Methods for Estimating Population Density in Data-Limited Areas: Evaluating Regression and Tree-Based Models in Peru

PubMed Central

Anderson, Weston; Guikema, Seth; Zaitchik, Ben; Pan, William

2014-01-01

Obtaining accurate small area estimates of population is essential for policy and health planning but is often difficult in countries with limited data. In lieu of available population data, small area estimate models draw information from previous time periods or from similar areas. This study focuses on model-based methods for estimating population when no direct samples are available in the area of interest. To explore the efficacy of tree-based models for estimating population density, we compare six different model structures including Random Forest and Bayesian Additive Regression Trees. Results demonstrate that without information from prior time periods, non-parametric tree-based models produced more accurate predictions than did conventional regression methods. Improving estimates of population density in non-sampled areas is important for regions with incomplete census data and has implications for economic, health and development policies. PMID:24992657

Population size estimation of female sex workers in Iran: Synthesis of methods and results

PubMed Central

Sharifi, Hamid; Karamouzian, Mohammad; Baneshi, Mohammad Reza; Shokoohi, Mostafa; Haghdoost, AliAkbar; McFarland, Willi

2017-01-01

Introduction Estimating the number of key populations at risk of HIV is essential for planning, monitoring, and evaluating prevention, care, and treatment programmes. We conducted this study to estimate the number of female sex workers (FSW) in major cities of Iran. Methods We used three population size estimation methods (i.e., wisdom of the crowds, multiplier method, and network scale-up) to calculate the number of FSW in 13 cities in Iran. The wisdom of the crowds and multiplier methods were integrated into a nationwide bio-behavioural surveillance survey in 2015, and the network scale-up method was included in a national survey of the general population in 2014. The median of the three methods was used to calculate the proportion of the adult female population who practice sex work in the 13 cities. These figures were then extrapolated to provide a national population size estimation of FSW across urban areas. Results The population size of FSW was 91,500 (95% Uncertainty Intervals [UIs] 61,400–117,700), corresponding to 1.43% (95% UIs 0.96–1.84) of the adult (i.e., 15–49 year-old) female population living in these 13 cities. The projected numbers of FSW for all 31 provincial capital cities were 130,800 (95% UIs 87,800–168,200) and 228,700 (95% UIs 153,500–294,300) for all urban settings in Iran. Conclusions Using methods of comparable rigor, our study provided a data-driven national estimate of the population size of FSW in urban areas of Iran. Our findings provide vital information for enhancing HIV programme planning and lay a foundation for assessing the impact of harm reduction efforts within this marginalized population. PMID:28796847

A review of the population estimation approach of the North American landbird conservation plan

USGS Publications Warehouse

Thogmartin, Wayne E.; Howe, Frank P.; James, Frances C.; Johnson, Douglas H.; Reed, Eric T.; Sauer, John R.; Thompson, Frank R.

2006-01-01

As part of their development of a continental plan for monitoring landbirds (Rich et al. 2004), Partners in Flight (PIF) applied a new method to make preliminary estimates of population size for all 448 species of landbirds present in the continental United States and Canada (Table 1). Estimation of the global population size of North American landbirds was intended to (1) identify the degree of vulnerability of each species, (2) provide estimates of the current population size for each species, and (3) provide a starting point for estimating population sizes in states, provinces, territories, and Bird Conservation Regions (Rich et al. 2004). A method proposed by Rosenberg and Blancher (2005) was used to derive population estimates from available survey data. To enhance the credibility of these estimates, PIF organized a review of the methodology used to estimate North American landbird population sizes. A planning committee selected members from the ornithological and biometrical communities (hereafter “the panel”), with the aim of selecting individuals from academia, state natural-resource agencies, and the U.S. and Canadian federal governments, including the Canadian Wildlife Service, the U.S. Geological Survey, and the U.S. Department of Agriculture Forest Service.The panel addressed three questions: (1) Were the methods of population estimation proposed by PIF reasonable? (2) What actions could be taken to improve the data or analyses on which the PIF population estimates were based? and (3) How should the PIF population estimates be interpreted?

Efficacy of time-lapse photography and repeated counts abundance estimation for white-tailed deer populations

USGS Publications Warehouse

Keever, Allison; McGowan, Conor P.; Ditchkoff, Stephen S.; Acker, S.A.; Grand, James B.; Newbolt, Chad H.

2017-01-01

Automated cameras have become increasingly common for monitoring wildlife populations and estimating abundance. Most analytical methods, however, fail to account for incomplete and variable detection probabilities, which biases abundance estimates. Methods which do account for detection have not been thoroughly tested, and those that have been tested were compared to other methods of abundance estimation. The goal of this study was to evaluate the accuracy and effectiveness of the N-mixture method, which explicitly incorporates detection probability, to monitor white-tailed deer (Odocoileus virginianus) by using camera surveys and a known, marked population to collect data and estimate abundance. Motion-triggered camera surveys were conducted at Auburn University’s deer research facility in 2010. Abundance estimates were generated using N-mixture models and compared to the known number of marked deer in the population. We compared abundance estimates generated from a decreasing number of survey days used in analysis and by time periods (DAY, NIGHT, SUNRISE, SUNSET, CREPUSCULAR, ALL TIMES). Accurate abundance estimates were generated using 24 h of data and nighttime only data. Accuracy of abundance estimates increased with increasing number of survey days until day 5, and there was no improvement with additional data. This suggests that, for our system, 5-day camera surveys conducted at night were adequate for abundance estimation and population monitoring. Further, our study demonstrates that camera surveys and N-mixture models may be a highly effective method for estimation and monitoring of ungulate populations.

Developing accurate survey methods for estimating population sizes and trends of the critically endangered Nihoa Millerbird and Nihoa Finch.

USGS Publications Warehouse

Gorresen, P. Marcos; Camp, Richard J.; Brinck, Kevin W.; Farmer, Chris

2012-01-01

Point-transect surveys indicated that millerbirds were more abundant than shown by the striptransect method, and were estimated at 802 birds in 2010 (95%CI = 652 – 964) and 704 birds in 2011 (95%CI = 579 – 837). Point-transect surveys yielded population estimates with improved precision which will permit trends to be detected in shorter time periods and with greater statistical power than is available from strip-transect survey methods. Mean finch population estimates and associated uncertainty were not markedly different among the three survey methods, but the performance of models used to estimate density and population size are expected to improve as the data from additional surveys are incorporated. Using the pointtransect survey, the mean finch population size was estimated at 2,917 birds in 2010 (95%CI = 2,037 – 3,965) and 2,461 birds in 2011 (95%CI = 1,682 – 3,348). Preliminary testing of the line-transect method in 2011 showed that it would not generate sufficient detections to effectively model bird density, and consequently, relatively precise population size estimates. Both species were fairly evenly distributed across Nihoa and appear to occur in all or nearly all available habitat. The time expended and area traversed by observers was similar among survey methods; however, point-transect surveys do not require that observers walk a straight transect line, thereby allowing them to avoid culturally or biologically sensitive areas and minimize the adverse effects of recurrent travel to any particular area. In general, pointtransect surveys detect more birds than strip-survey methods, thereby improving precision and resulting population size and trend estimation. The method is also better suited for the steep and uneven terrain of Nihoa

Population size estimation of female sex workers in Iran: Synthesis of methods and results.

PubMed

Sharifi, Hamid; Karamouzian, Mohammad; Baneshi, Mohammad Reza; Shokoohi, Mostafa; Haghdoost, AliAkbar; McFarland, Willi; Mirzazadeh, Ali

2017-01-01

Estimating the number of key populations at risk of HIV is essential for planning, monitoring, and evaluating prevention, care, and treatment programmes. We conducted this study to estimate the number of female sex workers (FSW) in major cities of Iran. We used three population size estimation methods (i.e., wisdom of the crowds, multiplier method, and network scale-up) to calculate the number of FSW in 13 cities in Iran. The wisdom of the crowds and multiplier methods were integrated into a nationwide bio-behavioural surveillance survey in 2015, and the network scale-up method was included in a national survey of the general population in 2014. The median of the three methods was used to calculate the proportion of the adult female population who practice sex work in the 13 cities. These figures were then extrapolated to provide a national population size estimation of FSW across urban areas. The population size of FSW was 91,500 (95% Uncertainty Intervals [UIs] 61,400-117,700), corresponding to 1.43% (95% UIs 0.96-1.84) of the adult (i.e., 15-49 year-old) female population living in these 13 cities. The projected numbers of FSW for all 31 provincial capital cities were 130,800 (95% UIs 87,800-168,200) and 228,700 (95% UIs 153,500-294,300) for all urban settings in Iran. Using methods of comparable rigor, our study provided a data-driven national estimate of the population size of FSW in urban areas of Iran. Our findings provide vital information for enhancing HIV programme planning and lay a foundation for assessing the impact of harm reduction efforts within this marginalized population.

Change-in-ratio density estimator for feral pigs is less biased than closed mark-recapture estimates

USGS Publications Warehouse

Hanson, L.B.; Grand, J.B.; Mitchell, M.S.; Jolley, D.B.; Sparklin, B.D.; Ditchkoff, S.S.

2008-01-01

Closed-population capture-mark-recapture (CMR) methods can produce biased density estimates for species with low or heterogeneous detection probabilities. In an attempt to address such biases, we developed a density-estimation method based on the change in ratio (CIR) of survival between two populations where survival, calculated using an open-population CMR model, is known to differ. We used our method to estimate density for a feral pig (Sus scrofa) population on Fort Benning, Georgia, USA. To assess its validity, we compared it to an estimate of the minimum density of pigs known to be alive and two estimates based on closed-population CMR models. Comparison of the density estimates revealed that the CIR estimator produced a density estimate with low precision that was reasonable with respect to minimum known density. By contrast, density point estimates using the closed-population CMR models were less than the minimum known density, consistent with biases created by low and heterogeneous capture probabilities for species like feral pigs that may occur in low density or are difficult to capture. Our CIR density estimator may be useful for tracking broad-scale, long-term changes in species, such as large cats, for which closed CMR models are unlikely to work. ?? CSIRO 2008.

Estimating numbers of females with cubs-of-the-year in the Yellowstone grizzly bear population

USGS Publications Warehouse

Keating, K.A.; Schwartz, C.C.; Haroldson, M.A.; Moody, D.

2001-01-01

For grizzly bears (Ursus arctos horribilis) in the Greater Yellowstone Ecosystem (GYE), minimum population size and allowable numbers of human-caused mortalities have been calculated as a function of the number of unique females with cubs-of-the-year (FCUB) seen during a 3- year period. This approach underestimates the total number of FCUB, thereby biasing estimates of population size and sustainable mortality. Also, it does not permit calculation of valid confidence bounds. Many statistical methods can resolve or mitigate these problems, but there is no universal best method. Instead, relative performances of different methods can vary with population size, sample size, and degree of heterogeneity among sighting probabilities for individual animals. We compared 7 nonparametric estimators, using Monte Carlo techniques to assess performances over the range of sampling conditions deemed plausible for the Yellowstone population. Our goal was to estimate the number of FCUB present in the population each year. Our evaluation differed from previous comparisons of such estimators by including sample coverage methods and by treating individual sightings, rather than sample periods, as the sample unit. Consequently, our conclusions also differ from earlier studies. Recommendations regarding estimators and necessary sample sizes are presented, together with estimates of annual numbers of FCUB in the Yellowstone population with bootstrap confidence bounds.

Empirical Bayes approach to the estimation of "unsafety": the multivariate regression method.

PubMed

Hauer, E

1992-10-01

There are two kinds of clues to the unsafety of an entity: its traits (such as traffic, geometry, age, or gender) and its historical accident record. The Empirical Bayes approach to unsafety estimation makes use of both kinds of clues. It requires information about the mean and the variance of the unsafety in a "reference population" of similar entities. The method now in use for this purpose suffers from several shortcomings. First, a very large reference population is required. Second, the choice of reference population is to some extent arbitrary. Third, entities in the reference population usually cannot match the traits of the entity the unsafety of which is estimated. To alleviate these shortcomings the multivariate regression method for estimating the mean and variance of unsafety in reference populations is offered. Its logical foundations are described and its soundness is demonstrated. The use of the multivariate method makes the Empirical Bayes approach to unsafety estimation applicable to a wider range of circumstances and yields better estimates of unsafety. The application of the method to the tasks of identifying deviant entities and of estimating the effect of interventions on unsafety are discussed and illustrated by numerical examples.

A probabilistic method for testing and estimating selection differences between populations

PubMed Central

He, Yungang; Wang, Minxian; Huang, Xin; Li, Ran; Xu, Hongyang; Xu, Shuhua; Jin, Li

2015-01-01

Human populations around the world encounter various environmental challenges and, consequently, develop genetic adaptations to different selection forces. Identifying the differences in natural selection between populations is critical for understanding the roles of specific genetic variants in evolutionary adaptation. Although numerous methods have been developed to detect genetic loci under recent directional selection, a probabilistic solution for testing and quantifying selection differences between populations is lacking. Here we report the development of a probabilistic method for testing and estimating selection differences between populations. By use of a probabilistic model of genetic drift and selection, we showed that logarithm odds ratios of allele frequencies provide estimates of the differences in selection coefficients between populations. The estimates approximate a normal distribution, and variance can be estimated using genome-wide variants. This allows us to quantify differences in selection coefficients and to determine the confidence intervals of the estimate. Our work also revealed the link between genetic association testing and hypothesis testing of selection differences. It therefore supplies a solution for hypothesis testing of selection differences. This method was applied to a genome-wide data analysis of Han and Tibetan populations. The results confirmed that both the EPAS1 and EGLN1 genes are under statistically different selection in Han and Tibetan populations. We further estimated differences in the selection coefficients for genetic variants involved in melanin formation and determined their confidence intervals between continental population groups. Application of the method to empirical data demonstrated the outstanding capability of this novel approach for testing and quantifying differences in natural selection. PMID:26463656

Estimating population size with correlated sampling unit estimates

Treesearch

David C. Bowden; Gary C. White; Alan B. Franklin; Joseph L. Ganey

2003-01-01

Finite population sampling theory is useful in estimating total population size (abundance) from abundance estimates of each sampled unit (quadrat). We develop estimators that allow correlated quadrat abundance estimates, even for quadrats in different sampling strata. Correlated quadrat abundance estimates based on mark–recapture or distance sampling methods occur...

Estimating population sizes for elusive animals: the forest elephants of Kakum National Park, Ghana.

PubMed

Eggert, L S; Eggert, J A; Woodruff, D S

2003-06-01

African forest elephants are difficult to observe in the dense vegetation, and previous studies have relied upon indirect methods to estimate population sizes. Using multilocus genotyping of noninvasively collected samples, we performed a genetic survey of the forest elephant population at Kakum National Park, Ghana. We estimated population size, sex ratio and genetic variability from our data, then combined this information with field observations to divide the population into age groups. Our population size estimate was very close to that obtained using dung counts, the most commonly used indirect method of estimating the population sizes of forest elephant populations. As their habitat is fragmented by expanding human populations, management will be increasingly important to the persistence of forest elephant populations. The data that can be obtained from noninvasively collected samples will help managers plan for the conservation of this keystone species.

Inferring the temperature dependence of population parameters: the effects of experimental design and inference algorithm

PubMed Central

Palamara, Gian Marco; Childs, Dylan Z; Clements, Christopher F; Petchey, Owen L; Plebani, Marco; Smith, Matthew J

2014-01-01

Understanding and quantifying the temperature dependence of population parameters, such as intrinsic growth rate and carrying capacity, is critical for predicting the ecological responses to environmental change. Many studies provide empirical estimates of such temperature dependencies, but a thorough investigation of the methods used to infer them has not been performed yet. We created artificial population time series using a stochastic logistic model parameterized with the Arrhenius equation, so that activation energy drives the temperature dependence of population parameters. We simulated different experimental designs and used different inference methods, varying the likelihood functions and other aspects of the parameter estimation methods. Finally, we applied the best performing inference methods to real data for the species Paramecium caudatum. The relative error of the estimates of activation energy varied between 5% and 30%. The fraction of habitat sampled played the most important role in determining the relative error; sampling at least 1% of the habitat kept it below 50%. We found that methods that simultaneously use all time series data (direct methods) and methods that estimate population parameters separately for each temperature (indirect methods) are complementary. Indirect methods provide a clearer insight into the shape of the functional form describing the temperature dependence of population parameters; direct methods enable a more accurate estimation of the parameters of such functional forms. Using both methods, we found that growth rate and carrying capacity of Paramecium caudatum scale with temperature according to different activation energies. Our study shows how careful choice of experimental design and inference methods can increase the accuracy of the inferred relationships between temperature and population parameters. The comparison of estimation methods provided here can increase the accuracy of model predictions, with important implications in understanding and predicting the effects of temperature on the dynamics of populations. PMID:25558365

Inferring recent outcrossing rates using multilocus individual heterozygosity: application to evolving wheat populations.

PubMed Central

Enjalbert, J; David, J L

2000-01-01

Using multilocus individual heterozygosity, a method is developed to estimate the outcrossing rates of a population over a few previous generations. Considering that individuals originate either from outcrossing or from n successive selfing generations from an outbred ancestor, a maximum-likelihood (ML) estimator is described that gives estimates of past outcrossing rates in terms of proportions of individuals with different n values. Heterozygosities at several unlinked codominant loci are used to assign n values to each individual. This method also allows a test of whether populations are in inbreeding equilibrium. The estimator's reliability was checked using simulations for different mating histories. We show that this ML estimator can provide estimates of outcrossing rates for the final generation outcrossing rate (t(0)) and a mean of the preceding rates (t(p)) and can detect major temporal variation in the mating system. The method is most efficient for low to intermediate outcrossing levels. Applied to nine populations of wheat, this method gave estimates of t(0) and t(p). These estimates confirmed the absence of outcrossing t(0) = 0 in the two populations subjected to manual selfing. For free-mating wheat populations, it detected lower final generation outcrossing rates t(0) = 0-0.06 than those expected from global heterozygosity t = 0.02-0.09. This estimator appears to be a new and efficient way to describe the multilocus heterozygosity of a population, complementary to Fis and progeny analysis approaches. PMID:11102388

Assessment of the effect of population and diary sampling methods on estimation of school-age children exposure to fine particles.

PubMed

Che, W W; Frey, H Christopher; Lau, Alexis K H

2014-12-01

Population and diary sampling methods are employed in exposure models to sample simulated individuals and their daily activity on each simulation day. Different sampling methods may lead to variations in estimated human exposure. In this study, two population sampling methods (stratified-random and random-random) and three diary sampling methods (random resampling, diversity and autocorrelation, and Markov-chain cluster [MCC]) are evaluated. Their impacts on estimated children's exposure to ambient fine particulate matter (PM2.5 ) are quantified via case studies for children in Wake County, NC for July 2002. The estimated mean daily average exposure is 12.9 μg/m(3) for simulated children using the stratified population sampling method, and 12.2 μg/m(3) using the random sampling method. These minor differences are caused by the random sampling among ages within census tracts. Among the three diary sampling methods, there are differences in the estimated number of individuals with multiple days of exposures exceeding a benchmark of concern of 25 μg/m(3) due to differences in how multiday longitudinal diaries are estimated. The MCC method is relatively more conservative. In case studies evaluated here, the MCC method led to 10% higher estimation of the number of individuals with repeated exposures exceeding the benchmark. The comparisons help to identify and contrast the capabilities of each method and to offer insight regarding implications of method choice. Exposure simulation results are robust to the two population sampling methods evaluated, and are sensitive to the choice of method for simulating longitudinal diaries, particularly when analyzing results for specific microenvironments or for exposures exceeding a benchmark of concern. © 2014 Society for Risk Analysis.

Winter bird population studies and project prairie birds for surveying grassland birds

USGS Publications Warehouse

Twedt, D.J.; Hamel, P.B.; Woodrey, M.S.

2008-01-01

We compared 2 survey methods for assessing winter bird communities in temperate grasslands: Winter Bird Population Study surveys are area-searches that have long been used in a variety of habitats whereas Project Prairie Bird surveys employ active-flushing techniques on strip-transects and are intended for use in grasslands. We used both methods to survey birds on 14 herbaceous reforested sites and 9 coastal pine savannas during winter and compared resultant estimates of species richness and relative abundance. These techniques did not yield similar estimates of avian populations. We found Winter Bird Population Studies consistently produced higher estimates of species richness, whereas Project Prairie Birds produced higher estimates of avian abundance for some species. When it is important to identify all species within the winter bird community, Winter Bird Population Studies should be the survey method of choice. If estimates of the abundance of relatively secretive grassland bird species are desired, the use of Project Prairie Birds protocols is warranted. However, we suggest that both survey techniques, as currently employed, are deficient and recommend distance- based survey methods that provide species-specific estimates of detection probabilities be incorporated into these survey methods.

The efficacy of respondent-driven sampling for the health assessment of minority populations.

PubMed

Badowski, Grazyna; Somera, Lilnabeth P; Simsiman, Brayan; Lee, Hye-Ryeon; Cassel, Kevin; Yamanaka, Alisha; Ren, JunHao

2017-10-01

Respondent driven sampling (RDS) is a relatively new network sampling technique typically employed for hard-to-reach populations. Like snowball sampling, initial respondents or "seeds" recruit additional respondents from their network of friends. Under certain assumptions, the method promises to produce a sample independent from the biases that may have been introduced by the non-random choice of "seeds." We conducted a survey on health communication in Guam's general population using the RDS method, the first survey that has utilized this methodology in Guam. It was conducted in hopes of identifying a cost-efficient non-probability sampling strategy that could generate reasonable population estimates for both minority and general populations. RDS data was collected in Guam in 2013 (n=511) and population estimates were compared with 2012 BRFSS data (n=2031) and the 2010 census data. The estimates were calculated using the unweighted RDS sample and the weighted sample using RDS inference methods and compared with known population characteristics. The sample size was reached in 23days, providing evidence that the RDS method is a viable, cost-effective data collection method, which can provide reasonable population estimates. However, the results also suggest that the RDS inference methods used to reduce bias, based on self-reported estimates of network sizes, may not always work. Caution is needed when interpreting RDS study findings. For a more diverse sample, data collection should not be conducted in just one location. Fewer questions about network estimates should be asked, and more careful consideration should be given to the kind of incentives offered to participants. Copyright © 2017. Published by Elsevier Ltd.

Multiple data sources improve DNA-based mark-recapture population estimates of grizzly bears.

PubMed

Boulanger, John; Kendall, Katherine C; Stetz, Jeffrey B; Roon, David A; Waits, Lisette P; Paetkau, David

2008-04-01

A fundamental challenge to estimating population size with mark-recapture methods is heterogeneous capture probabilities and subsequent bias of population estimates. Confronting this problem usually requires substantial sampling effort that can be difficult to achieve for some species, such as carnivores. We developed a methodology that uses two data sources to deal with heterogeneity and applied this to DNA mark-recapture data from grizzly bears (Ursus arctos). We improved population estimates by incorporating additional DNA "captures" of grizzly bears obtained by collecting hair from unbaited bear rub trees concurrently with baited, grid-based, hair snag sampling. We consider a Lincoln-Petersen estimator with hair snag captures as the initial session and rub tree captures as the recapture session and develop an estimator in program MARK that treats hair snag and rub tree samples as successive sessions. Using empirical data from a large-scale project in the greater Glacier National Park, Montana, USA, area and simulation modeling we evaluate these methods and compare the results to hair-snag-only estimates. Empirical results indicate that, compared with hair-snag-only data, the joint hair-snag-rub-tree methods produce similar but more precise estimates if capture and recapture rates are reasonably high for both methods. Simulation results suggest that estimators are potentially affected by correlation of capture probabilities between sample types in the presence of heterogeneity. Overall, closed population Huggins-Pledger estimators showed the highest precision and were most robust to sparse data, heterogeneity, and capture probability correlation among sampling types. Results also indicate that these estimators can be used when a segment of the population has zero capture probability for one of the methods. We propose that this general methodology may be useful for other species in which mark-recapture data are available from multiple sources.

A probabilistic method for testing and estimating selection differences between populations.

PubMed

He, Yungang; Wang, Minxian; Huang, Xin; Li, Ran; Xu, Hongyang; Xu, Shuhua; Jin, Li

2015-12-01

Human populations around the world encounter various environmental challenges and, consequently, develop genetic adaptations to different selection forces. Identifying the differences in natural selection between populations is critical for understanding the roles of specific genetic variants in evolutionary adaptation. Although numerous methods have been developed to detect genetic loci under recent directional selection, a probabilistic solution for testing and quantifying selection differences between populations is lacking. Here we report the development of a probabilistic method for testing and estimating selection differences between populations. By use of a probabilistic model of genetic drift and selection, we showed that logarithm odds ratios of allele frequencies provide estimates of the differences in selection coefficients between populations. The estimates approximate a normal distribution, and variance can be estimated using genome-wide variants. This allows us to quantify differences in selection coefficients and to determine the confidence intervals of the estimate. Our work also revealed the link between genetic association testing and hypothesis testing of selection differences. It therefore supplies a solution for hypothesis testing of selection differences. This method was applied to a genome-wide data analysis of Han and Tibetan populations. The results confirmed that both the EPAS1 and EGLN1 genes are under statistically different selection in Han and Tibetan populations. We further estimated differences in the selection coefficients for genetic variants involved in melanin formation and determined their confidence intervals between continental population groups. Application of the method to empirical data demonstrated the outstanding capability of this novel approach for testing and quantifying differences in natural selection. © 2015 He et al.; Published by Cold Spring Harbor Laboratory Press.

Multi-population Genomic Relationships for Estimating Current Genetic Variances Within and Genetic Correlations Between Populations.

PubMed

Wientjes, Yvonne C J; Bijma, Piter; Vandenplas, Jérémie; Calus, Mario P L

2017-10-01

Different methods are available to calculate multi-population genomic relationship matrices. Since those matrices differ in base population, it is anticipated that the method used to calculate genomic relationships affects the estimate of genetic variances, covariances, and correlations. The aim of this article is to define the multi-population genomic relationship matrix to estimate current genetic variances within and genetic correlations between populations. The genomic relationship matrix containing two populations consists of four blocks, one block for population 1, one block for population 2, and two blocks for relationships between the populations. It is known, based on literature, that by using current allele frequencies to calculate genomic relationships within a population, current genetic variances are estimated. In this article, we theoretically derived the properties of the genomic relationship matrix to estimate genetic correlations between populations and validated it using simulations. When the scaling factor of across-population genomic relationships is equal to the product of the square roots of the scaling factors for within-population genomic relationships, the genetic correlation is estimated unbiasedly even though estimated genetic variances do not necessarily refer to the current population. When this property is not met, the correlation based on estimated variances should be multiplied by a correction factor based on the scaling factors. In this study, we present a genomic relationship matrix which directly estimates current genetic variances as well as genetic correlations between populations. Copyright © 2017 by the Genetics Society of America.

Sample Size Calculations for Population Size Estimation Studies Using Multiplier Methods With Respondent-Driven Sampling Surveys.

PubMed

Fearon, Elizabeth; Chabata, Sungai T; Thompson, Jennifer A; Cowan, Frances M; Hargreaves, James R

2017-09-14

While guidance exists for obtaining population size estimates using multiplier methods with respondent-driven sampling surveys, we lack specific guidance for making sample size decisions. To guide the design of multiplier method population size estimation studies using respondent-driven sampling surveys to reduce the random error around the estimate obtained. The population size estimate is obtained by dividing the number of individuals receiving a service or the number of unique objects distributed (M) by the proportion of individuals in a representative survey who report receipt of the service or object (P). We have developed an approach to sample size calculation, interpreting methods to estimate the variance around estimates obtained using multiplier methods in conjunction with research into design effects and respondent-driven sampling. We describe an application to estimate the number of female sex workers in Harare, Zimbabwe. There is high variance in estimates. Random error around the size estimate reflects uncertainty from M and P, particularly when the estimate of P in the respondent-driven sampling survey is low. As expected, sample size requirements are higher when the design effect of the survey is assumed to be greater. We suggest a method for investigating the effects of sample size on the precision of a population size estimate obtained using multipler methods and respondent-driven sampling. Uncertainty in the size estimate is high, particularly when P is small, so balancing against other potential sources of bias, we advise researchers to consider longer service attendance reference periods and to distribute more unique objects, which is likely to result in a higher estimate of P in the respondent-driven sampling survey. ©Elizabeth Fearon, Sungai T Chabata, Jennifer A Thompson, Frances M Cowan, James R Hargreaves. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 14.09.2017.

Differential estimates of southern flying squirrel (Glaucomys volans) population structure based on capture method

Treesearch

Kevin S. Laves; Susan C. Loeb

2005-01-01

It is commonly assumed that population estimates derived from trapping small mammals are accurate and unbiased or that estimates derived from different capture methods are comparable. We captured southern flying squirrels (Glaucmrtys volam) using two methods to study their effect on red-cockaded woodpecker (Picoides bumah) reproductive success. Southern flying...

Estimating Population Cause-Specific Mortality Fractions from in-Hospital Mortality: Validation of a New Method

PubMed Central

Murray, Christopher J. L; Lopez, Alan D; Barofsky, Jeremy T; Bryson-Cahn, Chloe; Lozano, Rafael

2007-01-01

Background Cause-of-death data for many developing countries are not available. Information on deaths in hospital by cause is available in many low- and middle-income countries but is not a representative sample of deaths in the population. We propose a method to estimate population cause-specific mortality fractions (CSMFs) using data already collected in many middle-income and some low-income developing nations, yet rarely used: in-hospital death records. Methods and Findings For a given cause of death, a community's hospital deaths are equal to total community deaths multiplied by the proportion of deaths occurring in hospital. If we can estimate the proportion dying in hospital, we can estimate the proportion dying in the population using deaths in hospital. We propose to estimate the proportion of deaths for an age, sex, and cause group that die in hospital from the subset of the population where vital registration systems function or from another population. We evaluated our method using nearly complete vital registration (VR) data from Mexico 1998–2005, which records whether a death occurred in a hospital. In this validation test, we used 45 disease categories. We validated our method in two ways: nationally and between communities. First, we investigated how the method's accuracy changes as we decrease the amount of Mexican VR used to estimate the proportion of each age, sex, and cause group dying in hospital. Decreasing VR data used for this first step from 100% to 9% produces only a 12% maximum relative error between estimated and true CSMFs. Even if Mexico collected full VR information only in its capital city with 9% of its population, our estimation method would produce an average relative error in CSMFs across the 45 causes of just over 10%. Second, we used VR data for the capital zone (Distrito Federal and Estado de Mexico) and estimated CSMFs for the three lowest-development states. Our estimation method gave an average relative error of 20%, 23%, and 31% for Guerrero, Chiapas, and Oaxaca, respectively. Conclusions Where accurate International Classification of Diseases (ICD)-coded cause-of-death data are available for deaths in hospital and for VR covering a subset of the population, we demonstrated that population CSMFs can be estimated with low average error. In addition, we showed in the case of Mexico that this method can substantially reduce error from biased hospital data, even when applied to areas with widely different levels of development. For countries with ICD-coded deaths in hospital, this method potentially allows the use of existing data to inform health policy. PMID:18031195

Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies.

PubMed

Palacios, Julia A; Minin, Vladimir N

2013-03-01

Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past population dynamics from genomic data. We start with a standard framework based on the coalescent, a stochastic process that generates genealogies connecting randomly sampled individuals from the population of interest. These genealogies serve as a glue between the population demographic history and genomic sequences. It turns out that only the times of genealogical lineage coalescences contain information about population size dynamics. Viewing these coalescent times as a point process, estimating population size trajectories is equivalent to estimating a conditional intensity of this point process. Therefore, our inverse problem is similar to estimating an inhomogeneous Poisson process intensity function. We demonstrate how recent advances in Gaussian process-based nonparametric inference for Poisson processes can be extended to Bayesian nonparametric estimation of population size dynamics under the coalescent. We compare our Gaussian process (GP) approach to one of the state-of-the-art Gaussian Markov random field (GMRF) methods for estimating population trajectories. Using simulated data, we demonstrate that our method has better accuracy and precision. Next, we analyze two genealogies reconstructed from real sequences of hepatitis C and human Influenza A viruses. In both cases, we recover more believed aspects of the viral demographic histories than the GMRF approach. We also find that our GP method produces more reasonable uncertainty estimates than the GMRF method. Copyright © 2013, The International Biometric Society.

Validity and feasibility of a satellite imagery-based method for rapid estimation of displaced populations

PubMed Central

2013-01-01

Background Estimating the size of forcibly displaced populations is key to documenting their plight and allocating sufficient resources to their assistance, but is often not done, particularly during the acute phase of displacement, due to methodological challenges and inaccessibility. In this study, we explored the potential use of very high resolution satellite imagery to remotely estimate forcibly displaced populations. Methods Our method consisted of multiplying (i) manual counts of assumed residential structures on a satellite image and (ii) estimates of the mean number of people per structure (structure occupancy) obtained from publicly available reports. We computed population estimates for 11 sites in Bangladesh, Chad, Democratic Republic of Congo, Ethiopia, Haiti, Kenya and Mozambique (six refugee camps, three internally displaced persons’ camps and two urban neighbourhoods with a mixture of residents and displaced) ranging in population from 1,969 to 90,547, and compared these to “gold standard” reference population figures from census or other robust methods. Results Structure counts by independent analysts were reasonably consistent. Between one and 11 occupancy reports were available per site and most of these reported people per household rather than per structure. The imagery-based method had a precision relative to reference population figures of <10% in four sites and 10–30% in three sites, but severely over-estimated the population in an Ethiopian camp with implausible occupancy data and two post-earthquake Haiti sites featuring dense and complex residential layout. For each site, estimates were produced in 2–5 working person-days. Conclusions In settings with clearly distinguishable individual structures, the remote, imagery-based method had reasonable accuracy for the purposes of rapid estimation, was simple and quick to implement, and would likely perform better in more current application. However, it may have insurmountable limitations in settings featuring connected buildings or shelters, a complex pattern of roofs and multi-level buildings. Based on these results, we discuss possible ways forward for the method’s development. PMID:23343099

Validity and feasibility of a satellite imagery-based method for rapid estimation of displaced populations.

PubMed

Checchi, Francesco; Stewart, Barclay T; Palmer, Jennifer J; Grundy, Chris

2013-01-23

Estimating the size of forcibly displaced populations is key to documenting their plight and allocating sufficient resources to their assistance, but is often not done, particularly during the acute phase of displacement, due to methodological challenges and inaccessibility. In this study, we explored the potential use of very high resolution satellite imagery to remotely estimate forcibly displaced populations. Our method consisted of multiplying (i) manual counts of assumed residential structures on a satellite image and (ii) estimates of the mean number of people per structure (structure occupancy) obtained from publicly available reports. We computed population estimates for 11 sites in Bangladesh, Chad, Democratic Republic of Congo, Ethiopia, Haiti, Kenya and Mozambique (six refugee camps, three internally displaced persons' camps and two urban neighbourhoods with a mixture of residents and displaced) ranging in population from 1,969 to 90,547, and compared these to "gold standard" reference population figures from census or other robust methods. Structure counts by independent analysts were reasonably consistent. Between one and 11 occupancy reports were available per site and most of these reported people per household rather than per structure. The imagery-based method had a precision relative to reference population figures of <10% in four sites and 10-30% in three sites, but severely over-estimated the population in an Ethiopian camp with implausible occupancy data and two post-earthquake Haiti sites featuring dense and complex residential layout. For each site, estimates were produced in 2-5 working person-days. In settings with clearly distinguishable individual structures, the remote, imagery-based method had reasonable accuracy for the purposes of rapid estimation, was simple and quick to implement, and would likely perform better in more current application. However, it may have insurmountable limitations in settings featuring connected buildings or shelters, a complex pattern of roofs and multi-level buildings. Based on these results, we discuss possible ways forward for the method's development.

Accurate reconstruction of viral quasispecies spectra through improved estimation of strain richness

PubMed Central

2015-01-01

Background Estimating the number of different species (richness) in a mixed microbial population has been a main focus in metagenomic research. Existing methods of species richness estimation ride on the assumption that the reads in each assembled contig correspond to only one of the microbial genomes in the population. This assumption and the underlying probabilistic formulations of existing methods are not useful for quasispecies populations where the strains are highly genetically related. The lack of knowledge on the number of different strains in a quasispecies population is observed to hinder the precision of existing Viral Quasispecies Spectrum Reconstruction (QSR) methods due to the uncontrolled reconstruction of a large number of in silico false positives. In this work, we formulated a novel probabilistic method for strain richness estimation specifically targeting viral quasispecies. By using this approach we improved our recently proposed spectrum reconstruction pipeline ViQuaS to achieve higher levels of precision in reconstructed quasispecies spectra without compromising the recall rates. We also discuss how one other existing popular QSR method named ShoRAH can be improved using this new approach. Results On benchmark data sets, our estimation method provided accurate richness estimates (< 0.2 median estimation error) and improved the precision of ViQuaS by 2%-13% and F-score by 1%-9% without compromising the recall rates. We also demonstrate that our estimation method can be used to improve the precision and F-score of ShoRAH by 0%-7% and 0%-5% respectively. Conclusions The proposed probabilistic estimation method can be used to estimate the richness of viral populations with a quasispecies behavior and to improve the accuracy of the quasispecies spectra reconstructed by the existing methods ViQuaS and ShoRAH in the presence of a moderate level of technical sequencing errors. Availability http://sourceforge.net/projects/viquas/ PMID:26678073

Comparing population size estimators for plethodontid salamanders

USGS Publications Warehouse

Bailey, L.L.; Simons, T.R.; Pollock, K.H.

2004-01-01

Despite concern over amphibian declines, few studies estimate absolute abundances because of logistic and economic constraints and previously poor estimator performance. Two estimation approaches recommended for amphibian studies are mark-recapture and depletion (or removal) sampling. We compared abundance estimation via various mark-recapture and depletion methods, using data from a three-year study of terrestrial salamanders in Great Smoky Mountains National Park. Our results indicate that short-term closed-population, robust design, and depletion methods estimate surface population of salamanders (i.e., those near the surface and available for capture during a given sampling occasion). In longer duration studies, temporary emigration violates assumptions of both open- and closed-population mark-recapture estimation models. However, if the temporary emigration is completely random, these models should yield unbiased estimates of the total population (superpopulation) of salamanders in the sampled area. We recommend using Pollock's robust design in mark-recapture studies because of its flexibility to incorporate variation in capture probabilities and to estimate temporary emigration probabilities.

Improving size estimates of open animal populations by incorporating information on age

USGS Publications Warehouse

Manly, Bryan F.J.; McDonald, Trent L.; Amstrup, Steven C.; Regehr, Eric V.

2003-01-01

Around the world, a great deal of effort is expended each year to estimate the sizes of wild animal populations. Unfortunately, population size has proven to be one of the most intractable parameters to estimate. The capture-recapture estimation models most commonly used (of the Jolly-Seber type) are complicated and require numerous, sometimes questionable, assumptions. The derived estimates usually have large variances and lack consistency over time. In capture–recapture studies of long-lived animals, the ages of captured animals can often be determined with great accuracy and relative ease. We show how to incorporate age information into size estimates for open populations, where the size changes through births, deaths, immigration, and emigration. The proposed method allows more precise estimates of population size than the usual models, and it can provide these estimates from two sample occasions rather than the three usually required. Moreover, this method does not require specialized programs for capture-recapture data; researchers can derive their estimates using the logistic regression module in any standard statistical package.

Estimating the population of female sex workers in two Chinese cities on the basis of the HIV/AIDS behavioural surveillance approach combined with a multiplier method

PubMed Central

Zhang, Dapeng; Lv, Fan; Wang, Liyan; Sun, Liangxian; Zhou, Jian; Su, Wenyi; Bi, Peng

2007-01-01

Objective To estimate the size of the population of female sex workers (FSWs) on the basis of the HIV/AIDS behavioural surveillance approach in two Chinese cities, using a multiplier method. Method Relevant questions were inserted into the questionnaires given to two behavioural surveillance groups—female attendees of sexually transmitted disease (STD) clinics and FSWs. The size of the FSW population was derived by multiplying the number of FSWs in selected STD clinics during the study period by the proportion of FSW population who reported having attended the selected STD clinics during the same period. Results The size of the FSW population in the urban area of Xingyi, China, was estimated to be about 2500 (95% CI 2000 to 3400). This accounted for 3.6% of the total urban adult female population. There were an estimated 17 500 FSWs in the urban area of Guiyang, China (95% CI 10 300 to 31 900) or about 3.4% of its total urban adult female population (rounded to the nearest 100). Conclusions The multiplier method could be a useful and cost‐effective approach to estimate the FSW population, especially suitable in countries where HIV behavioural surveillance has been established in high‐risk populations. PMID:17090568

Population growth rates of reef sharks with and without fishing on the great barrier reef: robust estimation with multiple models.

PubMed

Hisano, Mizue; Connolly, Sean R; Robbins, William D

2011-01-01

Overfishing of sharks is a global concern, with increasing numbers of species threatened by overfishing. For many sharks, both catch rates and underwater visual surveys have been criticized as indices of abundance. In this context, estimation of population trends using individual demographic rates provides an important alternative means of assessing population status. However, such estimates involve uncertainties that must be appropriately characterized to credibly and effectively inform conservation efforts and management. Incorporating uncertainties into population assessment is especially important when key demographic rates are obtained via indirect methods, as is often the case for mortality rates of marine organisms subject to fishing. Here, focusing on two reef shark species on the Great Barrier Reef, Australia, we estimated natural and total mortality rates using several indirect methods, and determined the population growth rates resulting from each. We used bootstrapping to quantify the uncertainty associated with each estimate, and to evaluate the extent of agreement between estimates. Multiple models produced highly concordant natural and total mortality rates, and associated population growth rates, once the uncertainties associated with the individual estimates were taken into account. Consensus estimates of natural and total population growth across multiple models support the hypothesis that these species are declining rapidly due to fishing, in contrast to conclusions previously drawn from catch rate trends. Moreover, quantitative projections of abundance differences on fished versus unfished reefs, based on the population growth rate estimates, are comparable to those found in previous studies using underwater visual surveys. These findings appear to justify management actions to substantially reduce the fishing mortality of reef sharks. They also highlight the potential utility of rigorously characterizing uncertainty, and applying multiple assessment methods, to obtain robust estimates of population trends in species threatened by overfishing.

Population Growth Rates of Reef Sharks with and without Fishing on the Great Barrier Reef: Robust Estimation with Multiple Models

PubMed Central

Hisano, Mizue; Connolly, Sean R.; Robbins, William D.

2011-01-01

Overfishing of sharks is a global concern, with increasing numbers of species threatened by overfishing. For many sharks, both catch rates and underwater visual surveys have been criticized as indices of abundance. In this context, estimation of population trends using individual demographic rates provides an important alternative means of assessing population status. However, such estimates involve uncertainties that must be appropriately characterized to credibly and effectively inform conservation efforts and management. Incorporating uncertainties into population assessment is especially important when key demographic rates are obtained via indirect methods, as is often the case for mortality rates of marine organisms subject to fishing. Here, focusing on two reef shark species on the Great Barrier Reef, Australia, we estimated natural and total mortality rates using several indirect methods, and determined the population growth rates resulting from each. We used bootstrapping to quantify the uncertainty associated with each estimate, and to evaluate the extent of agreement between estimates. Multiple models produced highly concordant natural and total mortality rates, and associated population growth rates, once the uncertainties associated with the individual estimates were taken into account. Consensus estimates of natural and total population growth across multiple models support the hypothesis that these species are declining rapidly due to fishing, in contrast to conclusions previously drawn from catch rate trends. Moreover, quantitative projections of abundance differences on fished versus unfished reefs, based on the population growth rate estimates, are comparable to those found in previous studies using underwater visual surveys. These findings appear to justify management actions to substantially reduce the fishing mortality of reef sharks. They also highlight the potential utility of rigorously characterizing uncertainty, and applying multiple assessment methods, to obtain robust estimates of population trends in species threatened by overfishing. PMID:21966402

The Demirjian versus the Willems method for dental age estimation in different populations: A meta-analysis of published studies

PubMed Central

2017-01-01

Background The accuracy of radiographic methods for dental age estimation is important for biological growth research and forensic applications. Accuracy of the two most commonly used systems (Demirjian and Willems) has been evaluated with conflicting results. This study investigates the accuracies of these methods for dental age estimation in different populations. Methods A search of PubMed, Scopus, Ovid, Database of Open Access Journals and Google Scholar was undertaken. Eligible studies published before December 28, 2016 were reviewed and analyzed. Meta-analysis was performed on 28 published articles using the Demirjian and/or Willems methods to estimate chronological age in 14,109 children (6,581 males, 7,528 females) age 3–18 years in studies using Demirjian’s method and 10,832 children (5,176 males, 5,656 females) age 4–18 years in studies using Willems’ method. The weighted mean difference at 95% confidence interval was used to assess accuracies of the two methods in predicting the chronological age. Results The Demirjian method significantly overestimated chronological age (p<0.05) in males age 3–15 and females age 4–16 when studies were pooled by age cohorts and sex. The majority of studies using Willems’ method did not report significant overestimation of ages in either sex. Overall, Demirjian’s method significantly overestimated chronological age compared to the Willems method (p<0.05). The weighted mean difference for the Demirjian method was 0.62 for males and 0.72 for females, while that of the Willems method was 0.26 for males and 0.29 for females. Conclusion The Willems method provides more accurate estimation of chronological age in different populations, while Demirjian’s method has a broad application in terms of determining maturity scores. However, accuracy of Demirjian age estimations is confounded by population variation when converting maturity scores to dental ages. For highest accuracy of age estimation, population-specific standards, rather than a universal standard or methods developed on other populations, need to be employed. PMID:29117240

Population Estimation Methods for Free-Ranging Dogs: A Systematic Review.

PubMed

Belo, Vinícius Silva; Werneck, Guilherme Loureiro; da Silva, Eduardo Sérgio; Barbosa, David Soeiro; Struchiner, Claudio José

2015-01-01

The understanding of the structure of free-roaming dog populations is of extreme importance for the planning and monitoring of populational control strategies and animal welfare. The methods used to estimate the abundance of this group of dogs are more complex than the ones used with domiciled owned dogs. In this systematic review, we analyze the techniques and the results obtained in studies that seek to estimate the size of free-ranging dog populations. Twenty-six studies were reviewed regarding the quality of execution and their capacity to generate valid estimates. Seven of the eight publications that take a simple count of the animal population did not consider the different probabilities of animal detection; only one study used methods based on distances; twelve relied on capture-recapture models for closed populations without considering heterogeneities in capture probabilities; six studies applied their own methods with different potential and limitations. Potential sources of bias in the studies were related to the inadequate description or implementation of animal capturing or viewing procedures and to inadequacies in the identification and registration of dogs. Thus, there was a predominance of estimates with low validity. Abundance and density estimates carried high variability, and all studies identified a greater number of male dogs. We point to enhancements necessary for the implementation of future studies and to potential updates and revisions to the recommendations of the World Health Organization with respect to the estimation of free-ranging dog populations.

Combining nutrient intake from food/beverages and vitamin/mineral supplements.

PubMed

Garriguet, Didier

2010-12-01

To calculate total intake of a nutrient and estimate inadequate intake for a population, the amounts derived from food/beverages and from vitamin/mineral supplements must be combined. The two methods Statistics Canada has suggested present problems of interpretation. Data collected from 34,386 respondents to the 2004 Canadian Community Health Survey-Nutrition were used to compare four methods of combining nutrient intake from food/beverages and vitamin/mineral supplements: adding average intake from supplements to the 24-hour food/beverage recall and estimating the usual distribution in the population (Method 1); estimating usual individual intake from food? beverages and adding intake from supplements (Method 2); and dividing the population into supplement users and non-users and applying Method 1 or Method 2 and combining the estimates based on the percentages of users and non-users (Methods 3 and 4). Interpretation problems arise with Methods 1 and 2; for example, the percentage of the population with inadequate intake of vitamin C and folate equivalents falls outside the expected minimum-maximum range. These interpretation problems are not observed with Methods 3 and 4. Interpretation problems that may arise in combining food and supplement intake of a given nutrient are overcome if the population is divided into supplement users and non-users before Method 1 or Method 2 is applied.

cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms.

PubMed

Ali, Sajid; Soubeyrand, Samuel; Gladieux, Pierre; Giraud, Tatiana; Leconte, Marc; Gautier, Angélique; Mboup, Mamadou; Chen, Wanquan; de Vallavieille-Pope, Claude; Enjalbert, Jérôme

2016-07-01

Inferring reproductive and demographic parameters of populations is crucial to our understanding of species ecology and evolutionary potential but can be challenging, especially in partially clonal organisms. Here, we describe a new and accurate method, cloncase, for estimating both the rate of sexual vs. asexual reproduction and the effective population size, based on the frequency of clonemate resampling across generations. Simulations showed that our method provides reliable estimates of sex frequency and effective population size for a wide range of parameters. The cloncase method was applied to Puccinia striiformis f.sp. tritici, a fungal pathogen causing stripe/yellow rust, an important wheat disease. This fungus is highly clonal in Europe but has been suggested to recombine in Asia. Using two temporally spaced samples of P. striiformis f.sp. tritici in China, the estimated sex frequency was 75% (i.e. three-quarter of individuals being sexually derived during the yearly sexual cycle), indicating strong contribution of sexual reproduction to the life cycle of the pathogen in this area. The inferred effective population size of this partially clonal organism (Nc  = 998) was in good agreement with estimates obtained using methods based on temporal variations in allelic frequencies. The cloncase estimator presented herein is the first method allowing accurate inference of both sex frequency and effective population size from population data without knowledge of recombination or mutation rates. cloncase can be applied to population genetic data from any organism with cyclical parthenogenesis and should in particular be very useful for improving our understanding of pest and microbial population biology. © 2016 John Wiley & Sons Ltd.

Estimating the coverage of mental health programmes: a systematic review

PubMed Central

De Silva, Mary J; Lee, Lucy; Fuhr, Daniela C; Rathod, Sujit; Chisholm, Dan; Schellenberg, Joanna; Patel, Vikram

2014-01-01

Background The large treatment gap for people suffering from mental disorders has led to initiatives to scale up mental health services. In order to track progress, estimates of programme coverage, and changes in coverage over time, are needed. Methods Systematic review of mental health programme evaluations that assess coverage, measured either as the proportion of the target population in contact with services (contact coverage) or as the proportion of the target population who receive appropriate and effective care (effective coverage). We performed a search of electronic databases and grey literature up to March 2013 and contacted experts in the field. Methods to estimate the numerator (service utilization) and the denominator (target population) were reviewed to explore methods which could be used in programme evaluations. Results We identified 15 735 unique records of which only seven met the inclusion criteria. All studies reported contact coverage. No study explicitly measured effective coverage, but it was possible to estimate this for one study. In six studies the numerator of coverage, service utilization, was estimated using routine clinical information, whereas one study used a national community survey. The methods for estimating the denominator, the population in need of services, were more varied and included national prevalence surveys case registers, and estimates from the literature. Conclusions Very few coverage estimates are available. Coverage could be estimated at low cost by combining routine programme data with population prevalence estimates from national surveys. PMID:24760874

Counting the stunted children in a population: a criticism of old and new approaches and a conciliatory proposal.

PubMed

Monteiro, C A

1991-01-01

Two methods for estimating the prevalence of growth retardation in a population are evaluated: the classical method, which is based on the proportion of children whose height is more than 2 standard deviations below the expected mean of a reference population; and a new method recently proposed by Mora, which is based on the whole height distribution of observed and reference populations. Application of the classical method to several simulated populations leads to the conclusion that in most situations in developing countries the prevalence of growth retardation is grossly underestimated, and reflects only the presence of severe growth deficits. A second constraint with this method is a marked reduction of the relative differentials between more and less exposed strata. Application of Mora's method to the same simulated populations reduced but did not eliminate these constraints. A novel method for estimating the prevalence of growth retardation, which is based also on the whole height distribution of observed and reference populations, is also described and evaluated. This method produces better estimates of the true prevalence of growth retardation with no reduction in relative differentials.

Confidence intervals for population allele frequencies: the general case of sampling from a finite diploid population of any size.

PubMed

Fung, Tak; Keenan, Kevin

2014-01-01

The estimation of population allele frequencies using sample data forms a central component of studies in population genetics. These estimates can be used to test hypotheses on the evolutionary processes governing changes in genetic variation among populations. However, existing studies frequently do not account for sampling uncertainty in these estimates, thus compromising their utility. Incorporation of this uncertainty has been hindered by the lack of a method for constructing confidence intervals containing the population allele frequencies, for the general case of sampling from a finite diploid population of any size. In this study, we address this important knowledge gap by presenting a rigorous mathematical method to construct such confidence intervals. For a range of scenarios, the method is used to demonstrate that for a particular allele, in order to obtain accurate estimates within 0.05 of the population allele frequency with high probability (> or = 95%), a sample size of > 30 is often required. This analysis is augmented by an application of the method to empirical sample allele frequency data for two populations of the checkerspot butterfly (Melitaea cinxia L.), occupying meadows in Finland. For each population, the method is used to derive > or = 98.3% confidence intervals for the population frequencies of three alleles. These intervals are then used to construct two joint > or = 95% confidence regions, one for the set of three frequencies for each population. These regions are then used to derive a > or = 95%% confidence interval for Jost's D, a measure of genetic differentiation between the two populations. Overall, the results demonstrate the practical utility of the method with respect to informing sampling design and accounting for sampling uncertainty in studies of population genetics, important for scientific hypothesis-testing and also for risk-based natural resource management.

Joint Inference of Population Assignment and Demographic History

PubMed Central

Choi, Sang Chul; Hey, Jody

2011-01-01

A new approach to assigning individuals to populations using genetic data is described. Most existing methods work by maximizing Hardy–Weinberg and linkage equilibrium within populations, neither of which will apply for many demographic histories. By including a demographic model, within a likelihood framework based on coalescent theory, we can jointly study demographic history and population assignment. Genealogies and population assignments are sampled from a posterior distribution using a general isolation-with-migration model for multiple populations. A measure of partition distance between assignments facilitates not only the summary of a posterior sample of assignments, but also the estimation of the posterior density for the demographic history. It is shown that joint estimates of assignment and demographic history are possible, including estimation of population phylogeny for samples from three populations. The new method is compared to results of a widely used assignment method, using simulated and published empirical data sets. PMID:21775468

Generalizing the Network Scale-Up Method: A New Estimator for the Size of Hidden Populations*

PubMed Central

Feehan, Dennis M.; Salganik, Matthew J.

2018-01-01

The network scale-up method enables researchers to estimate the size of hidden populations, such as drug injectors and sex workers, using sampled social network data. The basic scale-up estimator offers advantages over other size estimation techniques, but it depends on problematic modeling assumptions. We propose a new generalized scale-up estimator that can be used in settings with non-random social mixing and imperfect awareness about membership in the hidden population. Further, the new estimator can be used when data are collected via complex sample designs and from incomplete sampling frames. However, the generalized scale-up estimator also requires data from two samples: one from the frame population and one from the hidden population. In some situations these data from the hidden population can be collected by adding a small number of questions to already planned studies. For other situations, we develop interpretable adjustment factors that can be applied to the basic scale-up estimator. We conclude with practical recommendations for the design and analysis of future studies. PMID:29375167

Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches

Treesearch

Gordon Luikart; Nils Ryman; David A. Tallmon; Michael K. Schwartz; Fred W. Allendorf

2010-01-01

Population census size (NC) and effective population sizes (Ne) are two crucial parameters that influence population viability, wildlife management decisions, and conservation planning. Genetic estimators of both NC and Ne are increasingly widely used because molecular markers are increasingly available, statistical methods are improving rapidly, and genetic estimators...

Capture-recapture to estimate the number of street children in a city in Brazil

PubMed Central

Gurgel, R; da Fonseca, J D C; Neyra-Castaneda, D; Gill, G; Cuevas, L

2004-01-01

Background: Street children are an increasing problem in Latin America. It is however difficult to estimate the number of children in the street as this is a highly mobile population. Aims: To estimate the number of street children in Aracaju, northeast Brazil, and describe the characteristics of this population. Methods: Three independent lists of street children were constructed from a non-governmental organisation and cross-sectional surveys. The number of street children was estimated using the capture-recapture method. The characteristics of the children were recorded during the surveys. Results: The estimated number of street children was 1456. The estimated number of street children before these surveys was 526, although non-official estimates suggested that there was a much larger population. Most street children are male, maintain contact with their families, and are attending school. Children contribute to the family budget a weekly average of R$21.2 (£4.25, €6.0, US$7.5) for boys and R$17.7 (£3.55, €5.0, US$6.3) for girls. Conclusion: Street children of Aracaju have similar characteristics to street children from other cities in Brazil. The capture-recapture method could be a useful method to estimate the size of this highly mobile population. The major advantage of the method is its reproducibility, which makes it more acceptable than estimates from interested parties. PMID:14977695

Estimating numbers of greater prairie-chickens using mark-resight techniques

USGS Publications Warehouse

Clifton, A.M.; Krementz, D.G.

2006-01-01

Current monitoring efforts for greater prairie-chicken (Tympanuchus cupido pinnatus) populations indicate that populations are declining across their range. Monitoring the population status of greater prairie-chickens is based on traditional lek surveys (TLS) that provide an index without considering detectability. Estimators, such as immigration-emigration joint maximum-likelihood estimator from a hypergeometric distribution (IEJHE), can account for detectability and provide reliable population estimates based on resightings. We evaluated the use of mark-resight methods using radiotelemetry to estimate population size and density of greater prairie-chickens on 2 sites at a tallgrass prairie in the Flint Hills of Kansas, USA. We used average distances traveled from lek of capture to estimate density. Population estimates and confidence intervals at the 2 sites were 54 (CI 50-59) on 52.9 km 2 and 87 (CI 82-94) on 73.6 km2. The TLS performed at the same sites resulted in population ranges of 7-34 and 36-63 and always produced a lower population index than the mark-resight population estimate with a larger range. Mark-resight simulations with varying male:female ratios of marks indicated that this ratio was important in designing a population study on prairie-chickens. Confidence intervals for estimates when no marks were placed on females at the 2 sites (CI 46-50, 76-84) did not overlap confidence intervals when 40% of marks were placed on females (CI 54-64, 91-109). Population estimates derived using this mark-resight technique were apparently more accurate than traditional methods and would be more effective in detecting changes in prairie-chicken populations. Our technique could improve prairie-chicken management by providing wildlife biologists and land managers with a tool to estimate the population size and trends of lekking bird species, such as greater prairie-chickens.

Determining population size of territorial red-winged blackbirds

USGS Publications Warehouse

Albers, P.H.

1976-01-01

Population sizes of territorial male red-winged blackbirds (Agelaius phoeniceus) were determined with counts of territorial males (area count) and a Petersen-Lincoln Index method for roadsides (roadside estimate). Weather conditions and time of day did not influence either method. Combined roadside estimates had smaller error bounds than the individual transect estimates and were not hindered by the problem of zero recaptures. Roadside estimates were usually one-half as large as the area counts, presumably due to an observer bias for marked birds. The roadside estimate provides only an index of major changes in populations of territorial male redwings. When the roadside estimate is employed, the area count should be used to determine the amount and nature of observer bias. For small population surveys, the area count is probably more reliable and accurate than the roadside estimate.

A review of life expectancy and infant mortality estimations for Australian Aboriginal people

PubMed Central

2014-01-01

Background Significant variation exists in published Aboriginal mortality and life expectancy (LE) estimates due to differing and evolving methodologies required to correct for inadequate recording of Aboriginality in death data, under-counting of Aboriginal people in population censuses, and unexplained growth in the Aboriginal population attributed to changes in the propensity of individuals to identify as Aboriginal at population censuses. The objective of this paper is to analyse variation in reported Australian Aboriginal mortality in terms of LE and infant mortality rates (IMR), compared with all Australians. Methods Published data for Aboriginal LE and IMR were obtained and analysed for data quality and method of estimation. Trends in reported LE and IMR estimates were assessed and compared with those in the entire Australian population. Results LE estimates derived from different methodologies vary by as much as 7.2 years for the same comparison period. Indirect methods for estimating Aboriginal LE have produced LE estimates sensitive to small changes in underlying assumptions, some of which are subject to circular reasoning. Most indirect methods appear to under-estimate Aboriginal LE. Estimated LE gaps between Aboriginal people and the overall Australian population have varied between 11 and 20 years. Latest mortality estimates, based on linking census and death data, are likely to over-estimate Aboriginal LE. Temporal LE changes by each methodology indicate that Aboriginal LE has improved at rates similar to the Australian population overall. Consequently the gap in LE between Aboriginal people and the total Australian population appears to be unchanged since the early 1980s, and at the end of the first decade of the 21st century remains at least 11–12 years. In contrast, focussing on the 1990–2010 period Aboriginal IMR declined steeply over 2001–08, from more than 12 to around 8 deaths per 1,000 live births, the same level as Australia overall in 1993–95. The IMR gap between Aboriginal people and the total Australian population, while still unacceptable, has declined considerably, from over 8 before 2000 to around 4 per 1,000 live births by 2008. Conclusions Regardless of estimation method used, mortality and LE gaps between Aboriginal and non-Aboriginal people are substantial, but remain difficult to estimate accurately. PMID:24383435

A Spatio-Temporally Explicit Random Encounter Model for Large-Scale Population Surveys

PubMed Central

Jousimo, Jussi; Ovaskainen, Otso

2016-01-01

Random encounter models can be used to estimate population abundance from indirect data collected by non-invasive sampling methods, such as track counts or camera-trap data. The classical Formozov–Malyshev–Pereleshin (FMP) estimator converts track counts into an estimate of mean population density, assuming that data on the daily movement distances of the animals are available. We utilize generalized linear models with spatio-temporal error structures to extend the FMP estimator into a flexible Bayesian modelling approach that estimates not only total population size, but also spatio-temporal variation in population density. We also introduce a weighting scheme to estimate density on habitats that are not covered by survey transects, assuming that movement data on a subset of individuals is available. We test the performance of spatio-temporal and temporal approaches by a simulation study mimicking the Finnish winter track count survey. The results illustrate how the spatio-temporal modelling approach is able to borrow information from observations made on neighboring locations and times when estimating population density, and that spatio-temporal and temporal smoothing models can provide improved estimates of total population size compared to the FMP method. PMID:27611683

Population Estimation Using a 3D City Model: A Multi-Scale Country-Wide Study in the Netherlands

PubMed Central

Arroyo Ohori, Ken; Ledoux, Hugo; Peters, Ravi; Stoter, Jantien

2016-01-01

The remote estimation of a region’s population has for decades been a key application of geographic information science in demography. Most studies have used 2D data (maps, satellite imagery) to estimate population avoiding field surveys and questionnaires. As the availability of semantic 3D city models is constantly increasing, we investigate to what extent they can be used for the same purpose. Based on the assumption that housing space is a proxy for the number of its residents, we use two methods to estimate the population with 3D city models in two directions: (1) disaggregation (areal interpolation) to estimate the population of small administrative entities (e.g. neighbourhoods) from that of larger ones (e.g. municipalities); and (2) a statistical modelling approach to estimate the population of large entities from a sample composed of their smaller ones (e.g. one acquired by a government register). Starting from a complete Dutch census dataset at the neighbourhood level and a 3D model of all 9.9 million buildings in the Netherlands, we compare the population estimates obtained by both methods with the actual population as reported in the census, and use it to evaluate the quality that can be achieved by estimations at different administrative levels. We also analyse how the volume-based estimation enabled by 3D city models fares in comparison to 2D methods using building footprints and floor areas, as well as how it is affected by different levels of semantic detail in a 3D city model. We conclude that 3D city models are useful for estimations of large areas (e.g. for a country), and that the 3D approach has clear advantages over the 2D approach. PMID:27254151

Population Estimation in Singapore Based on Remote Sensing and Open Data

NASA Astrophysics Data System (ADS)

Guo, H.; Cao, K.; Wang, P.

2017-09-01

Population estimation statistics are widely used in government, commercial and educational sectors for a variety of purposes. With growing emphases on real-time and detailed population information, data users nowadays have switched from traditional census data to more technology-based data source such as LiDAR point cloud and High-Resolution Satellite Imagery. Nevertheless, such data are costly and periodically unavailable. In this paper, the authors use West Coast District, Singapore as a case study to investigate the applicability and effectiveness of using satellite image from Google Earth for extraction of building footprint and population estimation. At the same time, volunteered geographic information (VGI) is also utilized as ancillary data for building footprint extraction. Open data such as Open Street Map OSM could be employed to enhance the extraction process. In view of challenges in building shadow extraction, this paper discusses several methods including buffer, mask and shape index to improve accuracy. It also illustrates population estimation methods based on building height and number of floor estimates. The results show that the accuracy level of housing unit method on population estimation can reach 92.5 %, which is remarkably accurate. This paper thus provides insights into techniques for building extraction and fine-scale population estimation, which will benefit users such as urban planners in terms of policymaking and urban planning of Singapore.

Estimates of population change in selected species of tropical birds using mark-recapture data

USGS Publications Warehouse

Brawn, J.; Nichols, J.D.; Hines, J.E.; Nesbitt, J.

2000-01-01

The population biology of tropical birds is known for a only small sample of species; especially in the Neotropics. Robust estimates of parameters such as survival rate and finite rate of population change (A) are crucial for conservation purposes and useful for studies of avian life histories. We used methods developed by Pradel (1996, Biometrics 52:703-709) to estimate A for 10 species of tropical forest lowland birds using data from a long-term (> 20 yr) banding study in Panama. These species constitute a ecologically and phylogenetically diverse sample. We present these estimates and explore if they are consistent with what we know from selected studies of banded birds and from 5 yr of estimating nesting success (i.e., an important component of A). A major goal of these analyses is to assess if the mark-recapture methods generate reliable and reasonably precise estimates of population change than traditional methods that require more sampling effort.

Shell productivity of the large benthic foraminifer Baculogypsina sphaerulata, based on the population dynamics in a tropical reef environment

NASA Astrophysics Data System (ADS)

Fujita, Kazuhiko; Otomaru, Maki; Lopati, Paeniu; Hosono, Takashi; Kayanne, Hajime

2016-03-01

Carbonate production by large benthic foraminifers is sometimes comparable to that of corals and coralline algae, and contributes to sedimentation on reef islands and beaches in the tropical Pacific. Population dynamic data, such as population density and size structure (size-frequency distribution), are vital for an accurate estimation of shell production of foraminifers. However, previous production estimates in tropical environments were based on a limited sampling period with no consideration of seasonality. In addition, no comparisons were made of various estimation methods to determine more accurate estimates. Here we present the annual gross shell production rate of Baculogypsina sphaerulata, estimated based on population dynamics studied over a 2-yr period on an ocean reef flat of Funafuti Atoll (Tuvalu, tropical South Pacific). The population density of B. sphaerulata increased from January to March, when northwest winds predominated and the study site was on the leeward side of reef islands, compared to other seasons when southeast trade winds predominated and the study site was on the windward side. This result suggested that wind-driven flows controlled the population density at the study site. The B. sphaerulata population had a relatively stationary size-frequency distribution throughout the study period, indicating no definite intensive reproductive period in the tropical population. Four methods were applied to estimate the annual gross shell production rates of B. sphaerulata. The production rates estimated by three of the four methods (using monthly biomass, life tables and growth increment rates) were in the order of hundreds of g CaCO3 m-2 yr-1 or cm-3 m-2 yr-1, and the simple method using turnover rates overestimated the values. This study suggests that seasonal surveys should be undertaken of population density and size structure as these can produce more accurate estimates of shell productivity of large benthic foraminifers.

Estimating the coverage of mental health programmes: a systematic review.

PubMed

De Silva, Mary J; Lee, Lucy; Fuhr, Daniela C; Rathod, Sujit; Chisholm, Dan; Schellenberg, Joanna; Patel, Vikram

2014-04-01

The large treatment gap for people suffering from mental disorders has led to initiatives to scale up mental health services. In order to track progress, estimates of programme coverage, and changes in coverage over time, are needed. Systematic review of mental health programme evaluations that assess coverage, measured either as the proportion of the target population in contact with services (contact coverage) or as the proportion of the target population who receive appropriate and effective care (effective coverage). We performed a search of electronic databases and grey literature up to March 2013 and contacted experts in the field. Methods to estimate the numerator (service utilization) and the denominator (target population) were reviewed to explore methods which could be used in programme evaluations. We identified 15 735 unique records of which only seven met the inclusion criteria. All studies reported contact coverage. No study explicitly measured effective coverage, but it was possible to estimate this for one study. In six studies the numerator of coverage, service utilization, was estimated using routine clinical information, whereas one study used a national community survey. The methods for estimating the denominator, the population in need of services, were more varied and included national prevalence surveys case registers, and estimates from the literature. Very few coverage estimates are available. Coverage could be estimated at low cost by combining routine programme data with population prevalence estimates from national surveys.

Estimating abundance of an open population with an N-mixture model using auxiliary data on animal movements.

PubMed

Ketz, Alison C; Johnson, Therese L; Monello, Ryan J; Mack, John A; George, Janet L; Kraft, Benjamin R; Wild, Margaret A; Hooten, Mevin B; Hobbs, N Thompson

2018-04-01

Accurate assessment of abundance forms a central challenge in population ecology and wildlife management. Many statistical techniques have been developed to estimate population sizes because populations change over time and space and to correct for the bias resulting from animals that are present in a study area but not observed. The mobility of individuals makes it difficult to design sampling procedures that account for movement into and out of areas with fixed jurisdictional boundaries. Aerial surveys are the gold standard used to obtain data of large mobile species in geographic regions with harsh terrain, but these surveys can be prohibitively expensive and dangerous. Estimating abundance with ground-based census methods have practical advantages, but it can be difficult to simultaneously account for temporary emigration and observer error to avoid biased results. Contemporary research in population ecology increasingly relies on telemetry observations of the states and locations of individuals to gain insight on vital rates, animal movements, and population abundance. Analytical models that use observations of movements to improve estimates of abundance have not been developed. Here we build upon existing multi-state mark-recapture methods using a hierarchical N-mixture model with multiple sources of data, including telemetry data on locations of individuals, to improve estimates of population sizes. We used a state-space approach to model animal movements to approximate the number of marked animals present within the study area at any observation period, thereby accounting for a frequently changing number of marked individuals. We illustrate the approach using data on a population of elk (Cervus elaphus nelsoni) in Northern Colorado, USA. We demonstrate substantial improvement compared to existing abundance estimation methods and corroborate our results from the ground based surveys with estimates from aerial surveys during the same seasons. We develop a hierarchical Bayesian N-mixture model using multiple sources of data on abundance, movement and survival to estimate the population size of a mobile species that uses remote conservation areas. The model improves accuracy of inference relative to previous methods for estimating abundance of open populations. © 2018 by the Ecological Society of America.

Assessing and adjusting for differences between HIV prevalence estimates derived from national population-based surveys and antenatal care surveillance, with applications for Spectrum 2013

PubMed Central

Marsh, Kimberly; Mahy, Mary; Salomon, Joshua A.; Hogan, Daniel R.

2014-01-01

Objective(s): To assess differences between HIV prevalence estimates derived from national population surveys and antenatal care (ANC) surveillance sites and to improve the calibration of ANC-derived estimates in Spectrum 2013 to more appropriately account for differences between these data. Design: Retrospective analysis of national population survey and ANC surveillance data from 25 countries with generalized epidemics in sub-Saharan Africa and 8 countries with concentrated epidemics. Methods: Adult national population survey and ANC surveillance HIV prevalence estimates were compared for all available national population survey data points for the years 1999–2012. For sub-Saharan Africa, a mixed-effects linear regression model determined whether the relationship between national population and ANC estimates was constant across surveys. A new calibration method was developed to incorporate national population survey data directly into the likelihood for HIV prevalence in countries with generalized epidemics. Results were used to develop default rules for adjusting ANC data for countries with no national population surveys. Results: ANC surveillance data typically overestimate population prevalence, although a wide variation, particularly in rural areas, is observed across countries and survey years. The new calibration method yields similar point estimates to previous approaches, but leads to an average 44% increase in the width of 95% uncertainty intervals. Conclusion: Important biases remain in ANC surveillance data for HIV prevalence. The new approach to model-fitting in Spectrum 2013 more appropriately accounts for this bias when producing national estimates in countries with generalized epidemics. In countries with concentrated epidemics, local sex ratios should be used to calibrate ANC surveillance estimates. PMID:25203158

Estimating survival rates with time series of standing age‐structure data

USGS Publications Warehouse

Udevitz, Mark S.; Gogan, Peter J.

2012-01-01

It has long been recognized that age‐structure data contain useful information for assessing the status and dynamics of wildlife populations. For example, age‐specific survival rates can be estimated with just a single sample from the age distribution of a stable, stationary population. For a population that is not stable, age‐specific survival rates can be estimated using techniques such as inverse methods that combine time series of age‐structure data with other demographic data. However, estimation of survival rates using these methods typically requires numerical optimization, a relatively long time series of data, and smoothing or other constraints to provide useful estimates. We developed general models for possibly unstable populations that combine time series of age‐structure data with other demographic data to provide explicit maximum likelihood estimators of age‐specific survival rates with as few as two years of data. As an example, we applied these methods to estimate survival rates for female bison (Bison bison) in Yellowstone National Park, USA. This approach provides a simple tool for monitoring survival rates based on age‐structure data.

Analysis options for estimating status and trends in long-term monitoring

USGS Publications Warehouse

Bart, Jonathan; Beyer, Hawthorne L.

2012-01-01

This chapter describes methods for estimating long-term trends in ecological parameters. Other chapters in this volume discuss more advanced methods for analyzing monitoring data, but these methods may be relatively inaccessible to some readers. Therefore, this chapter provides an introduction to trend analysis for managers and biologists while also discussing general issues relevant to trend assessment in any long-term monitoring program. For simplicity, we focus on temporal trends in population size across years. We refer to the survey results for each year as the “annual means” (e.g. mean per transect, per plot, per time period). The methods apply with little or no modification, however, to formal estimates of population size, other temporal units (e.g. a month), to spatial or other dimensions such as elevation or a north–south gradient, and to other quantities such as chemical or geological parameters. The chapter primarily discusses methods for estimating population-wide parameters rather than studying variation in trend within the population, which can be examined using methods presented in other chapters (e.g. Chapters 7, 12, 20). We begin by reviewing key concepts related to trend analysis. We then describe how to evaluate potential bias in trend estimates. An overview of the statistical models used to quantify trends is then presented. We conclude by showing ways to estimate trends using simple methods that can be implemented with spreadsheets.

Practical Bias Correction in Aerial Surveys of Large Mammals: Validation of Hybrid Double-Observer with Sightability Method against Known Abundance of Feral Horse (Equus caballus) Populations

PubMed Central

2016-01-01

Reliably estimating wildlife abundance is fundamental to effective management. Aerial surveys are one of the only spatially robust tools for estimating large mammal populations, but statistical sampling methods are required to address detection biases that affect accuracy and precision of the estimates. Although various methods for correcting aerial survey bias are employed on large mammal species around the world, these have rarely been rigorously validated. Several populations of feral horses (Equus caballus) in the western United States have been intensively studied, resulting in identification of all unique individuals. This provided a rare opportunity to test aerial survey bias correction on populations of known abundance. We hypothesized that a hybrid method combining simultaneous double-observer and sightability bias correction techniques would accurately estimate abundance. We validated this integrated technique on populations of known size and also on a pair of surveys before and after a known number was removed. Our analysis identified several covariates across the surveys that explained and corrected biases in the estimates. All six tests on known populations produced estimates with deviations from the known value ranging from -8.5% to +13.7% and <0.7 standard errors. Precision varied widely, from 6.1% CV to 25.0% CV. In contrast, the pair of surveys conducted around a known management removal produced an estimated change in population between the surveys that was significantly larger than the known reduction. Although the deviation between was only 9.1%, the precision estimate (CV = 1.6%) may have been artificially low. It was apparent that use of a helicopter in those surveys perturbed the horses, introducing detection error and heterogeneity in a manner that could not be corrected by our statistical models. Our results validate the hybrid method, highlight its potentially broad applicability, identify some limitations, and provide insight and guidance for improving survey designs. PMID:27139732

Practical Bias Correction in Aerial Surveys of Large Mammals: Validation of Hybrid Double-Observer with Sightability Method against Known Abundance of Feral Horse (Equus caballus) Populations.

PubMed

Lubow, Bruce C; Ransom, Jason I

2016-01-01

Reliably estimating wildlife abundance is fundamental to effective management. Aerial surveys are one of the only spatially robust tools for estimating large mammal populations, but statistical sampling methods are required to address detection biases that affect accuracy and precision of the estimates. Although various methods for correcting aerial survey bias are employed on large mammal species around the world, these have rarely been rigorously validated. Several populations of feral horses (Equus caballus) in the western United States have been intensively studied, resulting in identification of all unique individuals. This provided a rare opportunity to test aerial survey bias correction on populations of known abundance. We hypothesized that a hybrid method combining simultaneous double-observer and sightability bias correction techniques would accurately estimate abundance. We validated this integrated technique on populations of known size and also on a pair of surveys before and after a known number was removed. Our analysis identified several covariates across the surveys that explained and corrected biases in the estimates. All six tests on known populations produced estimates with deviations from the known value ranging from -8.5% to +13.7% and <0.7 standard errors. Precision varied widely, from 6.1% CV to 25.0% CV. In contrast, the pair of surveys conducted around a known management removal produced an estimated change in population between the surveys that was significantly larger than the known reduction. Although the deviation between was only 9.1%, the precision estimate (CV = 1.6%) may have been artificially low. It was apparent that use of a helicopter in those surveys perturbed the horses, introducing detection error and heterogeneity in a manner that could not be corrected by our statistical models. Our results validate the hybrid method, highlight its potentially broad applicability, identify some limitations, and provide insight and guidance for improving survey designs.

An Efficient Acoustic Density Estimation Method with Human Detectors Applied to Gibbons in Cambodia.

PubMed

Kidney, Darren; Rawson, Benjamin M; Borchers, David L; Stevenson, Ben C; Marques, Tiago A; Thomas, Len

2016-01-01

Some animal species are hard to see but easy to hear. Standard visual methods for estimating population density for such species are often ineffective or inefficient, but methods based on passive acoustics show more promise. We develop spatially explicit capture-recapture (SECR) methods for territorial vocalising species, in which humans act as an acoustic detector array. We use SECR and estimated bearing data from a single-occasion acoustic survey of a gibbon population in northeastern Cambodia to estimate the density of calling groups. The properties of the estimator are assessed using a simulation study, in which a variety of survey designs are also investigated. We then present a new form of the SECR likelihood for multi-occasion data which accounts for the stochastic availability of animals. In the context of gibbon surveys this allows model-based estimation of the proportion of groups that produce territorial vocalisations on a given day, thereby enabling the density of groups, instead of the density of calling groups, to be estimated. We illustrate the performance of this new estimator by simulation. We show that it is possible to estimate density reliably from human acoustic detections of visually cryptic species using SECR methods. For gibbon surveys we also show that incorporating observers' estimates of bearings to detected groups substantially improves estimator performance. Using the new form of the SECR likelihood we demonstrate that estimates of availability, in addition to population density and detection function parameters, can be obtained from multi-occasion data, and that the detection function parameters are not confounded with the availability parameter. This acoustic SECR method provides a means of obtaining reliable density estimates for territorial vocalising species. It is also efficient in terms of data requirements since since it only requires routine survey data. We anticipate that the low-tech field requirements will make this method an attractive option in many situations where populations can be surveyed acoustically by humans.

When are genetic methods useful for estimating contemporary abundance and detecting population trends?

Treesearch

David A. Tallmon; Dave Gregovich; Robin S. Waples; C. Scott Baker; Jennifer Jackson; Barbara L. Taylor; Eric Archer; Karen K. Martien; Fred W. Allendorf; Michael K. Schwartz

2010-01-01

The utility of microsatellite markers for inferring population size and trend has not been rigorously examined, even though these markers are commonly used to monitor the demography of natural populations. We assessed the ability of a linkage disequilibrium estimator of effective population size (Ne) and a simple capture-recapture estimator of abundance (N) to quantify...

The Effects of Population Size Histories on Estimates of Selection Coefficients from Time-Series Genetic Data

PubMed Central

Jewett, Ethan M.; Steinrücken, Matthias; Song, Yun S.

2016-01-01

Many approaches have been developed for inferring selection coefficients from time series data while accounting for genetic drift. These approaches have been motivated by the intuition that properly accounting for the population size history can significantly improve estimates of selective strengths. However, the improvement in inference accuracy that can be attained by modeling drift has not been characterized. Here, by comparing maximum likelihood estimates of selection coefficients that account for the true population size history with estimates that ignore drift by assuming allele frequencies evolve deterministically in a population of infinite size, we address the following questions: how much can modeling the population size history improve estimates of selection coefficients? How much can mis-inferred population sizes hurt inferences of selection coefficients? We conduct our analysis under the discrete Wright–Fisher model by deriving the exact probability of an allele frequency trajectory in a population of time-varying size and we replicate our results under the diffusion model. For both models, we find that ignoring drift leads to estimates of selection coefficients that are nearly as accurate as estimates that account for the true population history, even when population sizes are small and drift is high. This result is of interest because inference methods that ignore drift are widely used in evolutionary studies and can be many orders of magnitude faster than methods that account for population sizes. PMID:27550904

Evaluation of a method using survey counts and tag data to estimate the number of Pacific walruses (Odobenus rosmarus divergens) using a coastal haulout in northwestern Alaska

USGS Publications Warehouse

Battaile, Brian; Jay, Chadwick V.; Udevitz, Mark S.; Fischbach, Anthony S.

2017-01-01

Increased periods of sparse sea ice over the continental shelf of the Chukchi Sea in late summer have reduced offshore haulout habitat for Pacific walruses (Odobenus rosmarus divergens) and increased opportunities for human activities in the region. Knowing how many walruses could be affected by human activities would be useful to conservation decisions. Currently, there are no adequate estimates of walrus abundance in the northeastern Chukchi Sea during summer–early autumn. Estimating abundance in autumn might be possible from coastal surveys of hauled out walruses during periods when offshore sea ice is unavailable to walruses. We evaluated methods to estimate the size of the walrus population that was using a haulout on the coast of northwestern Alaska in autumn by using aerial photography to count the number of hauled out walruses (herd size) and data from 37 tagged walruses to estimate availability (proportion of population hauled out). We used two methods to estimate availability, direct proportions of hauled out tagged walruses and smoothed proportions using local polynomial regression. Point estimates of herd size (4200–38,000 walruses) and total population size (76,000–287,000 walruses) ranged widely among days and between the two methods of estimating availability. Estimates of population size were influenced most by variation in estimates of availability. Coastal surveys might be improved most by counting walruses when the greatest numbers are hauled out, thereby reducing the influence of availability on population size estimates. The chance of collecting data during peak haulout periods would be improved by conducting multiple surveys.

An Empirical Analysis of the Impact of Recruitment Patterns on RDS Estimates among a Socially Ordered Population of Female Sex Workers in China

PubMed Central

Yamanis, Thespina J.; Merli, M. Giovanna; Neely, William Whipple; Tian, Felicia Feng; Moody, James; Tu, Xiaowen; Gao, Ersheng

2013-01-01

Respondent-driven sampling (RDS) is a method for recruiting “hidden” populations through a network-based, chain and peer referral process. RDS recruits hidden populations more effectively than other sampling methods and promises to generate unbiased estimates of their characteristics. RDS’s faithful representation of hidden populations relies on the validity of core assumptions regarding the unobserved referral process. With empirical recruitment data from an RDS study of female sex workers (FSWs) in Shanghai, we assess the RDS assumption that participants recruit nonpreferentially from among their network alters. We also present a bootstrap method for constructing the confidence intervals around RDS estimates. This approach uniquely incorporates real-world features of the population under study (e.g., the sample’s observed branching structure). We then extend this approach to approximate the distribution of RDS estimates under various peer recruitment scenarios consistent with the data as a means to quantify the impact of recruitment bias and of rejection bias on the RDS estimates. We find that the hierarchical social organization of FSWs leads to recruitment biases by constraining RDS recruitment across social classes and introducing bias in the RDS estimates. PMID:24288418

A modified cluster-sampling method for post-disaster rapid assessment of needs.

PubMed Central

Malilay, J.; Flanders, W. D.; Brogan, D.

1996-01-01

The cluster-sampling method can be used to conduct rapid assessment of health and other needs in communities affected by natural disasters. It is modelled on WHO's Expanded Programme on Immunization method of estimating immunization coverage, but has been modified to provide (1) estimates of the population remaining in an area, and (2) estimates of the number of people in the post-disaster area with specific needs. This approach differs from that used previously in other disasters where rapid needs assessments only estimated the proportion of the population with specific needs. We propose a modified n x k survey design to estimate the remaining population, severity of damage, the proportion and number of people with specific needs, the number of damaged or destroyed and remaining housing units, and the changes in these estimates over a period of time as part of the survey. PMID:8823962

Population trends, survival, and sampling methodologies for a population of Rana draytonii

USGS Publications Warehouse

Fellers, Gary M.; Kleeman, Patrick M.; Miller, David A.W.; Halstead, Brian J.

2017-01-01

Estimating population trends provides valuable information for resource managers, but monitoring programs face trade-offs between the quality and quantity of information gained and the number of sites surveyed. We compared the effectiveness of monitoring techniques for estimating population trends of Rana draytonii (California Red-legged Frog) at Point Reyes National Seashore, California, USA, over a 13-yr period. Our primary goals were to: 1) estimate trends for a focal pond at Point Reyes National Seashore, and 2) evaluate whether egg mass counts could reliably estimate an index of abundance relative to more-intensive capture–mark–recapture methods. Capture–mark–recapture (CMR) surveys of males indicated a stable population from 2005 to 2009, despite low annual apparent survival (26.3%). Egg mass counts from 2000 to 2012 indicated that despite some large fluctuations, the breeding female population was generally stable or increasing, with annual abundance varying between 26 and 130 individuals. Minor modifications to egg mass counts, such as marking egg masses, can allow estimation of egg mass detection probabilities necessary to convert counts to abundance estimates, even when closure of egg mass abundance cannot be assumed within a breeding season. High egg mass detection probabilities (mean per-survey detection probability = 0.98 [0.89–0.99]) indicate that egg mass surveys can be an efficient and reliable method for monitoring population trends of federally threatened R. draytonii. Combining egg mass surveys to estimate trends at many sites with CMR methods to evaluate factors affecting adult survival at focal populations is likely a profitable path forward to enhance understanding and conservation of R. draytonii.

Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study.

PubMed

Fan, Ming; Kuwahara, Hiroyuki; Wang, Xiaolei; Wang, Suojin; Gao, Xin

2015-11-01

Parameter estimation is a challenging computational problem in the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter estimation of gene circuit models from such time-series mRNA data has become an important method for quantitatively dissecting the regulation of gene expression. By focusing on the modeling of gene circuits, we examine here the performance of three types of state-of-the-art parameter estimation methods: population-based methods, online methods and model-decomposition-based methods. Our results show that certain population-based methods are able to generate high-quality parameter solutions. The performance of these methods, however, is heavily dependent on the size of the parameter search space, and their computational requirements substantially increase as the size of the search space increases. In comparison, online methods and model decomposition-based methods are computationally faster alternatives and are less dependent on the size of the search space. Among other things, our results show that a hybrid approach that augments computationally fast methods with local search as a subsequent refinement procedure can substantially increase the quality of their parameter estimates to the level on par with the best solution obtained from the population-based methods while maintaining high computational speed. These suggest that such hybrid methods can be a promising alternative to the more commonly used population-based methods for parameter estimation of gene circuit models when limited prior knowledge about the underlying regulatory mechanisms makes the size of the parameter search space vastly large. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Advantage of population pharmacokinetic method for evaluating the bioequivalence and accuracy of parameter estimation of pidotimod.

PubMed

Huang, Jihan; Li, Mengying; Lv, Yinghua; Yang, Juan; Xu, Ling; Wang, Jingjing; Chen, Junchao; Wang, Kun; He, Yingchun; Zheng, Qingshan

2016-09-01

This study was aimed at exploring the accuracy of population pharmacokinetic method in evaluating the bioequivalence of pidotimod with sparse data profiles and whether this method is suitable for bioequivalence evaluation in special populations such as children with fewer samplings. Methods In this single-dose, two-period crossover study, 20 healthy male Chinese volunteers were randomized 1 : 1 to receive either the test or reference formulation, with a 1-week washout before receiving the alternative formulation. Noncompartmental and population compartmental pharmacokinetic analyses were conducted. Simulated data were analyzed to graphically evaluate the model and the pharmacokinetic characteristics of the two pidotimod formulations. Various sparse sampling scenarios were generated from the real bioequivalence clinical trial data and evaluated by population pharmacokinetic method. The 90% confidence intervals (CIs) for AUC0-12h, AUC0-∞, and Cmax were 97.3 - 118.7%, 96.9 - 118.7%, and 95.1 - 109.8%, respectively, within the 80 - 125% range for bioequivalence using noncompartmental analysis. The population compartmental pharmacokinetics of pidotimod were described using a one-compartment model with first-order absorption and lag time. In the comparison of estimations in different dataset, the estimation of random three- and< fixed four-point sampling strategies can provide results similar to those obtained through rich sampling. The nonlinear mixed-effects model requires fewer data points. Moreover, compared with the noncompartmental analysis method, the pharmacokinetic parameters can be more accurately estimated using nonlinear mixed-effects model. The population pharmacokinetic modeling method was used to assess the bioequivalence of two pidotimod formulations with relatively few sampling points and further validated the bioequivalence of the two formulations. This method may provide useful information for regulating bioequivalence evaluation in special populations.

Multinomial N-mixture models improve the applicability of electrofishing for developing population estimates of stream-dwelling Smallmouth Bass

USGS Publications Warehouse

Mollenhauer, Robert; Brewer, Shannon K.

2017-01-01

Failure to account for variable detection across survey conditions constrains progressive stream ecology and can lead to erroneous stream fish management and conservation decisions. In addition to variable detection’s confounding long-term stream fish population trends, reliable abundance estimates across a wide range of survey conditions are fundamental to establishing species–environment relationships. Despite major advancements in accounting for variable detection when surveying animal populations, these approaches remain largely ignored by stream fish scientists, and CPUE remains the most common metric used by researchers and managers. One notable advancement for addressing the challenges of variable detection is the multinomial N-mixture model. Multinomial N-mixture models use a flexible hierarchical framework to model the detection process across sites as a function of covariates; they also accommodate common fisheries survey methods, such as removal and capture–recapture. Effective monitoring of stream-dwelling Smallmouth Bass Micropterus dolomieu populations has long been challenging; therefore, our objective was to examine the use of multinomial N-mixture models to improve the applicability of electrofishing for estimating absolute abundance. We sampled Smallmouth Bass populations by using tow-barge electrofishing across a range of environmental conditions in streams of the Ozark Highlands ecoregion. Using an information-theoretic approach, we identified effort, water clarity, wetted channel width, and water depth as covariates that were related to variable Smallmouth Bass electrofishing detection. Smallmouth Bass abundance estimates derived from our top model consistently agreed with baseline estimates obtained via snorkel surveys. Additionally, confidence intervals from the multinomial N-mixture models were consistently more precise than those of unbiased Petersen capture–recapture estimates due to the dependency among data sets in the hierarchical framework. We demonstrate the application of this contemporary population estimation method to address a longstanding stream fish management issue. We also detail the advantages and trade-offs of hierarchical population estimation methods relative to CPUE and estimation methods that model each site separately.

Application of a hybrid model to reduce bias and improve precision in population estimates for elk (Cervus elaphus) inhabiting a cold desert ecosystem

USGS Publications Warehouse

Schoenecker, Kathryn A.; Lubow, Bruce C.

2016-01-01

Accurately estimating the size of wildlife populations is critical to wildlife management and conservation of species. Raw counts or “minimum counts” are still used as a basis for wildlife management decisions. Uncorrected raw counts are not only negatively biased due to failure to account for undetected animals, but also provide no estimate of precision on which to judge the utility of counts. We applied a hybrid population estimation technique that combined sightability modeling, radio collar-based mark-resight, and simultaneous double count (double-observer) modeling to estimate the population size of elk in a high elevation desert ecosystem. Combining several models maximizes the strengths of each individual model while minimizing their singular weaknesses. We collected data with aerial helicopter surveys of the elk population in the San Luis Valley and adjacent mountains in Colorado State, USA in 2005 and 2007. We present estimates from 7 alternative analyses: 3 based on different methods for obtaining a raw count and 4 based on different statistical models to correct for sighting probability bias. The most reliable of these approaches is a hybrid double-observer sightability model (model MH), which uses detection patterns of 2 independent observers in a helicopter plus telemetry-based detections of radio collared elk groups. Data were fit to customized mark-resight models with individual sighting covariates. Error estimates were obtained by a bootstrapping procedure. The hybrid method was an improvement over commonly used alternatives, with improved precision compared to sightability modeling and reduced bias compared to double-observer modeling. The resulting population estimate corrected for multiple sources of undercount bias that, if left uncorrected, would have underestimated the true population size by as much as 22.9%. Our comparison of these alternative methods demonstrates how various components of our method contribute to improving the final estimate and demonstrates why each is necessary.

Ancestry estimation and control of population stratification for sequence-based association studies.

PubMed

Wang, Chaolong; Zhan, Xiaowei; Bragg-Gresham, Jennifer; Kang, Hyun Min; Stambolian, Dwight; Chew, Emily Y; Branham, Kari E; Heckenlively, John; Fulton, Robert; Wilson, Richard K; Mardis, Elaine R; Lin, Xihong; Swaroop, Anand; Zöllner, Sebastian; Abecasis, Gonçalo R

2014-04-01

Estimating individual ancestry is important in genetic association studies where population structure leads to false positive signals, although assigning ancestry remains challenging with targeted sequence data. We propose a new method for the accurate estimation of individual genetic ancestry, based on direct analysis of off-target sequence reads, and implement our method in the publicly available LASER software. We validate the method using simulated and empirical data and show that the method can accurately infer worldwide continental ancestry when used with sequencing data sets with whole-genome shotgun coverage as low as 0.001×. For estimates of fine-scale ancestry within Europe, the method performs well with coverage of 0.1×. On an even finer scale, the method improves discrimination between exome-sequenced study participants originating from different provinces within Finland. Finally, we show that our method can be used to improve case-control matching in genetic association studies and to reduce the risk of spurious findings due to population structure.

Change-in-ratio estimators for populations with more than two subclasses

USGS Publications Warehouse

Udevitz, Mark S.; Pollock, Kenneth H.

1991-01-01

Change-in-ratio methods have been developed to estimate the size of populations with two or three population subclasses. Most of these methods require the often unreasonable assumption of equal sampling probabilities for individuals in all subclasses. This paper presents new models based on the weaker assumption that ratios of sampling probabilities are constant over time for populations with three or more subclasses. Estimation under these models requires that a value be assumed for one of these ratios when there are two samples. Explicit expressions are given for the maximum likelihood estimators under models for two samples with three or more subclasses and for three samples with two subclasses. A numerical method using readily available statistical software is described for obtaining the estimators and their standard errors under all of the models. Likelihood ratio tests that can be used in model selection are discussed. Emphasis is on the two-sample, three-subclass models for which Monte-Carlo simulation results and an illustrative example are presented.

Analysis of mating system parameters and population structure in Douglas-fir using single-locus and multilocus methods

Treesearch

D. V. Shaw; R. W. Allard

1981-01-01

Two methods of estimating the proportion of self-fertilization as opposed to outcrossing in plant populations are described. The first method makes use of marker loci one at a time; the second method makes use of multiple marker loci simultaneously. Comparisons of the estimates of proportions of selfing and outcrossing obtained using the two methods are shown to yield...

Estimation of effective population size in continuously distributed populations: There goes the neighborhood

Treesearch

M. C. Neel; K. McKelvey; N. Ryman; M. W. Lloyd; R. Short Bull; F. W. Allendorf; M. K. Schwartz; R. S. Waples

2013-01-01

Use of genetic methods to estimate effective population size (Ne) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating...

Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population.

PubMed

Cros, David; Sánchez, Leopoldo; Cochard, Benoit; Samper, Patrick; Denis, Marie; Bouvet, Jean-Marc; Fernández, Jesús

2014-04-01

Explicit pedigree reconstruction by simulated annealing gave reliable estimates of genealogical coancestry in plant species, especially when selfing rate was lower than 0.6, using a realistic number of markers. Genealogical coancestry information is crucial in plant breeding to estimate genetic parameters and breeding values. The approach of Fernández and Toro (Mol Ecol 15:1657-1667, 2006) to estimate genealogical coancestries from molecular data through pedigree reconstruction was limited to species with separate sexes. In this study it was extended to plants, allowing hermaphroditism and monoecy, with possible selfing. Moreover, some improvements were made to take previous knowledge on the population demographic history into account. The new method was validated using simulated and real datasets. Simulations showed that accuracy of estimates was high with 30 microsatellites, with the best results obtained for selfing rates below 0.6. In these conditions, the root mean square error (RMSE) between the true and estimated genealogical coancestry was small (<0.07), although the number of ancestors was overestimated and the selfing rate could be biased. Simulations also showed that linkage disequilibrium between markers and departure from the Hardy-Weinberg equilibrium in the founder population did not affect the efficiency of the method. Real oil palm data confirmed the simulation results, with a high correlation between the true and estimated genealogical coancestry (>0.9) and a low RMSE (<0.08) using 38 markers. The method was applied to the Deli oil palm population for which pedigree data were scarce. The estimated genealogical coancestries were highly correlated (>0.9) with the molecular coancestries using 100 markers. Reconstructed pedigrees were used to estimate effective population sizes. In conclusion, this method gave reliable genealogical coancestry estimates. The strategy was implemented in the software MOLCOANC 3.0.

Estimating the size of an open population using sparse capture-recapture data.

PubMed

Huggins, Richard; Stoklosa, Jakub; Roach, Cameron; Yip, Paul

2018-03-01

Sparse capture-recapture data from open populations are difficult to analyze using currently available frequentist statistical methods. However, in closed capture-recapture experiments, the Chao sparse estimator (Chao, 1989, Biometrics 45, 427-438) may be used to estimate population sizes when there are few recaptures. Here, we extend the Chao (1989) closed population size estimator to the open population setting by using linear regression and extrapolation techniques. We conduct a small simulation study and apply the models to several sparse capture-recapture data sets. © 2017, The International Biometric Society.

A Monte Carlo Evaluation of Estimated Parameters of Five Shrinkage Estimate Formuli.

ERIC Educational Resources Information Center

Newman, Isadore; And Others

A Monte Carlo study was conducted to estimate the efficiency of and the relationship between five equations and the use of cross validation as methods for estimating shrinkage in multiple correlations. Two of the methods were intended to estimate shrinkage to population values and the other methods were intended to estimate shrinkage from sample…

Sample size planning for composite reliability coefficients: accuracy in parameter estimation via narrow confidence intervals.

PubMed

Terry, Leann; Kelley, Ken

2012-11-01

Composite measures play an important role in psychology and related disciplines. Composite measures almost always have error. Correspondingly, it is important to understand the reliability of the scores from any particular composite measure. However, the point estimates of the reliability of composite measures are fallible and thus all such point estimates should be accompanied by a confidence interval. When confidence intervals are wide, there is much uncertainty in the population value of the reliability coefficient. Given the importance of reporting confidence intervals for estimates of reliability, coupled with the undesirability of wide confidence intervals, we develop methods that allow researchers to plan sample size in order to obtain narrow confidence intervals for population reliability coefficients. We first discuss composite reliability coefficients and then provide a discussion on confidence interval formation for the corresponding population value. Using the accuracy in parameter estimation approach, we develop two methods to obtain accurate estimates of reliability by planning sample size. The first method provides a way to plan sample size so that the expected confidence interval width for the population reliability coefficient is sufficiently narrow. The second method ensures that the confidence interval width will be sufficiently narrow with some desired degree of assurance (e.g., 99% assurance that the 95% confidence interval for the population reliability coefficient will be less than W units wide). The effectiveness of our methods was verified with Monte Carlo simulation studies. We demonstrate how to easily implement the methods with easy-to-use and freely available software. ©2011 The British Psychological Society.

Comparison of methods used to estimate numbers of walruses on sea ice

USGS Publications Warehouse

Udevitz, Mark S.; Gilbert, James R.; Fedoseev, Gennadii A.

2001-01-01

The US and former USSR conducted joint surveys of Pacific walruses on sea ice and at land haul-outs in 1975, 1980, 1985, and 1990. One of the difficulties in interpreting results of these surveys has been that, except for the 1990 survey, the Americans and Soviets used different methods for estimating population size from their respective portions of the sea ice data. We used data exchanged between Soviet and American scientists to compare and evaluate the two estimation procedures and to derive a set of alternative estimates from the 1975, 1980, and 1985 surveys based on a single consistent procedure. Estimation method had only a small effect on total population estimates because most walruses were found at land haul-outs. However, the Soviet method is subject to bias that depends on the distribution of the population on the sea ice and this has important implications for interpreting the ice portions of previously reported surveys for walruses and other pinniped species. We recommend that the American method be used in future surveys. Future research on survey methods for walruses should focus on other potential sources of bias and variation.

Hierarchical modeling of population stability and species group attributes from survey data

USGS Publications Warehouse

Sauer, J.R.; Link, W.A.

2002-01-01

Many ecological studies require analysis of collections of estimates. For example, population change is routinely estimated for many species from surveys such as the North American Breeding Bird Survey (BBS), and the species are grouped and used in comparative analyses. We developed a hierarchical model for estimation of group attributes from a collection of estimates of population trend. The model uses information from predefined groups of species to provide a context and to supplement data for individual species; summaries of group attributes are improved by statistical methods that simultaneously analyze collections of trend estimates. The model is Bayesian; trends are treated as random variables rather than fixed parameters. We use Markov Chain Monte Carlo (MCMC) methods to fit the model. Standard assessments of population stability cannot distinguish magnitude of trend and statistical significance of trend estimates, but the hierarchical model allows us to legitimately describe the probability that a trend is within given bounds. Thus we define population stability in terms of the probability that the magnitude of population change for a species is less than or equal to a predefined threshold. We applied the model to estimates of trend for 399 species from the BBS to estimate the proportion of species with increasing populations and to identify species with unstable populations. Analyses are presented for the collection of all species and for 12 species groups commonly used in BBS summaries. Overall, we estimated that 49% of species in the BBS have positive trends and 33 species have unstable populations. However, the proportion of species with increasing trends differs among habitat groups, with grassland birds having only 19% of species with positive trend estimates and wetland birds having 68% of species with positive trend estimates.

A conceptual guide to detection probability for point counts and other count-based survey methods

Treesearch

D. Archibald McCallum

2005-01-01

Accurate and precise estimates of numbers of animals are vitally needed both to assess population status and to evaluate management decisions. Various methods exist for counting birds, but most of those used with territorial landbirds yield only indices, not true estimates of population size. The need for valid density estimates has spawned a number of models for...

Comparison of an automated Most Probable Number (MPN) technique to traditional plating methods for estimating populations of total aerobes, coliforms and E. coli associated with freshly processed broiler chickens

USDA-ARS?s Scientific Manuscript database

Recently, an instrument (TEMPOTM) has been developed to automate the Most Probable Number (MPN) technique and reduce the effort required to estimate some bacterial populations. We compared the automated MPN technique to traditional microbiological plating methods or PetrifilmTM for estimating the t...

Gene Flow and the Measurement of Dispersal in Plant Populations.

ERIC Educational Resources Information Center

Nicholls, Marc S.

1986-01-01

Reviews methods of estimating pollen and seed dispersals and discusses the extent and frequency of gene exchange within and between populations. Offers suggestions for designing exercises suitable for estimating dispersal distances in natural plant populations. (ML)

Nose profile morphology and accuracy study of nose profile estimation method in Scottish subadult and Indonesian adult populations.

PubMed

Sarilita, Erli; Rynn, Christopher; Mossey, Peter A; Black, Sue; Oscandar, Fahmi

2018-05-01

This study investigated nose profile morphology and its relationship to the skull in Scottish subadult and Indonesian adult populations, with the aim of improving the accuracy of forensic craniofacial reconstruction. Samples of 86 lateral head cephalograms from Dundee Dental School (mean age, 11.8 years) and 335 lateral head cephalograms from the Universitas Padjadjaran Dental Hospital, Bandung, Indonesia (mean age 24.2 years), were measured. The method of nose profile estimation based on skull morphology previously proposed by Rynn and colleagues in 2010 (FSMP 6:20-34) was tested in this study. Following this method, three nasal aperture-related craniometrics and six nose profile dimensions were measured from the cephalograms. To assess the accuracy of the method, six nose profile dimensions were estimated from the three craniometric parameters using the published method and then compared to the actual nose profile dimensions.In the Scottish subadult population, no sexual dimorphism was evident in the measured dimensions. In contrast, sexual dimorphism of the Indonesian adult population was evident in all craniometric and nose profile dimensions; notably, males exhibited statistically significant larger values than females. The published method by Rynn and colleagues (FSMP 6:20-34, 2010) performed better in the Scottish subadult population (mean difference of maximum, 2.35 mm) compared to the Indonesian adult population (mean difference of maximum, 5.42 mm in males and 4.89 mm in females).In addition, regression formulae were derived to estimate nose profile dimensions based on the craniometric measurements for the Indonesian adult population. The published method is not sufficiently accurate for use on the Indonesian population, so the derived method should be used. The accuracy of the published method by Rynn and colleagues (FSMP 6:20-34, 2010) was sufficiently reliable to be applied in Scottish subadult population.

Evaluation of respondent-driven sampling.

PubMed

McCreesh, Nicky; Frost, Simon D W; Seeley, Janet; Katongole, Joseph; Tarsh, Matilda N; Ndunguse, Richard; Jichi, Fatima; Lunel, Natasha L; Maher, Dermot; Johnston, Lisa G; Sonnenberg, Pam; Copas, Andrew J; Hayes, Richard J; White, Richard G

2012-01-01

Respondent-driven sampling is a novel variant of link-tracing sampling for estimating the characteristics of hard-to-reach groups, such as HIV prevalence in sex workers. Despite its use by leading health organizations, the performance of this method in realistic situations is still largely unknown. We evaluated respondent-driven sampling by comparing estimates from a respondent-driven sampling survey with total population data. Total population data on age, tribe, religion, socioeconomic status, sexual activity, and HIV status were available on a population of 2402 male household heads from an open cohort in rural Uganda. A respondent-driven sampling (RDS) survey was carried out in this population, using current methods of sampling (RDS sample) and statistical inference (RDS estimates). Analyses were carried out for the full RDS sample and then repeated for the first 250 recruits (small sample). We recruited 927 household heads. Full and small RDS samples were largely representative of the total population, but both samples underrepresented men who were younger, of higher socioeconomic status, and with unknown sexual activity and HIV status. Respondent-driven sampling statistical inference methods failed to reduce these biases. Only 31%-37% (depending on method and sample size) of RDS estimates were closer to the true population proportions than the RDS sample proportions. Only 50%-74% of respondent-driven sampling bootstrap 95% confidence intervals included the population proportion. Respondent-driven sampling produced a generally representative sample of this well-connected nonhidden population. However, current respondent-driven sampling inference methods failed to reduce bias when it occurred. Whether the data required to remove bias and measure precision can be collected in a respondent-driven sampling survey is unresolved. Respondent-driven sampling should be regarded as a (potentially superior) form of convenience sampling method, and caution is required when interpreting findings based on the sampling method.

Assessment of public health impact of work-related asthma.

PubMed

Jaakkola, Maritta S; Jaakkola, Jouni J K

2012-03-05

Asthma is among the most common chronic diseases in working-aged populations and occupational exposures are important causal agents. Our aims were to evaluate the best methods to assess occurrence, public health impact, and burden to society related to occupational or work-related asthma and to achieve comparable estimates for different populations. We addressed three central questions: 1: What is the best method to assess the occurrence of occupational asthma? We evaluated: 1) assessment of the occurrence of occupational asthma per se, and 2) assessment of adult-onset asthma and the population attributable fractions due to specific occupational exposures. 2: What are the best methods to assess public health impact and burden to society related to occupational or work-related asthma? We evaluated methods based on assessment of excess burden of disease due to specific occupational exposures. 3: How to achieve comparable estimates for different populations? We evaluated comparability of estimates of occurrence and burden attributable to occupational asthma based on different methods. Assessment of the occurrence of occupational asthma per se can be used in countries with good coverage of the identification system for occupational asthma, i.e. countries with well-functioning occupational health services. Assessment based on adult-onset asthma and population attributable fractions due to specific occupational exposures is a good approach to estimate the occurrence of occupational asthma at the population level. For assessment of public health impact from work-related asthma we recommend assessing excess burden of disease due to specific occupational exposures, including excess incidence of asthma complemented by an assessment of disability from it. International comparability of estimates can be best achieved by methods based on population attributable fractions. Public health impact assessment for occupational asthma is central in prevention and health policy planning and could be improved by purposeful development of methods for assessing health benefits from preventive actions. Registry-based methods are suitable for evaluating time-trends of occurrence at a given population but for international comparisons they face serious limitations. Assessment of excess burden of disease due to specific occupational exposure is a useful measure, when there is valid information on population exposure and attributable fractions.

Estimating the Return of Persons Living With HIV/AIDS to New Orleans: Methods for Conducting Disease Surveillance in the Wake of a Natural Disaster

PubMed Central

Robinson, William T.; Wendell, Debbie; Gruber, DeAnn; Foxhood, Joseph; Scalco, M. Beth; Zapata, Amy

2008-01-01

Hurricane Katrina disrupted HIV/AIDS surveillance by invalidating the New Orleans, La, surveillance and population data on persons living with HIV/AIDS. We describes 2 methods—population return and HIV surveillance data—to estimate the return of the infected population to New Orleans. It is estimated that 58% to 64% of 7068 persons living with HIV/AIDS returned by summer 2006. Although developed for HIV planning, these methods could be used with other disease surveillance programs. PMID:18309138

The Effects of Population Size Histories on Estimates of Selection Coefficients from Time-Series Genetic Data.

PubMed

Jewett, Ethan M; Steinrücken, Matthias; Song, Yun S

2016-11-01

Many approaches have been developed for inferring selection coefficients from time series data while accounting for genetic drift. These approaches have been motivated by the intuition that properly accounting for the population size history can significantly improve estimates of selective strengths. However, the improvement in inference accuracy that can be attained by modeling drift has not been characterized. Here, by comparing maximum likelihood estimates of selection coefficients that account for the true population size history with estimates that ignore drift by assuming allele frequencies evolve deterministically in a population of infinite size, we address the following questions: how much can modeling the population size history improve estimates of selection coefficients? How much can mis-inferred population sizes hurt inferences of selection coefficients? We conduct our analysis under the discrete Wright-Fisher model by deriving the exact probability of an allele frequency trajectory in a population of time-varying size and we replicate our results under the diffusion model. For both models, we find that ignoring drift leads to estimates of selection coefficients that are nearly as accurate as estimates that account for the true population history, even when population sizes are small and drift is high. This result is of interest because inference methods that ignore drift are widely used in evolutionary studies and can be many orders of magnitude faster than methods that account for population sizes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The Foraging Ecology of Royal and Sandwich Terns in North Carolina, USA

USGS Publications Warehouse

McGinnis, T.W.; Emslie, S.D.

2001-01-01

Population sizes of territorial male red-winged blackbirds (Agelaius phoeniceus) were determined with counts of territorial males (area count) and a Petersen-Lincoln Index method for roadsides (roadside estimate). Weather conditions and time of day did not influence either method. Combined roadside estimates had smaller error bounds than the individual transect estimates and were not hindered by the problem of zero recaptures. Roadside estimates were usually one-half as large as the area counts, presumably due to an observer bias for marked birds. The roadside estimate provides only an index of major changes in populations of territorial male redwings. When the roadside estimate is employed, the area count should be used to determine the amount and nature of observer bias. For small population surveys, the area count is probably more reliable and accurate than the roadside estimate.

Sampling strategies for estimating brook trout effective population size

Treesearch

Andrew R. Whiteley; Jason A. Coombs; Mark Hudy; Zachary Robinson; Keith H. Nislow; Benjamin H. Letcher

2012-01-01

The influence of sampling strategy on estimates of effective population size (Ne) from single-sample genetic methods has not been rigorously examined, though these methods are increasingly used. For headwater salmonids, spatially close kin association among age-0 individuals suggests that sampling strategy (number of individuals and location from...

The direct cost of epilepsy in the United States: A systematic review of estimates.

PubMed

Begley, Charles E; Durgin, Tracy L

2015-09-01

To develop estimates of the direct cost of epilepsy in the United States for the general epilepsy population and sub-populations by systematically comparing similarities and differences in types of estimates and estimation methods from recently published studies. Papers published since 1995 were identified by systematic literature search. Information on types of estimates, study designs, data sources, types of epilepsy, and estimation methods was extracted from each study. Annual per person cost estimates from methodologically similar studies were identified, converted to 2013 U.S. dollars, and compared. From 4,104 publications discovered in the literature search, 21 were selected for review. Three were added that were published after the search. Eighteen were identified that reported estimates of average annual direct costs for the general epilepsy population in the United States. For general epilepsy populations (comprising all clinically defined subgroups), total direct healthcare costs per person ranged from $10,192 to $47,862 and epilepsy-specific costs ranged from $1,022 to $19,749. Four recent studies using claims data from large general populations yielded relatively similar epilepsy-specific annual cost estimates ranging from $8,412 to $11,354. Although more difficult to compare, studies examining direct cost differences for epilepsy sub-populations indicated a consistent pattern of markedly higher costs for those with uncontrolled or refractory epilepsy, and for those with comorbidities. This systematic review found that various approaches have been used to estimate the direct costs of epilepsy in the United States. However, recent studies using large claims databases and similar methods allow estimation of the direct cost burden of epilepsy for the general disease population, and show that it is greater for some patient subgroups. Additional research is needed to further understand the broader economic burden of epilepsy and how it varies across subpopulations. Wiley Periodicals, Inc. © 2015 International League Against Epilepsy.

Estimating fish populations by removal methods with minnow traps in southeast Alaska streams.

Treesearch

M.D. Bryant

2002-01-01

Passive capture methods, such as minnow traps, are commonly used to capture fish for mark-recapture population estimates; however, they have not been used for removal methods. Minnow traps set for 90-min periods during three or four sequential capture occasions during the summer of 1996 were used to capture coho salmon Oncorhynchus kisutch fry and...

Setting population targets for mammals using body mass as a predictor of population persistence.

PubMed

Hilbers, Jelle P; Santini, Luca; Visconti, Piero; Schipper, Aafke M; Pinto, Cecilia; Rondinini, Carlo; Huijbregts, Mark A J

2017-04-01

Conservation planning and biodiversity assessments need quantitative targets to optimize planning options and assess the adequacy of current species protection. However, targets aiming at persistence require population-specific data, which limit their use in favor of fixed and nonspecific targets, likely leading to unequal distribution of conservation efforts among species. We devised a method to derive equitable population targets; that is, quantitative targets of population size that ensure equal probabilities of persistence across a set of species and that can be easily inferred from species-specific traits. In our method, we used models of population dynamics across a range of life-history traits related to species' body mass to estimate minimum viable population targets. We applied our method to a range of body masses of mammals, from 2 g to 3825 kg. The minimum viable population targets decreased asymptotically with increasing body mass and were on the same order of magnitude as minimum viable population estimates from species- and context-specific studies. Our approach provides a compromise between pragmatic, nonspecific population targets and detailed context-specific estimates of population viability for which only limited data are available. It enables a first estimation of species-specific population targets based on a readily available trait and thus allows setting equitable targets for population persistence in large-scale and multispecies conservation assessments and planning. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Mark-recapture and mark-resight methods for estimating abundance with remote cameras: a carnivore case study

USGS Publications Warehouse

Alanso, Robert S.; McClintock, Brett T.; Lyren, Lisa M.; Boydston, Erin E.; Crooks, Kevin R.

2015-01-01

Abundance estimation of carnivore populations is difficult and has prompted the use of non-invasive detection methods, such as remotely-triggered cameras, to collect data. To analyze photo data, studies focusing on carnivores with unique pelage patterns have utilized a mark-recapture framework and studies of carnivores without unique pelage patterns have used a mark-resight framework. We compared mark-resight and mark-recapture estimation methods to estimate bobcat (Lynx rufus) population sizes, which motivated the development of a new "hybrid" mark-resight model as an alternative to traditional methods. We deployed a sampling grid of 30 cameras throughout the urban southern California study area. Additionally, we physically captured and marked a subset of the bobcat population with GPS telemetry collars. Since we could identify individual bobcats with photos of unique pelage patterns and a subset of the population was physically marked, we were able to use traditional mark-recapture and mark-resight methods, as well as the new “hybrid” mark-resight model we developed to estimate bobcat abundance. We recorded 109 bobcat photos during 4,669 camera nights and physically marked 27 bobcats with GPS telemetry collars. Abundance estimates produced by the traditional mark-recapture, traditional mark-resight, and “hybrid” mark-resight methods were similar, however precision differed depending on the models used. Traditional mark-recapture and mark-resight estimates were relatively imprecise with percent confidence interval lengths exceeding 100% of point estimates. Hybrid mark-resight models produced better precision with percent confidence intervals not exceeding 57%. The increased precision of the hybrid mark-resight method stems from utilizing the complete encounter histories of physically marked individuals (including those never detected by a camera trap) and the encounter histories of naturally marked individuals detected at camera traps. This new estimator may be particularly useful for estimating abundance of uniquely identifiable species that are difficult to sample using camera traps alone.

Population assessment of tropical tuna based on their associative behavior around floating objects.

PubMed

Capello, M; Deneubourg, J L; Robert, M; Holland, K N; Schaefer, K M; Dagorn, L

2016-11-03

Estimating the abundance of pelagic fish species is a challenging task, due to their vast and remote habitat. Despite the development of satellite, archival and acoustic tagging techniques that allow the tracking of marine animals in their natural environments, these technologies have so far been underutilized in developing abundance estimations. We developed a new method for estimating the abundance of tropical tuna that employs these technologies and exploits the aggregative behavior of tuna around floating objects (FADs). We provided estimates of abundance indices based on a simulated set of tagged fish and studied the sensitivity of our method to different association dynamics, FAD numbers, population sizes and heterogeneities of the FAD-array. Taking the case study of yellowfin tuna (Thunnus albacares) acoustically-tagged in Hawaii, we implemented our approach on field data and derived for the first time the ratio between the associated and the total population. With more extensive and long-term monitoring of FAD-associated tunas and good estimates of the numbers of fish at FADs, our method could provide fisheries-independent estimates of populations of tropical tuna. The same approach can be applied to obtain population assessments for any marine and terrestrial species that display associative behavior and from which behavioral data have been acquired using acoustic, archival or satellite tags.

Unified framework to evaluate panmixia and migration direction among multiple sampling locations.

PubMed

Beerli, Peter; Palczewski, Michal

2010-05-01

For many biological investigations, groups of individuals are genetically sampled from several geographic locations. These sampling locations often do not reflect the genetic population structure. We describe a framework using marginal likelihoods to compare and order structured population models, such as testing whether the sampling locations belong to the same randomly mating population or comparing unidirectional and multidirectional gene flow models. In the context of inferences employing Markov chain Monte Carlo methods, the accuracy of the marginal likelihoods depends heavily on the approximation method used to calculate the marginal likelihood. Two methods, modified thermodynamic integration and a stabilized harmonic mean estimator, are compared. With finite Markov chain Monte Carlo run lengths, the harmonic mean estimator may not be consistent. Thermodynamic integration, in contrast, delivers considerably better estimates of the marginal likelihood. The choice of prior distributions does not influence the order and choice of the better models when the marginal likelihood is estimated using thermodynamic integration, whereas with the harmonic mean estimator the influence of the prior is pronounced and the order of the models changes. The approximation of marginal likelihood using thermodynamic integration in MIGRATE allows the evaluation of complex population genetic models, not only of whether sampling locations belong to a single panmictic population, but also of competing complex structured population models.

The Ecological Genetics of Introduced Populations of the Giant Toad BUFO MARINUS. II. Effective Population Size

PubMed Central

Easteal, Simon

1985-01-01

The allele frequencies are described at ten polymorphic enzyme loci (of a total of 22 loci sampled) in 15 populations of the neotropical giant toad, Bufo marinus, introduced to Hawaii and Australia in the 1930s. The history of establishment of the ten populations is described and used as a framework for the analysis of allele frequency variances. The variances are used to determine the effective sizes of the populations. The estimates obtained (390 and 346) are reasonably precise, homogeneous between localities and much smaller than estimates of neighborhood size obtained previously using ecological methods. This discrepancy is discussed, and it is concluded that the estimates obtained here using genetic methods are the more reliable. PMID:3922852

Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis.

PubMed Central

Hey, Jody; Nielsen, Rasmus

2004-01-01

The genetic study of diverging, closely related populations is required for basic questions on demography and speciation, as well as for biodiversity and conservation research. However, it is often unclear whether divergence is due simply to separation or whether populations have also experienced gene flow. These questions can be addressed with a full model of population separation with gene flow, by applying a Markov chain Monte Carlo method for estimating the posterior probability distribution of model parameters. We have generalized this method and made it applicable to data from multiple unlinked loci. These loci can vary in their modes of inheritance, and inheritance scalars can be implemented either as constants or as parameters to be estimated. By treating inheritance scalars as parameters it is also possible to address variation among loci in the impact via linkage of recurrent selective sweeps or background selection. These methods are applied to a large multilocus data set from Drosophila pseudoobscura and D. persimilis. The species are estimated to have diverged approximately 500,000 years ago. Several loci have nonzero estimates of gene flow since the initial separation of the species, with considerable variation in gene flow estimates among loci, in both directions between the species. PMID:15238526

Reduction of feral cat (Felis catus Linnaeus 1758) colony size following hysterectomy of adult female cats.

PubMed

Mendes-de-Almeida, Flavya; Remy, Gabriella L; Gershony, Liza C; Rodrigues, Daniela P; Chame, Marcia; Labarthe, Norma V

2011-06-01

The size of urban cat colonies is limited only by the availability of food and shelter; therefore, their population growth challenges all known population control programs. To test a new population control method, a free-roaming feral cat colony at the Zoological Park in the city of Rio de Janeiro was studied, beginning in 2001. The novel method consisted of performing a hysterectomy on all captured female cats over 6 months of age. To estimate the size of the colony and compare population from year to year, a method of capture-mark-release-recapture was used. The aim was to capture as many individuals as possible, including cats of all ages and gender to estimate numbers of cats in all population categories. Results indicated that the feral cat population remained constant from 2001 to 2004. From 2004 to 2008, the hysterectomy program and population estimates were performed every other year (2006 and 2008). The population was estimated to be 40 cats in 2004, 26 in 2006, and 17 cats in 2008. Although pathogens tend to infect more individuals as the population grows older and maintains natural behavior, these results show that free-roaming feral cat colonies could have their population controlled by a biannual program that focuses on hysterectomy of sexually active female cats. Copyright © 2011 ISFM and AAFP. Published by Elsevier Ltd. All rights reserved.

Non-invasive genetic censusing and monitoring of primate populations.

PubMed

Arandjelovic, Mimi; Vigilant, Linda

2018-03-01

Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio-demographic and behavioral observations. When direct counts of animals are not possible, genetic analysis of non-invasive samples collected from wildlife populations allows estimates of population size with higher accuracy and precision than is possible using indirect signs. Furthermore, in contrast to traditional indirect survey methods, prolonged or periodic genetic sampling across months or years enables inference of group membership, movement, dynamics, and some kin relationships. Data may also be used to estimate sex ratios, sex differences in dispersal distances, and detect gene flow among locations. Recent advances in capture-recapture models have further improved the precision of population estimates derived from non-invasive samples. Simulations using these methods have shown that the confidence interval of point estimates includes the true population size when assumptions of the models are met, and therefore this range of population size minima and maxima should be emphasized in population monitoring studies. Innovations such as the use of sniffer dogs or anti-poaching patrols for sample collection are important to ensure adequate sampling, and the expected development of efficient and cost-effective genotyping by sequencing methods for DNAs derived from non-invasive samples will automate and speed analyses. © 2018 Wiley Periodicals, Inc.

Evaluation of terrestrial and streamside salamander monitoring techniques at Shenandoah National Park

USGS Publications Warehouse

Jung, R.E.; Droege, S.; Sauer, J.R.; Landy, R.B.

2000-01-01

In response to concerns about amphibian declines, a study evaluating and validating amphibian monitoring techniques was initiated in Shenandoah and Big Bend National Parks in the spring of 1998. We evaluate precision, bias, and efficiency of several sampling methods for terrestrial and streamside salamanders in Shenandoah National Park and assess salamander abundance in relation to environmental variables, notably soil and water pH. Terrestrial salamanders, primarily redback salamanders (Plethodon cinereus), were sampled by searching under cover objects during the day in square plots (10 to 35 m2). We compared population indices (mean daily and total counts) with adjusted population estimates from capture-recapture. Analyses suggested that the proportion of salamanders detected (p) during sampling varied among plots, necessitating the use of adjusted population estimates. However, adjusted population estimates were less precise than population indices, and may not be efficient in relating salamander populations to environmental variables. In future sampling, strategic use of capture-recapture to verify consistency of p's among sites may be a reasonable compromise between the possibility of bias in estimation of population size and deficiencies due to inefficiency associated with the estimation of p. The streamside two-lined salamander (Eurycea bislineata) was surveyed using four methods: leaf litter refugia bags, 1 m2 quadrats, 50 x 1 m visual encounter transects, and electric shocking. Comparison of survey methods at nine streams revealed congruent patterns of abundance among sites, suggesting that relative bias among the methods is similar, and that choice of survey method should be based on precision and logistical efficiency. Redback and two-lined salamander abundance were not significantly related to soil or water pH, respectively.

15 CFR 90.8 - Evidence required.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., DEPARTMENT OF COMMERCE PROCEDURE FOR CHALLENGING POPULATION ESTIMATES § 90.8 Evidence required. (a) The... the criteria, standards, and regular processes the Census Bureau employs to generate the population... uses a cohort-component of change method to produce population estimates. Each year, the components of...

On the estimation of spread rate for a biological population

Treesearch

Jim Clark; Lajos Horváth; Mark Lewis

2001-01-01

We propose a nonparametric estimator for the rate of spread of an introduced population. We prove that the limit distribution of the estimator is normal or stable, depending on the behavior of the moment generating function. We show that resampling methods can also be used to approximate the distribution of the estimators.

Appropriateness of the probability approach with a nutrient status biomarker to assess population inadequacy: a study using vitamin D123

PubMed Central

Carriquiry, Alicia L; Bailey, Regan L; Sempos, Christopher T; Yetley, Elizabeth A

2013-01-01

Background: There are questions about the appropriate method for the accurate estimation of the population prevalence of nutrient inadequacy on the basis of a biomarker of nutrient status (BNS). Objective: We determined the applicability of a statistical probability method to a BNS, specifically serum 25-hydroxyvitamin D [25(OH)D]. The ability to meet required statistical assumptions was the central focus. Design: Data on serum 25(OH)D concentrations in adults aged 19–70 y from the 2005–2006 NHANES were used (n = 3871). An Institute of Medicine report provided reference values. We analyzed key assumptions of symmetry, differences in variance, and the independence of distributions. We also corrected observed distributions for within-person variability (WPV). Estimates of vitamin D inadequacy were determined. Results: We showed that the BNS [serum 25(OH)D] met the criteria to use the method for the estimation of the prevalence of inadequacy. The difference between observations corrected compared with uncorrected for WPV was small for serum 25(OH)D but, nonetheless, showed enhanced accuracy because of correction. The method estimated a 19% prevalence of inadequacy in this sample, whereas misclassification inherent in the use of the more traditional 97.5th percentile high-end cutoff inflated the prevalence of inadequacy (36%). Conclusions: When the prevalence of nutrient inadequacy for a population is estimated by using serum 25(OH)D as an example of a BNS, a statistical probability method is appropriate and more accurate in comparison with a high-end cutoff. Contrary to a common misunderstanding, the method does not overlook segments of the population. The accuracy of population estimates of inadequacy is enhanced by the correction of observed measures for WPV. PMID:23097269

The effect of stochiastic technique on estimates of population viability from transition matrix models

USGS Publications Warehouse

Kaye, T.N.; Pyke, David A.

2003-01-01

Population viability analysis is an important tool for conservation biologists, and matrix models that incorporate stochasticity are commonly used for this purpose. However, stochastic simulations may require assumptions about the distribution of matrix parameters, and modelers often select a statistical distribution that seems reasonable without sufficient data to test its fit. We used data from long-term (5a??10 year) studies with 27 populations of five perennial plant species to compare seven methods of incorporating environmental stochasticity. We estimated stochastic population growth rate (a measure of viability) using a matrix-selection method, in which whole observed matrices were selected at random at each time step of the model. In addition, we drew matrix elements (transition probabilities) at random using various statistical distributions: beta, truncated-gamma, truncated-normal, triangular, uniform, or discontinuous/observed. Recruitment rates were held constant at their observed mean values. Two methods of constraining stage-specific survival to a??100% were also compared. Different methods of incorporating stochasticity and constraining matrix column sums interacted in their effects and resulted in different estimates of stochastic growth rate (differing by up to 16%). Modelers should be aware that when constraining stage-specific survival to 100%, different methods may introduce different levels of bias in transition element means, and when this happens, different distributions for generating random transition elements may result in different viability estimates. There was no species effect on the results and the growth rates derived from all methods were highly correlated with one another. We conclude that the absolute value of population viability estimates is sensitive to model assumptions, but the relative ranking of populations (and management treatments) is robust. Furthermore, these results are applicable to a range of perennial plants and possibly other life histories.

Estimating total population size for adult female sea turtles: Accounting for non-nesters

USGS Publications Warehouse

Kendall, W.L.; Richardson, J.I.; Rees, Alan F.

2008-01-01

Assessment of population size and changes therein is important to sea turtle management and population or life history research. Investigators might be interested in testing hypotheses about the effect of current population size or density (number of animals per unit resource) on future population processes. Decision makers might want to determine a level of allowable take of individual turtles of specified life stage. Nevertheless, monitoring most stages of sea turtle life histories is difficult, because obtaining access to individuals is difficult. Although in-water assessments are becoming more common, nesting females and their hatchlings remain the most accessible life stages. In some cases adult females of a given nesting population are sufficiently philopatric that the population itself can be well defined. If a well designed tagging study is conducted on this population, survival, breeding probability, and the size of the nesting population in a given year can be estimated. However, with published statistical methodology the size of the entire breeding population (including those females skipping nesting in that year) cannot be estimated without assuming that each adult female in this population has the same probability of nesting in a given year (even those that had just nested in the previous year). We present a method for estimating the total size of a breeding population (including nesters those skipping nesting) from a tagging study limited to the nesting population, allowing for the probability of nesting in a given year to depend on an individual's nesting status in the previous year (i.e., a Markov process). From this we further develop estimators for rate of growth from year to year in both nesting population and total breeding population, and the proportion of the breeding population that is breeding in a given year. We also discuss assumptions and apply these methods to a breeding population of hawksbill sea turtles (Eretmochelys imbricata) from the Caribbean. We anticipate that this method could also be useful for in-water studies of well defined populations.

The effects of spatial population dataset choice on estimates of population at risk of disease

PubMed Central

2011-01-01

Background The spatial modeling of infectious disease distributions and dynamics is increasingly being undertaken for health services planning and disease control monitoring, implementation, and evaluation. Where risks are heterogeneous in space or dependent on person-to-person transmission, spatial data on human population distributions are required to estimate infectious disease risks, burdens, and dynamics. Several different modeled human population distribution datasets are available and widely used, but the disparities among them and the implications for enumerating disease burdens and populations at risk have not been considered systematically. Here, we quantify some of these effects using global estimates of populations at risk (PAR) of P. falciparum malaria as an example. Methods The recent construction of a global map of P. falciparum malaria endemicity enabled the testing of different gridded population datasets for providing estimates of PAR by endemicity class. The estimated population numbers within each class were calculated for each country using four different global gridded human population datasets: GRUMP (~1 km spatial resolution), LandScan (~1 km), UNEP Global Population Databases (~5 km), and GPW3 (~5 km). More detailed assessments of PAR variation and accuracy were conducted for three African countries where census data were available at a higher administrative-unit level than used by any of the four gridded population datasets. Results The estimates of PAR based on the datasets varied by more than 10 million people for some countries, even accounting for the fact that estimates of population totals made by different agencies are used to correct national totals in these datasets and can vary by more than 5% for many low-income countries. In many cases, these variations in PAR estimates comprised more than 10% of the total national population. The detailed country-level assessments suggested that none of the datasets was consistently more accurate than the others in estimating PAR. The sizes of such differences among modeled human populations were related to variations in the methods, input resolution, and date of the census data underlying each dataset. Data quality varied from country to country within the spatial population datasets. Conclusions Detailed, highly spatially resolved human population data are an essential resource for planning health service delivery for disease control, for the spatial modeling of epidemics, and for decision-making processes related to public health. However, our results highlight that for the low-income regions of the world where disease burden is greatest, existing datasets display substantial variations in estimated population distributions, resulting in uncertainty in disease assessments that utilize them. Increased efforts are required to gather contemporary and spatially detailed demographic data to reduce this uncertainty, particularly in Africa, and to develop population distribution modeling methods that match the rigor, sophistication, and ability to handle uncertainty of contemporary disease mapping and spread modeling. In the meantime, studies that utilize a particular spatial population dataset need to acknowledge the uncertainties inherent within them and consider how the methods and data that comprise each will affect conclusions. PMID:21299885

Characterizing source-sink dynamics with genetic parentage assignments

Treesearch

M. Zachariah Peery; Steven R. Beissinger; Roger F. House; Martine Berube; Laurie A. Hall; Anna Sellas; Per J. Palsboll

2008-01-01

Source-sink dynamics have been suggested to characterize the population structure of many species, but the prevalence of source-sink systems in nature is uncertain because of inherent challenges in estimating migration rates among populations. Migration rates are often difficult to estimate directly with demographic methods, and indirect genetic methods are subject to...

Comparison of 3 estimation methods of mycophenolic acid AUC based on a limited sampling strategy in renal transplant patients.

PubMed

Hulin, Anne; Blanchet, Benoît; Audard, Vincent; Barau, Caroline; Furlan, Valérie; Durrbach, Antoine; Taïeb, Fabrice; Lang, Philippe; Grimbert, Philippe; Tod, Michel

2009-04-01

A significant relationship between mycophenolic acid (MPA) area under the plasma concentration-time curve (AUC) and the risk for rejection has been reported. Based on 3 concentration measurements, 3 approaches have been proposed for the estimation of MPA AUC, involving either a multilinear regression approach model (MLRA) or a Bayesian estimation using either gamma absorption or zero-order absorption population models. The aim of the study was to compare the 3 approaches for the estimation of MPA AUC in 150 renal transplant patients treated with mycophenolate mofetil and tacrolimus. The population parameters were determined in 77 patients (learning study). The AUC estimation methods were compared in the learning population and in 73 patients from another center (validation study). In the latter study, the reference AUCs were estimated by the trapezoidal rule on 8 measurements. MPA concentrations were measured by liquid chromatography. The gamma absorption model gave the best fit. In the learning study, the AUCs estimated by both Bayesian methods were very similar, whereas the multilinear approach was highly correlated but yielded estimates about 20% lower than Bayesian methods. This resulted in dosing recommendations differing by 250 mg/12 h or more in 27% of cases. In the validation study, AUC estimates based on the Bayesian method with gamma absorption model and multilinear regression approach model were, respectively, 12% higher and 7% lower than the reference values. To conclude, the bicompartmental model with gamma absorption rate gave the best fit. The 3 AUC estimation methods are highly correlated but not concordant. For a given patient, the same estimation method should always be used.

Estimating the number of female sex workers in Côte d'Ivoire: results and lessons learned.

PubMed

Vuylsteke, Bea; Sika, Lazare; Semdé, Gisèle; Anoma, Camille; Kacou, Elise; Laga, Marie

2017-09-01

To report on the results of three size estimations of the populations of female sex workers (FSW) in five cities in Côte d'Ivoire and on operational lessons learned, which may be relevant for key population programmes in other parts of the world. We applied three methods: mapping and census, capture-recapture and service multiplier. All were applied between 2008 and 2009 in Abidjan, San Pedro, Bouaké, Yamoussoukro and Abengourou. Abidjan was the city with the highest number of FSW by far, with estimations between 7880 (census) and 13 714 (service multiplier). The estimations in San Pedro, Bouaké and Yamoussoukro were very similar, with figures ranging from 1160 (Yamoussoukro, census) to 1916 (San Pedro, capture-recapture). Important operational lessons were learned, including strategies for mapping, the importance of involving peer sex workers for implementing the capture-recapture and the identification of the right question for the multiplier method. Successful application of three methods to estimate the population size of FSW in five cities in Côte d'Ivoire enabled us to make recommendations for size estimations of key population in low-income countries. © 2017 John Wiley & Sons Ltd.

Estimating the Population Size of Female Sex Worker Population in Tehran, Iran: Application of Direct Capture-Recapture Method.

PubMed

Karami, Manoochehr; Khazaei, Salman; Poorolajal, Jalal; Soltanian, Alireza; Sajadipoor, Mansour

2017-08-01

There is no reliable estimate of the size of female sex workers (FSWs). This study aimed to estimate the size of FSWs in south of Tehran, Iran in 2016 using direct capture-recapture method. In the capture phase, the hangouts of FSWs were mapped as their meeting places. FSWs who agreed to participate in the study tagged with a T-shirt. The recapture phase was implemented at the same places tagging FSWs with a blue bracelet. The total estimated size of FSWs was 690 (95% CI 633, 747). About 89.43% of FSWs experienced sexual intercourse prior to age 20. The prevalence of human immunodeficiency virus infection among FSWs was 4.60%. The estimated population size of FSWs was much more than our expectation. This issue must be the focus of special attention for planning prevention strategies. However, alternative estimates require to estimating the number FSWs, reliably.

Improving Estimation of Ground Casualty Risk From Reentering Space Objects

NASA Technical Reports Server (NTRS)

Ostrom, Chris L.

2017-01-01

A recent improvement to the long-term estimation of ground casualties from reentering space debris is the further refinement and update to the human population distribution. Previous human population distributions were based on global totals with simple scaling factors for future years, or a coarse grid of population counts in a subset of the world's countries, each cell having its own projected growth rate. The newest population model includes a 5-fold refinement in both latitude and longitude resolution. All areas along a single latitude are combined to form a global population distribution as a function of latitude, creating a more accurate population estimation based on non-uniform growth at the country and area levels. Previous risk probability calculations used simplifying assumptions that did not account for the ellipsoidal nature of the Earth. The new method uses first, a simple analytical method to estimate the amount of time spent above each latitude band for a debris object with a given orbit inclination and second, a more complex numerical method that incorporates the effects of a non-spherical Earth. These new results are compared with the prior models to assess the magnitude of the effects on reentry casualty risk.

Improving Estimation of Ground Casualty Risk from Reentering Space Objects

NASA Technical Reports Server (NTRS)

Ostrom, C.

2017-01-01

A recent improvement to the long-term estimation of ground casualties from reentering space debris is the further refinement and update to the human population distribution. Previous human population distributions were based on global totals with simple scaling factors for future years, or a coarse grid of population counts in a subset of the world's countries, each cell having its own projected growth rate. The newest population model includes a 5-fold refinement in both latitude and longitude resolution. All areas along a single latitude are combined to form a global population distribution as a function of latitude, creating a more accurate population estimation based on non-uniform growth at the country and area levels. Previous risk probability calculations used simplifying assumptions that did not account for the ellipsoidal nature of the earth. The new method uses first, a simple analytical method to estimate the amount of time spent above each latitude band for a debris object with a given orbit inclination, and second, a more complex numerical method that incorporates the effects of a non-spherical Earth. These new results are compared with the prior models to assess the magnitude of the effects on reentry casualty risk.

Tagging methods for estimating population size and mortality rates of inland striped bass populations

USGS Publications Warehouse

Hightower, Joseph E.; Pollock, Kenneth H.

2013-01-01

Striped bass Morone saxatilis in inland reservoirs play an important role ecologically and in supporting recreational fishing. To manage these populations, biologists need information about abundance and mortality. Abundance estimates can be used to assess the effectiveness of stocking programs that maintain most reservoir striped bass populations. Mortality estimates can indicate the relative impact of fishing versus natural mortality and the need for harvest regulation. The purpose of this chapter is to evaluate tagging studies as a way of obtaining information about abundance and mortality. These approaches can be grouped into three broad categories: tag recapture, tag return, and telemetry. Tag-recapture methods are typically used to estimate population size and other demographic parameters but are often difficult to apply in large systems. A fishing tournament can be an effective way of generating tagging or recapture effort in large systems, compared to using research sampling only. Tag-return methods that rely on angler harvest and catch and release can be used to estimate fishing (F) and natural (M) mortality rates and are a practical approach in large reservoirs. The key to success in tag-return studies is to build in auxiliary studies to estimate short-term tagging mortality, short- and longterm tag loss, reporting rate, and mortality associated with catch and release. F and M can also be estimated using telemetry tags. Advantages of this approach are that angler nonreporting does not bias estimates and fish with transmitters provide useful ecological data. Cost can be a disadvantage of telemetry studies; thus, combining telemetry tags with conventional tag returns in an integrated analysis is often the optimal approach. In summary, tagging methods can be a powerful tool for assessing the effectiveness of inland striped bass stocking programs and the relative impact of fishing versus natural mortality

Using effort information with change-in-ratio data for population estimation

USGS Publications Warehouse

Udevitz, Mark S.; Pollock, Kenneth H.

1995-01-01

Most change-in-ratio (CIR) methods for estimating fish and wildlife population sizes have been based only on assumptions about how encounter probabilities vary among population subclasses. When information on sampling effort is available, it is also possible to derive CIR estimators based on assumptions about how encounter probabilities vary over time. This paper presents a generalization of previous CIR models that allows explicit consideration of a range of assumptions about the variation of encounter probabilities among subclasses and over time. Explicit estimators are derived under this model for specific sets of assumptions about the encounter probabilities. Numerical methods are presented for obtaining estimators under the full range of possible assumptions. Likelihood ratio tests for these assumptions are described. Emphasis is on obtaining estimators based on assumptions about variation of encounter probabilities over time.

Developing population models with data from marked individuals

USGS Publications Warehouse

Hae Yeong Ryu,; Kevin T. Shoemaker,; Eva Kneip,; Anna Pidgeon,; Patricia Heglund,; Brooke Bateman,; Thogmartin, Wayne E.; Reşit Akçakaya,

2016-01-01

Population viability analysis (PVA) is a powerful tool for biodiversity assessments, but its use has been limited because of the requirements for fully specified population models such as demographic structure, density-dependence, environmental stochasticity, and specification of uncertainties. Developing a fully specified population model from commonly available data sources – notably, mark–recapture studies – remains complicated due to lack of practical methods for estimating fecundity, true survival (as opposed to apparent survival), natural temporal variability in both survival and fecundity, density-dependence in the demographic parameters, and uncertainty in model parameters. We present a general method that estimates all the key parameters required to specify a stochastic, matrix-based population model, constructed using a long-term mark–recapture dataset. Unlike standard mark–recapture analyses, our approach provides estimates of true survival rates and fecundities, their respective natural temporal variabilities, and density-dependence functions, making it possible to construct a population model for long-term projection of population dynamics. Furthermore, our method includes a formal quantification of parameter uncertainty for global (multivariate) sensitivity analysis. We apply this approach to 9 bird species and demonstrate the feasibility of using data from the Monitoring Avian Productivity and Survivorship (MAPS) program. Bias-correction factors for raw estimates of survival and fecundity derived from mark–recapture data (apparent survival and juvenile:adult ratio, respectively) were non-negligible, and corrected parameters were generally more biologically reasonable than their uncorrected counterparts. Our method allows the development of fully specified stochastic population models using a single, widely available data source, substantially reducing the barriers that have until now limited the widespread application of PVA. This method is expected to greatly enhance our understanding of the processes underlying population dynamics and our ability to analyze viability and project trends for species of conservation concern.

Differences in Movement Pattern and Detectability between Males and Females Influence How Common Sampling Methods Estimate Sex Ratio.

PubMed

Rodrigues, João Fabrício Mota; Coelho, Marco Túlio Pacheco

2016-01-01

Sampling the biodiversity is an essential step for conservation, and understanding the efficiency of sampling methods allows us to estimate the quality of our biodiversity data. Sex ratio is an important population characteristic, but until now, no study has evaluated how efficient are the sampling methods commonly used in biodiversity surveys in estimating the sex ratio of populations. We used a virtual ecologist approach to investigate whether active and passive capture methods are able to accurately sample a population's sex ratio and whether differences in movement pattern and detectability between males and females produce biased estimates of sex-ratios when using these methods. Our simulation allowed the recognition of individuals, similar to mark-recapture studies. We found that differences in both movement patterns and detectability between males and females produce biased estimates of sex ratios. However, increasing the sampling effort or the number of sampling days improves the ability of passive or active capture methods to properly sample sex ratio. Thus, prior knowledge regarding movement patterns and detectability for species is important information to guide field studies aiming to understand sex ratio related patterns.

Estimations of population density for selected periods between the Neolithic and AD 1800.

PubMed

Zimmermann, Andreas; Hilpert, Johanna; Wendt, Karl Peter

2009-04-01

Abstract We describe a combination of methods applied to obtain reliable estimations of population density using archaeological data. The combination is based on a hierarchical model of scale levels. The necessary data and methods used to obtain the results are chosen so as to define transfer functions from one scale level to another. We apply our method to data sets from western Germany that cover early Neolithic, Iron Age, Roman, and Merovingian times as well as historical data from AD 1800. Error margins and natural and historical variability are discussed. Our results for nonstate societies are always lower than conventional estimations compiled from the literature, and we discuss the reasons for this finding. At the end, we compare the calculated local and global population densities with other estimations from different parts of the world.

Methods of adjusting the stable estimates of fertility for the effects of mortality decline.

PubMed

Abou-Gamrah, H

1976-03-01

Summary The paper shows how stable population methods, based on the age structure and the rate of increase, may be used to estimate the demographic measures of a quasi-stable population. After a discussion of known methods for adjusting the stable estimates to allow for the effects of mortality decline two new methods are presented, the application of which requires less information. The first method does not need any supplementary information, and the second method requires an estimate of the difference between the last two five-year intercensal rates of increase, i.e. five times the annual change of the rate of increase during the last ten years. For these new methods we do not need to know the onset year of mortality decline as in the Coale-Demeny method, or a long series of rates of increase as in Zachariah's method.

Estimating HIV Incidence Using a Cross-Sectional Survey: Comparison of Three Approaches in a Hyperendemic Setting, Ndhiwa Subcounty, Kenya, 2012.

PubMed

Blaizot, Stéphanie; Kim, Andrea A; Zeh, Clement; Riche, Benjamin; Maman, David; De Cock, Kevin M; Etard, Jean-François; Ecochard, René

2017-05-01

Estimating HIV incidence is critical for identifying groups at risk for HIV infection, planning and targeting interventions, and evaluating these interventions over time. The use of reliable estimation methods for HIV incidence is thus of high importance. The aim of this study was to compare methods for estimating HIV incidence in a population-based cross-sectional survey. The incidence estimation methods evaluated included assay-derived methods, a testing history-derived method, and a probability-based method applied to data from the Ndhiwa HIV Impact in Population Survey (NHIPS). Incidence rates by sex and age and cumulative incidence as a function of age were presented. HIV incidence ranged from 1.38 [95% confidence interval (CI) 0.67-2.09] to 3.30 [95% CI 2.78-3.82] per 100 person-years overall; 0.59 [95% CI 0.00-1.34] to 2.89 [95% CI 0.86-6.45] in men; and 1.62 [95% CI 0.16-6.04] to 4.03 [95% CI 3.30-4.77] per 100 person-years in women. Women had higher incidence rates than men for all methods. Incidence rates were highest among women aged 15-24 and 25-34 years and highest among men aged 25-34 years. Comparison of different methods showed variations in incidence estimates, but they were in agreement to identify most-at-risk groups. The use and comparison of several distinct approaches for estimating incidence are important to provide the best-supported estimate of HIV incidence in the population.

Use of inequality constrained least squares estimation in small area estimation

NASA Astrophysics Data System (ADS)

Abeygunawardana, R. A. B.; Wickremasinghe, W. N.

2017-05-01

Traditional surveys provide estimates that are based only on the sample observations collected for the population characteristic of interest. However, these estimates may have unacceptably large variance for certain domains. Small Area Estimation (SAE) deals with determining precise and accurate estimates for population characteristics of interest for such domains. SAE usually uses least squares or maximum likelihood procedures incorporating prior information and current survey data. Many available methods in SAE use constraints in equality form. However there are practical situations where certain inequality restrictions on model parameters are more realistic. It will lead to Inequality Constrained Least Squares (ICLS) estimates if the method used is least squares. In this study ICLS estimation procedure is applied to many proposed small area estimates.

Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches.

PubMed

Skrbinšek, Tomaž; Jelenčič, Maja; Waits, Lisette; Kos, Ivan; Jerina, Klemen; Trontelj, Peter

2012-02-01

The effective population size (N(e) ) could be the ideal parameter for monitoring populations of conservation concern as it conveniently summarizes both the evolutionary potential of the population and its sensitivity to genetic stochasticity. However, tracing its change through time is difficult in natural populations. We applied four new methods for estimating N(e) from a single sample of genotypes to trace temporal change in N(e) for bears in the Northern Dinaric Mountains. We genotyped 510 bears using 20 microsatellite loci and determined their age. The samples were organized into cohorts with regard to the year when the animals were born and yearly samples with age categories for every year when they were alive. We used the Estimator by Parentage Assignment (EPA) to directly estimate both N(e) and generation interval for each yearly sample. For cohorts, we estimated the effective number of breeders (N(b) ) using linkage disequilibrium, sibship assignment and approximate Bayesian computation methods and extrapolated these estimates to N(e) using the generation interval. The N(e) estimate by EPA is 276 (183-350 95% CI), meeting the inbreeding-avoidance criterion of N(e) > 50 but short of the long-term minimum viable population goal of N(e) > 500. The results obtained by the other methods are highly consistent with this result, and all indicate a rapid increase in N(e) probably in the late 1990s and early 2000s. The new single-sample approaches to the estimation of N(e) provide efficient means for including N(e) in monitoring frameworks and will be of great importance for future management and conservation. © 2012 Blackwell Publishing Ltd.

Study design and the estimation of the size of key populations at risk of HIV: lessons from Viet Nam.

PubMed

Safarnejad, Ali; Groot, Wim; Pavlova, Milena

2018-01-30

Estimation of the size of populations at risk of HIV is a key activity in the surveillance of the HIV epidemic. The existing framework for considering future research needs may provide decision-makers with a basis for a fair process of deciding on the methods of the estimation of the size of key populations at risk of HIV. This study explores the extent to which stakeholders involved with population size estimation agree with this framework, and thus, the study updates the framework. We conducted 16 in-depth interviews with key informants from city and provincial governments, NGOs, research institutes, and the community of people at risk of HIV. Transcripts were analyzed and reviewed for significant statements pertaining to criteria. Variations and agreement around criteria were analyzed, and emerging criteria were validated against the existing framework. Eleven themes emerged which are relevant to the estimation of the size of populations at risk of HIV in Viet Nam. Findings on missing criteria, inclusive participation, community perspectives and conflicting weight and direction of criteria provide insights for an improved framework for the prioritization of population size estimation methods. The findings suggest that the exclusion of community members from decision-making on population size estimation methods in Viet Nam may affect the validity, use, and efficiency of the evidence generated. However, a wider group of decision-makers, including community members among others, may introduce diverse definitions, weight and direction of criteria. Although findings here may not apply to every country with a transitioning economy or to every emerging epidemic, the principles of fair decision-making, value of community participation in decision-making and the expected challenges faced, merit consideration in every situation.

Evaluation of Respondent-Driven Sampling

PubMed Central

McCreesh, Nicky; Frost, Simon; Seeley, Janet; Katongole, Joseph; Tarsh, Matilda Ndagire; Ndunguse, Richard; Jichi, Fatima; Lunel, Natasha L; Maher, Dermot; Johnston, Lisa G; Sonnenberg, Pam; Copas, Andrew J; Hayes, Richard J; White, Richard G

2012-01-01

Background Respondent-driven sampling is a novel variant of link-tracing sampling for estimating the characteristics of hard-to-reach groups, such as HIV prevalence in sex-workers. Despite its use by leading health organizations, the performance of this method in realistic situations is still largely unknown. We evaluated respondent-driven sampling by comparing estimates from a respondent-driven sampling survey with total-population data. Methods Total-population data on age, tribe, religion, socioeconomic status, sexual activity and HIV status were available on a population of 2402 male household-heads from an open cohort in rural Uganda. A respondent-driven sampling (RDS) survey was carried out in this population, employing current methods of sampling (RDS sample) and statistical inference (RDS estimates). Analyses were carried out for the full RDS sample and then repeated for the first 250 recruits (small sample). Results We recruited 927 household-heads. Full and small RDS samples were largely representative of the total population, but both samples under-represented men who were younger, of higher socioeconomic status, and with unknown sexual activity and HIV status. Respondent-driven-sampling statistical-inference methods failed to reduce these biases. Only 31%-37% (depending on method and sample size) of RDS estimates were closer to the true population proportions than the RDS sample proportions. Only 50%-74% of respondent-driven-sampling bootstrap 95% confidence intervals included the population proportion. Conclusions Respondent-driven sampling produced a generally representative sample of this well-connected non-hidden population. However, current respondent-driven-sampling inference methods failed to reduce bias when it occurred. Whether the data required to remove bias and measure precision can be collected in a respondent-driven sampling survey is unresolved. Respondent-driven sampling should be regarded as a (potentially superior) form of convenience-sampling method, and caution is required when interpreting findings based on the sampling method. PMID:22157309

Precision and accuracy of commonly used dental age estimation charts for the New Zealand population.

PubMed

Baylis, Stephanie; Bassed, Richard

2017-08-01

Little research has been undertaken for the New Zealand population in the field of dental age estimation. This research to date indicates there are differences in dental developmental rates between the New Zealand population and other global population groups, and within the New Zealand population itself. Dental age estimation methods range from dental development charts to complex biometric analysis. Dental development charts are not the most accurate method of dental age estimation, but are time saving in their use. They are an excellent screening tool, particularly for post-mortem identification purposes, and for assessing variation from population norms in living individuals. The aim of this study was to test the precision and accuracy of three dental development charts (Schour and Massler, Blenkin and Taylor, and the London Atlas), used to estimate dental age of a sample of New Zealand juveniles between the ages of 5 and 18 years old (n=875). Percentage 'best fit' to correct age category and to expected chart stage were calculated to determine which chart was the most precise for the sample. Chronological ages were compared to estimated dental ages using a two-tailed paired t-test (P<0.05) for each of the three methods. The mean differences between CA and DA were calculated to determine bias and the absolute mean differences were calculated to indicate accuracy. The results of this study show that while accuracy and precision were low for all charts tested against the New Zealand population sample, the Blenkin and Taylor Australian charts performed best overall. Copyright © 2017 Elsevier B.V. All rights reserved.

Estimation of the spatial autocorrelation function: consequences of sampling dynamic populations in space and time

Treesearch

Patrick C. Tobin

2004-01-01

The estimation of spatial autocorrelation in spatially- and temporally-referenced data is fundamental to understanding an organism's population biology. I used four sets of census field data, and developed an idealized space-time dynamic system, to study the behavior of spatial autocorrelation estimates when a practical method of sampling is employed. Estimates...

Quantification of HTLV-1 Clonality and TCR Diversity

PubMed Central

Laydon, Daniel J.; Melamed, Anat; Sim, Aaron; Gillet, Nicolas A.; Sim, Kathleen; Darko, Sam; Kroll, J. Simon; Douek, Daniel C.; Price, David A.; Bangham, Charles R. M.; Asquith, Becca

2014-01-01

Estimation of immunological and microbiological diversity is vital to our understanding of infection and the immune response. For instance, what is the diversity of the T cell repertoire? These questions are partially addressed by high-throughput sequencing techniques that enable identification of immunological and microbiological “species” in a sample. Estimators of the number of unseen species are needed to estimate population diversity from sample diversity. Here we test five widely used non-parametric estimators, and develop and validate a novel method, DivE, to estimate species richness and distribution. We used three independent datasets: (i) viral populations from subjects infected with human T-lymphotropic virus type 1; (ii) T cell antigen receptor clonotype repertoires; and (iii) microbial data from infant faecal samples. When applied to datasets with rarefaction curves that did not plateau, existing estimators systematically increased with sample size. In contrast, DivE consistently and accurately estimated diversity for all datasets. We identify conditions that limit the application of DivE. We also show that DivE can be used to accurately estimate the underlying population frequency distribution. We have developed a novel method that is significantly more accurate than commonly used biodiversity estimators in microbiological and immunological populations. PMID:24945836

Effects of social organization, trap arrangement and density, sampling scale, and population density on bias in population size estimation using some common mark-recapture estimators.

PubMed

Gupta, Manan; Joshi, Amitabh; Vidya, T N C

2017-01-01

Mark-recapture estimators are commonly used for population size estimation, and typically yield unbiased estimates for most solitary species with low to moderate home range sizes. However, these methods assume independence of captures among individuals, an assumption that is clearly violated in social species that show fission-fusion dynamics, such as the Asian elephant. In the specific case of Asian elephants, doubts have been raised about the accuracy of population size estimates. More importantly, the potential problem for the use of mark-recapture methods posed by social organization in general has not been systematically addressed. We developed an individual-based simulation framework to systematically examine the potential effects of type of social organization, as well as other factors such as trap density and arrangement, spatial scale of sampling, and population density, on bias in population sizes estimated by POPAN, Robust Design, and Robust Design with detection heterogeneity. In the present study, we ran simulations with biological, demographic and ecological parameters relevant to Asian elephant populations, but the simulation framework is easily extended to address questions relevant to other social species. We collected capture history data from the simulations, and used those data to test for bias in population size estimation. Social organization significantly affected bias in most analyses, but the effect sizes were variable, depending on other factors. Social organization tended to introduce large bias when trap arrangement was uniform and sampling effort was low. POPAN clearly outperformed the two Robust Design models we tested, yielding close to zero bias if traps were arranged at random in the study area, and when population density and trap density were not too low. Social organization did not have a major effect on bias for these parameter combinations at which POPAN gave more or less unbiased population size estimates. Therefore, the effect of social organization on bias in population estimation could be removed by using POPAN with specific parameter combinations, to obtain population size estimates in a social species.

Effects of social organization, trap arrangement and density, sampling scale, and population density on bias in population size estimation using some common mark-recapture estimators

PubMed Central

Joshi, Amitabh; Vidya, T. N. C.

2017-01-01

Mark-recapture estimators are commonly used for population size estimation, and typically yield unbiased estimates for most solitary species with low to moderate home range sizes. However, these methods assume independence of captures among individuals, an assumption that is clearly violated in social species that show fission-fusion dynamics, such as the Asian elephant. In the specific case of Asian elephants, doubts have been raised about the accuracy of population size estimates. More importantly, the potential problem for the use of mark-recapture methods posed by social organization in general has not been systematically addressed. We developed an individual-based simulation framework to systematically examine the potential effects of type of social organization, as well as other factors such as trap density and arrangement, spatial scale of sampling, and population density, on bias in population sizes estimated by POPAN, Robust Design, and Robust Design with detection heterogeneity. In the present study, we ran simulations with biological, demographic and ecological parameters relevant to Asian elephant populations, but the simulation framework is easily extended to address questions relevant to other social species. We collected capture history data from the simulations, and used those data to test for bias in population size estimation. Social organization significantly affected bias in most analyses, but the effect sizes were variable, depending on other factors. Social organization tended to introduce large bias when trap arrangement was uniform and sampling effort was low. POPAN clearly outperformed the two Robust Design models we tested, yielding close to zero bias if traps were arranged at random in the study area, and when population density and trap density were not too low. Social organization did not have a major effect on bias for these parameter combinations at which POPAN gave more or less unbiased population size estimates. Therefore, the effect of social organization on bias in population estimation could be removed by using POPAN with specific parameter combinations, to obtain population size estimates in a social species. PMID:28306735

Performance comparison of first-order conditional estimation with interaction and Bayesian estimation methods for estimating the population parameters and its distribution from data sets with a low number of subjects.

PubMed

Pradhan, Sudeep; Song, Byungjeong; Lee, Jaeyeon; Chae, Jung-Woo; Kim, Kyung Im; Back, Hyun-Moon; Han, Nayoung; Kwon, Kwang-Il; Yun, Hwi-Yeol

2017-12-01

Exploratory preclinical, as well as clinical trials, may involve a small number of patients, making it difficult to calculate and analyze the pharmacokinetic (PK) parameters, especially if the PK parameters show very high inter-individual variability (IIV). In this study, the performance of a classical first-order conditional estimation with interaction (FOCE-I) and expectation maximization (EM)-based Markov chain Monte Carlo Bayesian (BAYES) estimation methods were compared for estimating the population parameters and its distribution from data sets having a low number of subjects. In this study, 100 data sets were simulated with eight sampling points for each subject and with six different levels of IIV (5%, 10%, 20%, 30%, 50%, and 80%) in their PK parameter distribution. A stochastic simulation and estimation (SSE) study was performed to simultaneously simulate data sets and estimate the parameters using four different methods: FOCE-I only, BAYES(C) (FOCE-I and BAYES composite method), BAYES(F) (BAYES with all true initial parameters and fixed ω 2 ), and BAYES only. Relative root mean squared error (rRMSE) and relative estimation error (REE) were used to analyze the differences between true and estimated values. A case study was performed with a clinical data of theophylline available in NONMEM distribution media. NONMEM software assisted by Pirana, PsN, and Xpose was used to estimate population PK parameters, and R program was used to analyze and plot the results. The rRMSE and REE values of all parameter (fixed effect and random effect) estimates showed that all four methods performed equally at the lower IIV levels, while the FOCE-I method performed better than other EM-based methods at higher IIV levels (greater than 30%). In general, estimates of random-effect parameters showed significant bias and imprecision, irrespective of the estimation method used and the level of IIV. Similar performance of the estimation methods was observed with theophylline dataset. The classical FOCE-I method appeared to estimate the PK parameters more reliably than the BAYES method when using a simple model and data containing only a few subjects. EM-based estimation methods can be considered for adapting to the specific needs of a modeling project at later steps of modeling.

Population estimates of Nearctic shorebirds

USGS Publications Warehouse

Morrison, R.I.G.; Gill, Robert E.; Harrington, B.A.; Skagen, S.K.; Page, G.W.; Gratto-Trevor, C. L.; Haig, S.M.

2000-01-01

Estimates are presented for the population sizes of 53 species of Nearctic shorebirds occurring regularly in North America, plus four species that breed occasionally. Shorebird population sizes were derived from data obtained by a variety of methods from breeding, migration and wintering areas, and formal assessments of accuracy of counts or estimates are rarely available. Accurate estimates exist only for a few species that have been the subject of detailed investigation, and the likely accuracy of most estimates is considered poor or low. Population estimates range from a few tens to several millions. Overall, population estimates most commonly fell in the range of hundreds of thousands, particularly the low hundreds of thousands; estimated population sizes for large shorebird species currently all fall below 500,000. Population size was inversely related to size (mass) of the species, with a statistically significant negative regression between log (population size) and log (mass). Two outlying groups were evident on the regression graph: one, with populations lower than predicted, included species considered either to be "at risk" or particularly hard to count, and a second, with populations higher than predicted, included two species that are hunted. Population estimates are an integral part of conservation plans being developed for shorebirds in the United States and Canada, and may be used to identify areas of key international and regional importance.

Estimates of shorebird populations in North America

USGS Publications Warehouse

Morrison, R.I.G.; Gill, Robert E.; Harrington, B.A.; Skagen, S.K.; Page, G.W.; Gratto-Trevor, C. L.; Haig, S.M.

2001-01-01

Estimates are presented for the population sizes of 53 species of Nearctic shorebirds occurring regularly in North America, plus four species that breed occasionally. Population estimates range from a few tens to several millions. Overall, population estimates most commonly fall in the range of hundreds of thousands, particularly the low hundreds of thousands; estimated population sizes for large shorebird species currently all fall below 500 000. Population size is inversely related to size (mass) of the species, with a statistically significant negative regression between log(population size) and log(mass). Two outlying groups are evident on the regression graph: one, with populations lower than predicted, includes species considered to be either “at risk” or particularly hard to count, and a second, with populations higher than predicted, includes two species that are hunted. Shorebird population sizes were derived from data obtained by a variety of methods from breeding, migration, and wintering areas, and formal assessments of accuracy of counts or estimates are rarely available. Accurate estimates exist only for a few species that have been the subject of detailed investigation, and the likely accuracy of most estimates is considered poor or low. Population estimates are an integral part of conservation plans being developed for shorebirds in the United States and Canada and may be used to identify areas of key international and regional importance.

Comparing Bayesian estimates of genetic differentiation of molecular markers and quantitative traits: an application to Pinus sylvestris.

PubMed

Waldmann, P; García-Gil, M R; Sillanpää, M J

2005-06-01

Comparison of the level of differentiation at neutral molecular markers (estimated as F(ST) or G(ST)) with the level of differentiation at quantitative traits (estimated as Q(ST)) has become a standard tool for inferring that there is differential selection between populations. We estimated Q(ST) of timing of bud set from a latitudinal cline of Pinus sylvestris with a Bayesian hierarchical variance component method utilizing the information on the pre-estimated population structure from neutral molecular markers. Unfortunately, the between-family variances differed substantially between populations that resulted in a bimodal posterior of Q(ST) that could not be compared in any sensible way with the unimodal posterior of the microsatellite F(ST). In order to avoid publishing studies with flawed Q(ST) estimates, we recommend that future studies should present heritability estimates for each trait and population. Moreover, to detect variance heterogeneity in frequentist methods (ANOVA and REML), it is of essential importance to check also that the residuals are normally distributed and do not follow any systematically deviating trends.

Demography of a reintroduced population: moving toward management models for an endangered species, the whooping crane

USGS Publications Warehouse

Servanty, Sabrina; Converse, Sarah J.; Bailey, Larissa L.

2014-01-01

The reintroduction of threatened and endangered species is now a common method for reestablishing populations. Typically, a fundamental objective of reintroduction is to establish a self-sustaining population. Estimation of demographic parameters in reintroduced populations is critical, as these estimates serve multiple purposes. First, they support evaluation of progress toward the fundamental objective via construction of population viability analyses (PVAs) to predict metrics such as probability of persistence. Second, PVAs can be expanded to support evaluation of management actions, via management modeling. Third, the estimates themselves can support evaluation of the demographic performance of the reintroduced population, e.g., via comparison with wild populations. For each of these purposes, thorough treatment of uncertainties in the estimates is critical. Recently developed statistical methods - namely, hierarchical Bayesian implementations of state-space models - allow for effective integration of different types of uncertainty in estimation. We undertook a demographic estimation effort for a reintroduced population of endangered whooping cranes with the purpose of ultimately developing a Bayesian PVA for determining progress toward establishing a self-sustaining population, and for evaluating potential management actions via a Bayesian PVA-based management model. We evaluated individual and temporal variation in demographic parameters based upon a multi-state mark-recapture model. We found that survival was relatively high across time and varied little by sex. There was some indication that survival varied by release method. Survival was similar to that observed in the wild population. Although overall reproduction in this reintroduced population is poor, birds formed social pairs when relatively young, and once a bird was in a social pair, it had a nearly 50% chance of nesting the following breeding season. Also, once a bird had nested, it had a high probability of nesting again. These results are encouraging considering that survival and reproduction have been major challenges in past reintroductions of this species. The demographic estimates developed will support construction of a management model designed to facilitate exploration of management actions of interest, and will provide critical guidance in future planning for this reintroduction. An approach similar to what we describe could be usefully applied to many reintroduced populations.

Dutch population specific sex estimation formulae using the proximal femur.

PubMed

Colman, K L; Janssen, M C L; Stull, K E; van Rijn, R R; Oostra, R J; de Boer, H H; van der Merwe, A E

2018-05-01

Sex estimation techniques are frequently applied in forensic anthropological analyses of unidentified human skeletal remains. While morphological sex estimation methods are able to endure population differences, the classification accuracy of metric sex estimation methods are population-specific. No metric sex estimation method currently exists for the Dutch population. The purpose of this study is to create Dutch population specific sex estimation formulae by means of osteometric analyses of the proximal femur. Since the Netherlands lacks a representative contemporary skeletal reference population, 2D plane reconstructions, derived from clinical computed tomography (CT) data, were used as an alternative source for a representative reference sample. The first part of this study assesses the intra- and inter-observer error, or reliability, of twelve measurements of the proximal femur. The technical error of measurement (TEM) and relative TEM (%TEM) were calculated using 26 dry adult femora. In addition, the agreement, or accuracy, between the dry bone and CT-based measurements was determined by percent agreement. Only reliable and accurate measurements were retained for the logistic regression sex estimation formulae; a training set (n=86) was used to create the models while an independent testing set (n=28) was used to validate the models. Due to high levels of multicollinearity, only single variable models were created. Cross-validated classification accuracies ranged from 86% to 92%. The high cross-validated classification accuracies indicate that the developed formulae can contribute to the biological profile and specifically in sex estimation of unidentified human skeletal remains in the Netherlands. Furthermore, the results indicate that clinical CT data can be a valuable alternative source of data when representative skeletal collections are unavailable. Copyright © 2017 Elsevier B.V. All rights reserved.

Unauthorized Immigration to the United States: Annual Estimates and Components of Change, by State, 1990 to 2010.

PubMed

Warren, Robert; Warren, John Robert

2013-06-01

We describe a method for producing annual estimates of the unauthorized immigrant population in the United Sates and components of population change, for each state and D.C., for 1990 to 2010. We quantify a sharp drop in the number of unauthorized immigrants arriving since 2000, and we demonstrate the role of departures from the population (emigration, adjustment to legal status, removal by the Department of Homeland Security (DHS), and deaths) in reducing population growth from one million in 2000 to population losses in 2008 and 2009. The number arriving in the U.S. peaked at more than one million in 1999 to 2001, and then declined rapidly through 2009. We provide evidence that population growth stopped after 2007 primarily because entries declined and not because emigration increased during the economic crisis. Our estimates of the total unauthorized immigrant population in the U.S. and in the top ten states are comparable to those produced by DHS and the Pew Hispanic Center. For the remaining states and D.C., our data and methods produce estimates with smaller ranges of sampling error.

Estimating the size of key populations at higher risk of HIV infection: a summary of experiences and lessons presented during a technical meeting on size estimation among key populations in Asian countries

PubMed Central

Calleja, Jesus Maria Garcia; Zhao, Jinkou; Reddy, Amala; Seguy, Nicole

2014-01-01

Problem Size estimates of key populations at higher risk of HIV exposure are recognized as critical for understanding the trajectory of the HIV epidemic and planning and monitoring an effective response, especially for countries with concentrated and low epidemics such as those in Asia. Context To help countries estimate population sizes of key populations, global guidelines were updated in 2011 to reflect new technical developments and recent field experiences in applying these methods. Action In September 2013, a meeting of programme managers and experts experienced with population size estimates (PSE) for key populations was held for 13 Asian countries. This article summarizes the key results presented, shares practical lessons learnt and reviews the methodological approaches from implementing PSE in 13 countries. Lessons learnt It is important to build capacity to collect, analyse and use PSE data; establish a technical review group; and implement a transparent, well documented process. Countries should adapt global PSE guidelines and maintain operational definitions that are more relevant and useable for country programmes. Development of methods for non-venue-based key populations requires more investment and collaborative efforts between countries and among partners. PMID:25320676

Adaptive cluster sampling: An efficient method for assessing inconspicuous species

Treesearch

Andrea M. Silletti; Joan Walker

2003-01-01

Restorationistis typically evaluate the success of a project by estimating the population sizes of species that have been planted or seeded. Because total census is raely feasible, they must rely on sampling methods for population estimates. However, traditional random sampling designs may be inefficient for species that, for one reason or another, are challenging to...

Estimating the number of animals in wildlife populations

USGS Publications Warehouse

Lancia, R.A.; Kendall, W.L.; Pollock, K.H.; Nichols, J.D.; Braun, Clait E.

2005-01-01

INTRODUCTION In 1938, Howard M. Wight devoted 9 pages, which was an entire chapter in the first wildlife management techniques manual, to what he termed 'census' methods. As books and chapters such as this attest, the volume of literature on this subject has grown tremendously. Abundance estimation remains an active area of biometrical research, as reflected in the many differences between this chapter and the similar contribution in the previous manual. Our intent in this chapter is to present an overview of the basic and most widely used population estimation techniques and to provide an entree to the relevant literature. Several possible approaches could be taken in writing a chapter dealing with population estimation. For example, we could provide a detailed treatment focusing on statistical models and on derivation of estimators based on these models. Although a chapter using this approach might provide a valuable reference for quantitative biologists and biometricians, it would be of limited use to many field biologists and wildlife managers. Another approach would be to focus on details of actually applying different population estimation techniques. This approach would include both field application (e.g., how to set out a trapping grid or conduct an aerial survey) and detailed instructions on how to use the resulting data with appropriate estimation equations. We are reluctant to attempt such an approach, however, because of the tremendous diversity of real-world field situations defined by factors such as the animal being studied, habitat, available resources, and because of our resultant inability to provide detailed instructions for all possible cases. We believe it is more useful to provide the reader with the conceptual basis underlying estimation methods. Thus, we have tried to provide intuitive explanations for how basic methods work. In doing so, we present relevant estimation equations for many methods and provide citations of more detailed treatments covering both statistical considerations and field applications. We have chosen to present methods that are representative of classes of estimators, rather than address every available method. Our hope is that this chapter will provide the reader with enough background to make an informed decision about what general method(s) will likely perform well in any particular field situation. Readers with a more quantitative background may then be able to consult detailed references and tailor the selected method to suit their particular needs. Less quantitative readers should consult a biometrician, preferably one with experience in wildlife studies, for this 'tailoring,' with the hope they will be able to do so with a basic understanding of the general method, thereby permitting useful interaction and discussion with the biometrician. SUMMARY Estimating the abundance or density of animals in wild populations is not a trivial matter. Virtually all techniques involve the basic problem of estimating the probability of seeing, capturing, or otherwise detecting animals during some type of survey and, in many cases, sampling concerns as well. In the case of indices, the detection probability is assumed to be constant (but unknown). We caution against use of indices unless this assumption can be verified for the comparison(s) of interest. In the case of population estimation, many methods have been developed over the years to estimate the probability of detection associated with various kinds of count statistics. Techniques range from complete counts, where sampling concerns often dominate, to incomplete counts where detection probabilities are also important. Some examples of the latter are multiple observers, removal methods, and capture-recapture. Before embarking on a survey to estimate the size of a population, one must understand clearly what information is needed and for what purpose the information will be used. The key to derivin

Size matters: insights from an allometric approach to evaluate control methods for invasive Australian Rhinella marina.

PubMed

Beaty, Lynne E; Salice, Christopher J

2013-10-01

Invasive species are costly and difficult to control. In order to gain a mechanistic understanding of potential control measures, individual-based models uniquely parameterized to reflect the salient life-history characteristics of invasive species are useful. Using invasive Australian Rhinella marina as a case study, we constructed a cohort- and individual-based population simulation that incorporates growth and body size of terrestrial stages. We used this allometric approach to examine the efficacy of nontraditional control methods (i.e., tadpole alarm chemicals and native meat ants) that may have indirect effects on population dynamics mediated by effects on body size. We compared population estimates resulting from these control methods with traditional hand removal. We also conducted a sensitivity analysis to investigate the effect that model parameters, specifically those associated with growth and body size, had on adult population estimates. Incremental increases in hand removal of adults and juveniles caused nonlinear decreases in adult population estimates, suggesting less return with increased investment in hand-removal efforts. Applying tadpole alarm chemicals or meat ants decreased adult population estimates on the same level as removing 15-25% of adults and juveniles by hand. The combined application of tadpole alarm chemicals and meat ants resulted in approximately 80% decrease in adult abundance, the largest of any applied control method. In further support of the nontraditional control methods, which greatly affected the metamorph stage, our model was most sensitive to changes in metamorph survival, juvenile survival, metamorph growth rate, and adult survival. Our results highlight the use and insights that can be gained from individual-based models that incorporate growth and body size and the potential success that nontraditional control methods could have in controlling established, invasive Rhinella marina populations.

Dental age estimation of growing children by measurement of open apices: A Malaysian formula

PubMed Central

Cugati, Navaneetha; Kumaresan, Ramesh; Srinivasan, Balamanikanda; Karthikeyan, Priyadarshini

2015-01-01

Background: Age estimation is of prime importance in forensic science and clinical dentistry. Age estimation based on teeth development is one reliable approach. Many radiographic methods are proposed on the Western population for estimating dental age, and a similar assessment was found to be inadequate in Malaysian population. Hence, this study aims at formulating a regression model for dental age estimation in Malaysian children population using Cameriere's method. Materials and Methods: Orthopantomographs of 421 Malaysian children aged between 5 and 16 years involving all the three ethnic origins were digitalized and analyzed using Cameriere's method of age estimation. The subjects’ age was modeled as a function of the morphological variables, gender (g), ethnicity, sum of normalized open apices (s), number of tooth with completed root formation (N0) and the first-order interaction between s and N0. Results: The variables that contributed significantly to the fit were included in the regression model, yielding the following formula: Age = 11.368-0.345g + 0.553No -1.096s - 0.380s.No, where g is a variable, 1 for males and 2 for females. The equation explained 87.1% of total deviance. Conclusion: The results obtained insist on reframing the original Cameriere's formula to suit the population of the nation specifically. Further studies are to be conducted to evaluate the applicability of this formula on a larger sample size. PMID:26816464

Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity.

PubMed

Trask, Amanda E; Bignal, Eric M; McCracken, Davy I; Piertney, Stuart B; Reid, Jane M

2017-09-01

A population's effective size (N e ) is a key parameter that shapes rates of inbreeding and loss of genetic diversity, thereby influencing evolutionary processes and population viability. However, estimating N e , and identifying key demographic mechanisms that underlie the N e to census population size (N) ratio, remains challenging, especially for small populations with overlapping generations and substantial environmental and demographic stochasticity and hence dynamic age-structure. A sophisticated demographic method of estimating N e /N, which uses Fisher's reproductive value to account for dynamic age-structure, has been formulated. However, this method requires detailed individual- and population-level data on sex- and age-specific reproduction and survival, and has rarely been implemented. Here, we use the reproductive value method and detailed demographic data to estimate N e /N for a small and apparently isolated red-billed chough (Pyrrhocorax pyrrhocorax) population of high conservation concern. We additionally calculated two single-sample molecular genetic estimates of N e to corroborate the demographic estimate and examine evidence for unobserved immigration and gene flow. The demographic estimate of N e /N was 0.21, reflecting a high total demographic variance (σ2dg) of 0.71. Females and males made similar overall contributions to σ2dg. However, contributions varied among sex-age classes, with greater contributions from 3 year-old females than males, but greater contributions from ≥5 year-old males than females. The demographic estimate of N e was ~30, suggesting that rates of increase of inbreeding and loss of genetic variation per generation will be relatively high. Molecular genetic estimates of N e computed from linkage disequilibrium and approximate Bayesian computation were approximately 50 and 30, respectively, providing no evidence of substantial unobserved immigration which could bias demographic estimates of N e . Our analyses identify key sex-age classes contributing to demographic variance and thus decreasing N e /N in a small age-structured population inhabiting a variable environment. They thereby demonstrate how assessments of N e can incorporate stochastic sex- and age-specific demography and elucidate key demographic processes affecting a population's evolutionary trajectory and viability. Furthermore, our analyses show that N e for the focal chough population is critically small, implying that management to re-establish genetic connectivity may be required to ensure population viability. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Expected number of asbestos-related lung cancers in the Netherlands in the next two decades: a comparison of methods.

PubMed

Van der Bij, Sjoukje; Vermeulen, Roel C H; Portengen, Lützen; Moons, Karel G M; Koffijberg, Hendrik

2016-05-01

Exposure to asbestos fibres increases the risk of mesothelioma and lung cancer. Although the vast majority of mesothelioma cases are caused by asbestos exposure, the number of asbestos-related lung cancers is less clear. This number cannot be determined directly as lung cancer causes are not clinically distinguishable but may be estimated using varying modelling methods. We applied three different modelling methods to the Dutch population supplemented with uncertainty ranges (UR) due to uncertainty in model input values. The first method estimated asbestos-related lung cancer cases directly from observed and predicted mesothelioma cases in an age-period-cohort analysis. The second method used evidence on the fraction of lung cancer cases attributable (population attributable risk (PAR)) to asbestos exposure. The third method incorporated risk estimates and population exposure estimates to perform a life table analysis. The three methods varied substantially in incorporated evidence. Moreover, the estimated number of asbestos-related lung cancer cases in the Netherlands between 2011 and 2030 depended crucially on the actual method applied, as the mesothelioma method predicts 17 500 expected cases (UR 7000-57 000), the PAR method predicts 12 150 cases (UR 6700-19 000), and the life table analysis predicts 6800 cases (UR 6800-33 850). The three different methods described resulted in absolute estimates varying by a factor of ∼2.5. These results show that accurate estimation of the impact of asbestos exposure on the lung cancer burden remains a challenge. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Constructing stage-structured matrix population models from life tables: comparison of methods

PubMed Central

Diaz-Lopez, Jasmin

2017-01-01

A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates) of a population and can be used for calculating an asymptotic finite population growth rate (λ) and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism’s life history type and the true values of λ. In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ. Here, the weights are given by survivorship curve after discounting with λ. To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used for discounting the rate, was the best approach. However, stage-structured models performed poorly in estimating generation time, regardless of the methods used for constructing the models. Based on the results, we recommend using an age-structured matrix population model or the Euler-Lotka equation for calculating λ and generation time when life table data are available. Then, these age-structured vital rates can be converted into a stage-structured model for further analyses. PMID:29085763

Constructing stage-structured matrix population models from life tables: comparison of methods.

PubMed

Fujiwara, Masami; Diaz-Lopez, Jasmin

2017-01-01

A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates) of a population and can be used for calculating an asymptotic finite population growth rate ( λ ) and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism's life history type and the true values of λ . In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ . Here, the weights are given by survivorship curve after discounting with λ . To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used for discounting the rate, was the best approach. However, stage-structured models performed poorly in estimating generation time, regardless of the methods used for constructing the models. Based on the results, we recommend using an age-structured matrix population model or the Euler-Lotka equation for calculating λ and generation time when life table data are available. Then, these age-structured vital rates can be converted into a stage-structured model for further analyses.

Capture-recapture methodology

USGS Publications Warehouse

Gould, William R.; Kendall, William L.

2013-01-01

Capture-recapture methods were initially developed to estimate human population abundance, but since that time have seen widespread use for fish and wildlife populations to estimate and model various parameters of population, metapopulation, and disease dynamics. Repeated sampling of marked animals provides information for estimating abundance and tracking the fate of individuals in the face of imperfect detection. Mark types have evolved from clipping or tagging to use of noninvasive methods such as photography of natural markings and DNA collection from feces. Survival estimation has been emphasized more recently as have transition probabilities between life history states and/or geographical locations, even where some states are unobservable or uncertain. Sophisticated software has been developed to handle highly parameterized models, including environmental and individual covariates, to conduct model selection, and to employ various estimation approaches such as maximum likelihood and Bayesian approaches. With these user-friendly tools, complex statistical models for studying population dynamics have been made available to ecologists. The future will include a continuing trend toward integrating data types, both for tagged and untagged individuals, to produce more precise and robust population models.

Efficacy of using data from angler-caught Burbot to estimate population rate functions

USGS Publications Warehouse

Brauer, Tucker A.; Rhea, Darren T.; Walrath, John D.; Quist, Michael C.

2018-01-01

The effective management of a fish population depends on the collection of accurate demographic data from that population. Since demographic data are often expensive and difficult to obtain, developing cost‐effective and efficient collection methods is a high priority. This research evaluates the efficacy of using angler‐supplied data to monitor a nonnative population of Burbot Lota lota. Age and growth estimates were compared between Burbot collected by anglers and those collected in trammel nets from two Wyoming reservoirs. Collection methods produced different length‐frequency distributions, but no difference was observed in age‐frequency distributions. Mean back‐calculated lengths at age revealed that netted Burbot grew faster than angled Burbot in Fontenelle Reservoir. In contrast, angled Burbot grew slightly faster than netted Burbot in Flaming Gorge Reservoir. Von Bertalanffy growth models differed between collection methods, but differences in parameter estimates were minor. Estimates of total annual mortality (A) of Burbot in Fontenelle Reservoir were comparable between angled (A = 35.4%) and netted fish (33.9%); similar results were observed in Flaming Gorge Reservoir for angled (29.3%) and netted fish (30.5%). Beverton–Holt yield‐per‐recruit models were fit using data from both collection methods. Estimated yield differed by less than 15% between data sources and reservoir. Spawning potential ratios indicated that an exploitation rate of 20% would be required to induce recruitment overfishing in either reservoir, regardless of data source. Results of this study suggest that angler‐supplied data are useful for monitoring Burbot population dynamics in Wyoming and may be an option to efficiently monitor other fish populations in North America.

A systematic evaluation of different methods for calculating adolescent vaccination levels using immunization information system data.

PubMed

Gowda, Charitha; Dong, Shiming; Potter, Rachel C; Dombkowski, Kevin J; Stokley, Shannon; Dempsey, Amanda F

2013-01-01

Immunization information systems (IISs) are valuable surveillance tools; however, population relocation may introduce bias when determining immunization coverage. We explored alternative methods for estimating the vaccine-eligible population when calculating adolescent immunization levels using a statewide IIS. We performed a retrospective analysis of the Michigan State Care Improvement Registry (MCIR) for all adolescents aged 11-18 years registered in the MCIR as of October 2010. We explored four methods for determining denominators: (1) including all adolescents with MCIR records, (2) excluding adolescents with out-of-state residence, (3) further excluding those without MCIR activity ≥ 10 years prior to the evaluation date, and (4) using a denominator based on U.S. Census data. We estimated state- and county-specific coverage levels for four adolescent vaccines. We found a 20% difference in estimated vaccination coverage between the most inclusive and restrictive denominator populations. Although there was some variability among the four methods in vaccination at the state level (2%-11%), greater variation occurred at the county level (up to 21%). This variation was substantial enough to potentially impact public health assessments of immunization programs. Generally, vaccines with higher coverage levels had greater absolute variation, as did counties with smaller populations. At the county level, using the four denominator calculation methods resulted in substantial differences in estimated adolescent immunization rates that were less apparent when aggregated at the state level. Further research is needed to ascertain the most appropriate method for estimating vaccine coverage levels using IIS data.

An elusive paleodemography? A comparison of two methods for estimating the adult age distribution of deaths at late Classic Copan, Honduras.

PubMed

Storey, Rebecca

2007-01-01

Comparison of different adult age estimation methods on the same skeletal sample with unknown ages could forward paleodemographic inference, while researchers sort out various controversies. The original aging method for the auricular surface (Lovejoy et al., 1985a) assigned an age estimation based on several separate characteristics. Researchers have found this original method hard to apply. It is usually forgotten that before assigning an age, there was a seriation, an ordering of all available individuals from youngest to oldest. Thus, age estimation reflected the place of an individual within its sample. A recent article (Buckberry and Chamberlain, 2002) proposed a revised method that scores theses various characteristics into age stages, which can then be used with a Bayesian method to estimate an adult age distribution for the sample. Both methods were applied to the adult auricular surfaces of a Pre-Columbian Maya skeletal population from Copan, Honduras and resulted in age distributions with significant numbers of older adults. However, contrary to the usual paleodemographic distribution, one Bayesian estimation based on uniform prior probabilities yielded a population with 57% of the ages at death over 65, while another based on a high mortality life table still had 12% of the individuals aged over 75 years. The seriation method yielded an age distribution more similar to that known from preindustrial historical situations, without excessive longevity of adults. Paleodemography must still wrestle with its elusive goal of accurate adult age estimation from skeletons, a necessary base for demographic study of past populations. (c) 2006 Wiley-Liss, Inc

Monitoring Dolphins in an Urban Marine System: Total and Effective Population Size Estimates of Indo-Pacific Bottlenose Dolphins in Moreton Bay, Australia

PubMed Central

Ansmann, Ina C.; Lanyon, Janet M.; Seddon, Jennifer M.; Parra, Guido J.

2013-01-01

Moreton Bay, Queensland, Australia is an area of high biodiversity and conservation value and home to two sympatric sub-populations of Indo-Pacific bottlenose dolphins (Tursiops aduncus). These dolphins live in close proximity to major urban developments. Successful management requires information regarding their abundance. Here, we estimate total and effective population sizes of bottlenose dolphins in Moreton Bay using photo-identification and genetic data collected during boat-based surveys in 2008–2010. Abundance (N) was estimated using open population mark-recapture models based on sighting histories of distinctive individuals. Effective population size (Ne) was estimated using the linkage disequilibrium method based on nuclear genetic data at 20 microsatellite markers in skin samples, and corrected for bias caused by overlapping generations (Nec). A total of 174 sightings of dolphin groups were recorded and 365 different individuals identified. Over the whole of Moreton Bay, a population size N of 554±22.2 (SE) (95% CI: 510–598) was estimated. The southern bay sub-population was small at an estimated N = 193±6.4 (SE) (95% CI: 181–207), while the North sub-population was more numerous, with 446±56 (SE) (95% CI: 336–556) individuals. The small estimated effective population size of the southern sub-population (Nec = 56, 95% CI: 33–128) raises conservation concerns. A power analysis suggested that to reliably detect small (5%) declines in size of this population would require substantial survey effort (>4 years of annual mark-recapture surveys) at the precision levels achieved here. To ensure that ecological as well as genetic diversity within this population of bottlenose dolphins is preserved, we consider that North and South sub-populations should be treated as separate management units. Systematic surveys over smaller areas holding locally-adapted sub-populations are suggested as an alternative method for increasing ability to detect abundance trends. PMID:23755197

Transforming geographic scale: a comparison of combined population and areal weighting to other interpolation methods.

PubMed

Hallisey, Elaine; Tai, Eric; Berens, Andrew; Wilt, Grete; Peipins, Lucy; Lewis, Brian; Graham, Shannon; Flanagan, Barry; Lunsford, Natasha Buchanan

2017-08-07

Transforming spatial data from one scale to another is a challenge in geographic analysis. As part of a larger, primary study to determine a possible association between travel barriers to pediatric cancer facilities and adolescent cancer mortality across the United States, we examined methods to estimate mortality within zones at varying distances from these facilities: (1) geographic centroid assignment, (2) population-weighted centroid assignment, (3) simple areal weighting, (4) combined population and areal weighting, and (5) geostatistical areal interpolation. For the primary study, we used county mortality counts from the National Center for Health Statistics (NCHS) and population data by census tract for the United States to estimate zone mortality. In this paper, to evaluate the five mortality estimation methods, we employed address-level mortality data from the state of Georgia in conjunction with census data. Our objective here is to identify the simplest method that returns accurate mortality estimates. The distribution of Georgia county adolescent cancer mortality counts mirrors the Poisson distribution of the NCHS counts for the U.S. Likewise, zone value patterns, along with the error measures of hierarchy and fit, are similar for the state and the nation. Therefore, Georgia data are suitable for methods testing. The mean absolute value arithmetic differences between the observed counts for Georgia and the five methods were 5.50, 5.00, 4.17, 2.74, and 3.43, respectively. Comparing the methods through paired t-tests of absolute value arithmetic differences showed no statistical difference among the methods. However, we found a strong positive correlation (r = 0.63) between estimated Georgia mortality rates and combined weighting rates at zone level. Most importantly, Bland-Altman plots indicated acceptable agreement between paired arithmetic differences of Georgia rates and combined population and areal weighting rates. This research contributes to the literature on areal interpolation, demonstrating that combined population and areal weighting, compared to other tested methods, returns the most accurate estimates of mortality in transforming small counts by county to aggregated counts for large, non-standard study zones. This conceptually simple cartographic method should be of interest to public health practitioners and researchers limited to analysis of data for relatively large enumeration units.

Effects of scale of movement, detection probability, and true population density on common methods of estimating population density

DOE PAGES

Keiter, David A.; Davis, Amy J.; Rhodes, Olin E.; ...

2017-08-25

Knowledge of population density is necessary for effective management and conservation of wildlife, yet rarely are estimators compared in their robustness to effects of ecological and observational processes, which can greatly influence accuracy and precision of density estimates. For this study, we simulate biological and observational processes using empirical data to assess effects of animal scale of movement, true population density, and probability of detection on common density estimators. We also apply common data collection and analytical techniques in the field and evaluate their ability to estimate density of a globally widespread species. We find that animal scale of movementmore » had the greatest impact on accuracy of estimators, although all estimators suffered reduced performance when detection probability was low, and we provide recommendations as to when each field and analytical technique is most appropriately employed. The large influence of scale of movement on estimator accuracy emphasizes the importance of effective post-hoc calculation of area sampled or use of methods that implicitly account for spatial variation. In particular, scale of movement impacted estimators substantially, such that area covered and spacing of detectors (e.g. cameras, traps, etc.) must reflect movement characteristics of the focal species to reduce bias in estimates of movement and thus density.« less

Effects of scale of movement, detection probability, and true population density on common methods of estimating population density

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, David A.; Davis, Amy J.; Rhodes, Olin E.

Knowledge of population density is necessary for effective management and conservation of wildlife, yet rarely are estimators compared in their robustness to effects of ecological and observational processes, which can greatly influence accuracy and precision of density estimates. For this study, we simulate biological and observational processes using empirical data to assess effects of animal scale of movement, true population density, and probability of detection on common density estimators. We also apply common data collection and analytical techniques in the field and evaluate their ability to estimate density of a globally widespread species. We find that animal scale of movementmore » had the greatest impact on accuracy of estimators, although all estimators suffered reduced performance when detection probability was low, and we provide recommendations as to when each field and analytical technique is most appropriately employed. The large influence of scale of movement on estimator accuracy emphasizes the importance of effective post-hoc calculation of area sampled or use of methods that implicitly account for spatial variation. In particular, scale of movement impacted estimators substantially, such that area covered and spacing of detectors (e.g. cameras, traps, etc.) must reflect movement characteristics of the focal species to reduce bias in estimates of movement and thus density.« less

Estimating age at a specified length from the von Bertalanffy growth function

USGS Publications Warehouse

Ogle, Derek H.; Isermann, Daniel A.

2017-01-01

Estimating the time required (i.e., age) for fish in a population to reach a specific length (e.g., legal harvest length) is useful for understanding population dynamics and simulating the potential effects of length-based harvest regulations. The age at which a population reaches a specific mean length is typically estimated by fitting a von Bertalanffy growth function to length-at-age data and then rearranging the best-fit equation to solve for age at the specified length. This process precludes the use of standard frequentist methods to compute confidence intervals and compare estimates of age at the specified length among populations. We provide a parameterization of the von Bertalanffy growth function that has age at a specified length as a parameter. With this parameterization, age at a specified length is directly estimated, and standard methods can be used to construct confidence intervals and make among-group comparisons for this parameter. We demonstrate use of the new parameterization with two data sets.

Recalibration of the Klales et al. (2012) method of sexing the human innominate for Mexican populations.

PubMed

Gómez-Valdés, Jorge A; Menéndez Garmendia, Antinea; García-Barzola, Lizbeth; Sánchez-Mejorada, Gabriela; Karam, Carlos; Baraybar, José Pablo; Klales, Alexandra

2017-03-01

The aim of this study was to test the accuracy of the Klales et al. (2012) equation for sex estimation in contemporary Mexican population. Our investigation was carried out on a sample of 203 left innominates of identified adult skeletons from the UNAM-Collection and the Santa María Xigui Cemetery, in Central Mexico. The Klales' original equation produces a sex bias in sex estimation against males (86-92% accuracy versus 100% accuracy in females). Based on these results, the Klales et al. (2012) method was recalibrated for a new cutt-of-point for sex estimation in contemporary Mexican populations. The results show cross-validated classification accuracy rates as high as 100% after recalibrating the original logistic regression equation. Recalibration improved classification accuracy and eliminated sex bias. This new formula will improve sex estimation for Mexican contemporary populations. © 2017 Wiley Periodicals, Inc.

Estimation of distributional parameters for censored trace level water quality data: 2. Verification and applications

USGS Publications Warehouse

Helsel, Dennis R.; Gilliom, Robert J.

1986-01-01

Estimates of distributional parameters (mean, standard deviation, median, interquartile range) are often desired for data sets containing censored observations. Eight methods for estimating these parameters have been evaluated by R. J. Gilliom and D. R. Helsel (this issue) using Monte Carlo simulations. To verify those findings, the same methods are now applied to actual water quality data. The best method (lowest root-mean-squared error (rmse)) over all parameters, sample sizes, and censoring levels is log probability regression (LR), the method found best in the Monte Carlo simulations. Best methods for estimating moment or percentile parameters separately are also identical to the simulations. Reliability of these estimates can be expressed as confidence intervals using rmse and bias values taken from the simulation results. Finally, a new simulation study shows that best methods for estimating uncensored sample statistics from censored data sets are identical to those for estimating population parameters. Thus this study and the companion study by Gilliom and Helsel form the basis for making the best possible estimates of either population parameters or sample statistics from censored water quality data, and for assessments of their reliability.

Effective population size of korean populations.

PubMed

Park, Leeyoung

2014-12-01

Recently, new methods have been developed for estimating the current and recent changes in effective population sizes. Based on the methods, the effective population sizes of Korean populations were estimated using data from the Korean Association Resource (KARE) project. The overall changes in the population sizes of the total populations were similar to CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan) of the HapMap project. There were no differences in past changes in population sizes with a comparison between an urban area and a rural area. Age-dependent current and recent effective population sizes represent the modern history of Korean populations, including the effects of World War II, the Korean War, and urbanization. The oldest age group showed that the population growth of Koreans had already been substantial at least since the end of the 19th century.

Methods for estimating population coverage of mass distribution programmes: a review of practices in relation to trachoma control.

PubMed

Cromwell, Elizabeth A; Ngondi, Jeremiah; McFarland, Deborah; King, Jonathan D; Emerson, Paul M

2012-10-01

In the context of trachoma control, population coverage with mass drug administration (MDA) using antibiotics is measured using routine data. Due to the limitations of administrative records as well as the potential for bias from incomplete or incorrect records, a literature review of coverage survey methods applied in neglected tropical disease control programmes and immunisation outreach was conducted to inform the design of coverage surveys for trachoma control. Several methods were identified, including the '30 × 7' survey method for the Expanded Programme on Immunization (EPI 30×7), other cluster random sampling (CRS) methods, lot quality assurance sampling (LQAS), purposive sampling and routine data. When compared against one another, the EPI and other CRS methods produced similar population coverage estimates, whilst LQAS, purposive sampling and use of administrative data did not generate estimates consistent with CRS. In conclusion, CRS methods present a consistent approach for MDA coverage surveys despite different methods of household selection. They merit use until standard guidelines are available. CRS methods should be used to verify population coverage derived from LQAS, purposive sampling methods and administrative reports. Copyright © 2012 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved.

Estimation of walrus populations on sea ice with infrared imagery and aerial photography

USGS Publications Warehouse

Udevitz, M.S.; Burn, D.M.; Webber, M.A.

2008-01-01

Population sizes of ice-associated pinnipeds have often been estimated with visual or photographic aerial surveys, but these methods require relatively slow speeds and low altitudes, limiting the area they can cover. Recent developments in infrared imagery and its integration with digital photography could allow substantially larger areas to be surveyed and more accurate enumeration of individuals, thereby solving major problems with previous survey methods. We conducted a trial survey in April 2003 to estimate the number of Pacific walruses (Odobenus rosmarus divergens) hauled out on sea ice around St. Lawrence Island, Alaska. The survey used high altitude infrared imagery to detect groups of walruses on strip transects. Low altitude digital photography was used to determine the number of walruses in a sample of detected groups and calibrate the infrared imagery for estimating the total number of walruses. We propose a survey design incorporating this approach with satellite radio telemetry to estimate the proportion of the population in the water and additional low-level flights to estimate the proportion of the hauled-out population in groups too small to be detected in the infrared imagery. We believe that this approach offers the potential for obtaining reliable population estimates for walruses and other ice-associated pinnipeds. ?? 2007 by the Society for Marine Mammalogy.

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference

PubMed Central

Karcher, Michael D.; Palacios, Julia A.; Bedford, Trevor; Suchard, Marc A.; Minin, Vladimir N.

2016-01-01

Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting a coalescent model for the sampled individuals’ genealogy and then integrating over all possible genealogies via Monte Carlo or, less efficiently, by conditioning on one genealogy estimated from the sequence data. However, when analyzing sequences sampled serially through time, current methods implicitly assume either that sampling times are fixed deterministically by the data collection protocol or that their distribution does not depend on the size of the population. Through simulation, we first show that, when sampling times do probabilistically depend on effective population size, estimation methods may be systematically biased. To correct for this deficiency, we propose a new model that explicitly accounts for preferential sampling by modeling the sampling times as an inhomogeneous Poisson process dependent on effective population size. We demonstrate that in the presence of preferential sampling our new model not only reduces bias, but also improves estimation precision. Finally, we compare the performance of the currently used phylodynamic methods with our proposed model through clinically-relevant, seasonal human influenza examples. PMID:26938243

Making It Count: Improving Estimates of the Size of Transgender and Gender Nonconforming Populations.

PubMed

Deutsch, Madeline B

2016-06-01

An accurate estimate of the number of transgender and gender nonconforming people is essential to inform policy and funding priorities and decisions. Historical reports of population sizes of 1 in 4000 to 1 in 50,000 have been based on clinical populations and likely underestimate the size of the transgender population. More recent population-based studies have found a 10- to 100-fold increase in population size. Studies that estimate population size should be population based, employ the two-step method to allow for collection of both gender identity and sex assigned at birth, and include measures to capture the range of transgender people with nonbinary gender identities.

Properties of Endogenous Post-Stratified Estimation using remote sensing data

Treesearch

John Tipton; Jean Opsomer; Gretchen Moisen

2013-01-01

Post-stratification is commonly used to improve the precision of survey estimates. In traditional poststratification methods, the stratification variable must be known at the population level. When suitable covariates are available at the population level, an alternative approach consists of fitting a model on the covariates, making predictions for the population and...

A Systematic Evaluation of Different Methods for Calculating Adolescent Vaccination Levels Using Immunization Information System Data

PubMed Central

Gowda, Charitha; Dong, Shiming; Potter, Rachel C.; Dombkowski, Kevin J.; Stokley, Shannon

2013-01-01

Objective Immunization information systems (IISs) are valuable surveillance tools; however, population relocation may introduce bias when determining immunization coverage. We explored alternative methods for estimating the vaccine-eligible population when calculating adolescent immunization levels using a statewide IIS. Methods We performed a retrospective analysis of the Michigan State Care Improvement Registry (MCIR) for all adolescents aged 11–18 years registered in the MCIR as of October 2010. We explored four methods for determining denominators: (1) including all adolescents with MCIR records, (2) excluding adolescents with out-of-state residence, (3) further excluding those without MCIR activity ≥10 years prior to the evaluation date, and (4) using a denominator based on U.S. Census data. We estimated state- and county-specific coverage levels for four adolescent vaccines. Results We found a 20% difference in estimated vaccination coverage between the most inclusive and restrictive denominator populations. Although there was some variability among the four methods in vaccination at the state level (2%–11%), greater variation occurred at the county level (up to 21%). This variation was substantial enough to potentially impact public health assessments of immunization programs. Generally, vaccines with higher coverage levels had greater absolute variation, as did counties with smaller populations. Conclusion At the county level, using the four denominator calculation methods resulted in substantial differences in estimated adolescent immunization rates that were less apparent when aggregated at the state level. Further research is needed to ascertain the most appropriate method for estimating vaccine coverage levels using IIS data. PMID:24179260

Estimation of stream salamander (Plethodontidae, Desmognathinae and Plethodontinae) populations in Shenandoah National Park, Virginia, USA

USGS Publications Warehouse

Jung, R.E.; Royle, J. Andrew; Sauer, J.R.; Addison, C.; Rau, R.D.; Shirk, J.L.; Whissel, J.C.

2005-01-01

Stream salamanders in the family Plethodontidae constitute a large biomass in and near headwater streams in the eastern United States and are promising indicators of stream ecosystem health. Many studies of stream salamanders have relied on population indices based on counts rather than population estimates based on techniques such as capture-recapture and removal. Application of estimation procedures allows the calculation of detection probabilities (the proportion of total animals present that are detected during a survey) and their associated sampling error, and may be essential for determining salamander population sizes and trends. In 1999, we conducted capture-recapture and removal population estimation methods for Desmognathus salamanders at six streams in Shenandoah National Park, Virginia, USA. Removal sampling appeared more efficient and detection probabilities from removal data were higher than those from capture-recapture. During 2001-2004, we used removal estimation at eight streams in the park to assess the usefulness of this technique for long-term monitoring of stream salamanders. Removal detection probabilities ranged from 0.39 to 0.96 for Desmognathus, 0.27 to 0.89 for Eurycea and 0.27 to 0.75 for northern spring (Gyrinophilus porphyriticus) and northern red (Pseudotriton ruber) salamanders across stream transects. Detection probabilities did not differ across years for Desmognathus and Eurycea, but did differ among streams for Desmognathus. Population estimates of Desmognathus decreased between 2001-2002 and 2003-2004 which may be related to changes in stream flow conditions. Removal-based procedures may be a feasible approach for population estimation of salamanders, but field methods should be designed to meet the assumptions of the sampling procedures. New approaches to estimating stream salamander populations are discussed.

A log-linear model approach to estimation of population size using the line-transect sampling method

USGS Publications Warehouse

Anderson, D.R.; Burnham, K.P.; Crain, B.R.

1978-01-01

The technique of estimating wildlife population size and density using the belt or line-transect sampling method has been used in many past projects, such as the estimation of density of waterfowl nestling sites in marshes, and is being used currently in such areas as the assessment of Pacific porpoise stocks in regions of tuna fishing activity. A mathematical framework for line-transect methodology has only emerged in the last 5 yr. In the present article, we extend this mathematical framework to a line-transect estimator based upon a log-linear model approach.

A Method for Inferring an Individual’s Genetic Ancestry and Degree of Admixture Associated with Six Major Continental Populations

PubMed Central

Libiger, Ondrej; Schork, Nicholas J.

2013-01-01

The determination of the ancestry and genetic backgrounds of the subjects in genetic and general epidemiology studies is a crucial component in the analysis of relevant outcomes or associations. Although there are many methods for differentiating ancestral subgroups among individuals based on genetic markers only a few of these methods provide actual estimates of the fraction of an individual’s genome that is likely to be associated with different ancestral populations. We propose a method for assigning ancestry that works in stages to refine estimates of ancestral population contributions to individual genomes. The method leverages genotype data in the public domain obtained from individuals with known ancestries. Although we showcase the method in the assessment of ancestral genome proportions leveraging largely continental populations, the strategy can be used for assessing within-continent or more subtle ancestral origins with the appropriate data. PMID:23335941

Noninvasive methods for monitoring bear population trends

USGS Publications Warehouse

Kendall, Katherine

2010-01-01

The U.S. Geological Survey began a grizzly bear research project in 2009 in the Northern Continental Divide Ecosystem (NCDE) of northwestern Montana. This work uses hair collection and DNA analysis methods similar to those used in the 2004 Northern Divide Grizzly Bear Project. However, instead of producing a snapshot of population size, the objectives of this new work are to estimate population growth rates by collecting hair at natural bear rubs along trails, roads, and fence and power lines. This approach holds promise of providing reliable estimates of population trends in an efficient, cost-effective, and unobtrusive way.

Estimating the probability that the sample mean is within a desired fraction of the standard deviation of the true mean.

PubMed

Schillaci, Michael A; Schillaci, Mario E

2009-02-01

The use of small sample sizes in human and primate evolutionary research is commonplace. Estimating how well small samples represent the underlying population, however, is not commonplace. Because the accuracy of determinations of taxonomy, phylogeny, and evolutionary process are dependant upon how well the study sample represents the population of interest, characterizing the uncertainty, or potential error, associated with analyses of small sample sizes is essential. We present a method for estimating the probability that the sample mean is within a desired fraction of the standard deviation of the true mean using small (n<10) or very small (n < or = 5) sample sizes. This method can be used by researchers to determine post hoc the probability that their sample is a meaningful approximation of the population parameter. We tested the method using a large craniometric data set commonly used by researchers in the field. Given our results, we suggest that sample estimates of the population mean can be reasonable and meaningful even when based on small, and perhaps even very small, sample sizes.

Availability and Quality of Size Estimations of Female Sex Workers, Men Who Have Sex with Men, People Who Inject Drugs and Transgender Women in Low- and Middle-Income Countries

PubMed Central

Sabin, Keith; Zhao, Jinkou; Garcia Calleja, Jesus Maria; Sheng, Yaou; Arias Garcia, Sonia; Reinisch, Annette; Komatsu, Ryuichi

2016-01-01

Objective To assess the availability and quality of population size estimations of female sex workers (FSW), men who have sex with men (MSM), people who inject drug (PWID) and transgender women. Methods Size estimation data since 2010 were retrieved from global reporting databases, Global Fund grant application documents, and the peer-reviewed and grey literature. Overall quality and availability were assessed against a defined set of criteria, including estimation methods, geographic coverage, and extrapolation approaches. Estimates were compositely categorized into ‘nationally adequate’, ‘nationally inadequate but locally adequate’, ‘documented but inadequate methods’, ‘undocumented or untimely’ and ‘no data.’ Findings Of 140 countries assessed, 41 did not report any estimates since 2010. Among 99 countries with at least one estimate, 38 were categorized as having nationally adequate estimates and 30 as having nationally inadequate but locally adequate estimates. Multiplier, capture-recapture, census and enumeration, and programmatic mapping were the most commonly used methods. Most countries relied on only one estimate for a given population while about half of all reports included national estimates. A variety of approaches were applied to extrapolate from sites-level numbers to national estimates in two-thirds of countries. Conclusions Size estimates for FSW, MSM, PWID and transgender women are increasingly available but quality varies widely. The different approaches present challenges for data use in design, implementation and evaluation of programs for these populations in half of the countries assessed. Guidance should be further developed to recommend: a) applying multiple estimation methods; b) estimating size for a minimum number of sites; and, c) documenting extrapolation approaches. PMID:27163256

Estimation of the sensitive volume for gravitational-wave source populations using weighted Monte Carlo integration

NASA Astrophysics Data System (ADS)

Tiwari, Vaibhav

2018-07-01

The population analysis and estimation of merger rates of compact binaries is one of the important topics in gravitational wave astronomy. The primary ingredient in these analyses is the population-averaged sensitive volume. Typically, sensitive volume, of a given search to a given simulated source population, is estimated by drawing signals from the population model and adding them to the detector data as injections. Subsequently injections, which are simulated gravitational waveforms, are searched for by the search pipelines and their signal-to-noise ratio (SNR) is determined. Sensitive volume is estimated, by using Monte-Carlo (MC) integration, from the total number of injections added to the data, the number of injections that cross a chosen threshold on SNR and the astrophysical volume in which the injections are placed. So far, only fixed population models have been used in the estimation of binary black holes (BBH) merger rates. However, as the scope of population analysis broaden in terms of the methodologies and source properties considered, due to an increase in the number of observed gravitational wave (GW) signals, the procedure will need to be repeated multiple times at a large computational cost. In this letter we address the problem by performing a weighted MC integration. We show how a single set of generic injections can be weighted to estimate the sensitive volume for multiple population models; thereby greatly reducing the computational cost. The weights in this MC integral are the ratios of the output probabilities, determined by the population model and standard cosmology, and the injection probability, determined by the distribution function of the generic injections. Unlike analytical/semi-analytical methods, which usually estimate sensitive volume using single detector sensitivity, the method is accurate within statistical errors, comes at no added cost and requires minimal computational resources.

From blackbirds to black holes: Investigating capture-recapture methods for time domain astronomy

NASA Astrophysics Data System (ADS)

Laycock, Silas G. T.

2017-07-01

In time domain astronomy, recurrent transients present a special problem: how to infer total populations from limited observations. Monitoring observations may give a biassed view of the underlying population due to limitations on observing time, visibility and instrumental sensitivity. A similar problem exists in the life sciences, where animal populations (such as migratory birds) or disease prevalence, must be estimated from sparse and incomplete data. The class of methods termed Capture-Recapture is used to reconstruct population estimates from time-series records of encounters with the study population. This paper investigates the performance of Capture-Recapture methods in astronomy via a series of numerical simulations. The Blackbirds code simulates monitoring of populations of transients, in this case accreting binary stars (neutron star or black hole accreting from a stellar companion) under a range of observing strategies. We first generate realistic light-curves for populations of binaries with contrasting orbital period distributions. These models are then randomly sampled at observing cadences typical of existing and planned monitoring surveys. The classical capture-recapture methods, Lincoln-Peterson, Schnabel estimators, related techniques, and newer methods implemented in the Rcapture package are compared. A general exponential model based on the radioactive decay law is introduced which is demonstrated to recover (at 95% confidence) the underlying population abundance and duty cycle, in a fraction of the observing visits (10-50%) required to discover all the sources in the simulation. Capture-Recapture is a promising addition to the toolbox of time domain astronomy, and methods implemented in R by the biostats community can be readily called from within python.

The Game of Contacts: Estimating the Social Visibility of Groups.

PubMed

Salganik, Matthew J; Mello, Maeve B; Abdo, Alexandre H; Bertoni, Neilane; Fazito, Dimitri; Bastos, Francisco I

2011-01-01

Estimating the sizes of hard-to-count populations is a challenging and important problem that occurs frequently in social science, public health, and public policy. This problem is particularly pressing in HIV/AIDS research because estimates of the sizes of the most at-risk populations-illicit drug users, men who have sex with men, and sex workers-are needed for designing, evaluating, and funding programs to curb the spread of the disease. A promising new approach in this area is the network scale-up method, which uses information about the personal networks of respondents to make population size estimates. However, if the target population has low social visibility, as is likely to be the case in HIV/AIDS research, scale-up estimates will be too low. In this paper we develop a game-like activity that we call the game of contacts in order to estimate the social visibility of groups, and report results from a study of heavy drug users in Curitiba, Brazil (n = 294). The game produced estimates of social visibility that were consistent with qualitative expectations but of surprising magnitude. Further, a number of checks suggest that the data are high-quality. While motivated by the specific problem of population size estimation, our method could be used by researchers more broadly and adds to long-standing efforts to combine the richness of social network analysis with the power and scale of sample surveys.

Challenges in the Estimation of the Annual Risk of Mycobacterium tuberculosis Infection in Children Aged Less Than 5 Years.

PubMed

Khan, P Y; Glynn, Judith R; Mzembe, T; Mulawa, D; Chiumya, R; Crampin, Amelia C; Kranzer, Katharina; Fielding, Katherine L

2017-10-15

Accurate estimates of Mycobacterium tuberculosis infection in young children provide a critical indicator of ongoing community transmission of M. tuberculosis. Cross-reactions due to infection with environmental mycobacteria and/or bacille Calmette-Guérin (BCG) vaccination compromise the estimates derived from population-level tuberculin skin-test surveys using traditional cutoff methods. Newer statistical approaches are prone to failure of model convergence, especially in settings where the prevalence of M. tuberculosis infection is low and environmental sensitization is high. We conducted a tuberculin skin-test survey in 5,119 preschool children in the general population and among household contacts of tuberculosis cases in 2012-2014 in a district in northern Malawi where sensitization to environmental mycobacteria is common and almost all children are BCG-vaccinated. We compared different proposed methods of estimating M. tuberculosis prevalence, including a method described by Rust and Thomas more than 40 years ago. With the different methods, estimated prevalence in the general population was 0.7%-11.5% at ages <2 years and 0.8%-3.3% at ages 2-4 years. The Rust and Thomas method was the only method to give a lower estimate in the younger age group (0.7% vs 0.8%), suggesting that it was the only method that adjusted appropriately for the marked effect of BCG-attributable induration in the very young. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health.

Unauthorized Immigration to the United States: Annual Estimates and Components of Change, by State, 1990 to 2010

PubMed Central

Warren, Robert; Warren, John Robert

2013-01-01

We describe a method for producing annual estimates of the unauthorized immigrant population in the United Sates and components of population change, for each state and D.C., for 1990 to 2010. We quantify a sharp drop in the number of unauthorized immigrants arriving since 2000, and we demonstrate the role of departures from the population (emigration, adjustment to legal status, removal by the Department of Homeland Security (DHS), and deaths) in reducing population growth from one million in 2000 to population losses in 2008 and 2009. The number arriving in the U.S. peaked at more than one million in 1999 to 2001, and then declined rapidly through 2009. We provide evidence that population growth stopped after 2007 primarily because entries declined and not because emigration increased during the economic crisis. Our estimates of the total unauthorized immigrant population in the U.S. and in the top ten states are comparable to those produced by DHS and the Pew Hispanic Center. For the remaining states and D.C., our data and methods produce estimates with smaller ranges of sampling error. PMID:23956482

A method for estimating fall adult sex ratios from production and survival data

USGS Publications Warehouse

Wight, H.M.; Heath, R.G.; Geis, A.D.

1965-01-01

This paper presents a method of utilizing data relating to the production and survival of a bird population to estimate a basic fall adult sex ratio. This basic adult sex ratio is an average value derived from average production and survival rates. It is an estimate of the average sex ratio about which the fall adult ratios will fluctuate according to annual variations in production and survival. The basic fall adult sex ratio has been calculated as an asymptotic value which is the limit of an infinite series wherein average population characteristics are used as constants. Graphs are provided that allow the determination of basic sex ratios from production and survival data of a population. Where the respective asymptote has been determined, it may be possible to estimate various production and survival rates by use of variations of the formula for estimating the asymptote.

Network Model-Assisted Inference from Respondent-Driven Sampling Data

PubMed Central

Gile, Krista J.; Handcock, Mark S.

2015-01-01

Summary Respondent-Driven Sampling is a widely-used method for sampling hard-to-reach human populations by link-tracing over their social networks. Inference from such data requires specialized techniques because the sampling process is both partially beyond the control of the researcher, and partially implicitly defined. Therefore, it is not generally possible to directly compute the sampling weights for traditional design-based inference, and likelihood inference requires modeling the complex sampling process. As an alternative, we introduce a model-assisted approach, resulting in a design-based estimator leveraging a working network model. We derive a new class of estimators for population means and a corresponding bootstrap standard error estimator. We demonstrate improved performance compared to existing estimators, including adjustment for an initial convenience sample. We also apply the method and an extension to the estimation of HIV prevalence in a high-risk population. PMID:26640328

Network Model-Assisted Inference from Respondent-Driven Sampling Data.

PubMed

Gile, Krista J; Handcock, Mark S

2015-06-01

Respondent-Driven Sampling is a widely-used method for sampling hard-to-reach human populations by link-tracing over their social networks. Inference from such data requires specialized techniques because the sampling process is both partially beyond the control of the researcher, and partially implicitly defined. Therefore, it is not generally possible to directly compute the sampling weights for traditional design-based inference, and likelihood inference requires modeling the complex sampling process. As an alternative, we introduce a model-assisted approach, resulting in a design-based estimator leveraging a working network model. We derive a new class of estimators for population means and a corresponding bootstrap standard error estimator. We demonstrate improved performance compared to existing estimators, including adjustment for an initial convenience sample. We also apply the method and an extension to the estimation of HIV prevalence in a high-risk population.

Evaluating estimators for numbers of females with cubs-of-the-year in the Yellowstone grizzly bear population

USGS Publications Warehouse

Cherry, S.; White, G.C.; Keating, K.A.; Haroldson, Mark A.; Schwartz, Charles C.

2007-01-01

Current management of the grizzly bear (Ursus arctos) population in Yellowstone National Park and surrounding areas requires annual estimation of the number of adult female bears with cubs-of-the-year. We examined the performance of nine estimators of population size via simulation. Data were simulated using two methods for different combinations of population size, sample size, and coefficient of variation of individual sighting probabilities. We show that the coefficient of variation does not, by itself, adequately describe the effects of capture heterogeneity, because two different distributions of capture probabilities can have the same coefficient of variation. All estimators produced biased estimates of population size with bias decreasing as effort increased. Based on the simulation results we recommend the Chao estimator for model M h be used to estimate the number of female bears with cubs of the year; however, the estimator of Chao and Shen may also be useful depending on the goals of the research.

Mapping Air Population

NASA Astrophysics Data System (ADS)

Peterson, Michael P.; Hunt, Paul; Weiß, Konrad

2018-05-01

"Air population" refers to the total number of people flying above the earth at any point in time. The total number of passengers can then be estimated by multiplying the number of seats for each aircraft by the current seat occupancy rate. Using this method, the estimated air population is determined by state for the airspace over the United States. In the interactive, real-time mapping system, maps are provided to show total air population, the density of air population (air population / area of state), and the ratio of air population to ground population.

Dasymetric high resolution population distribution estimates for improved decision making, with a case study of sea-level rise vulnerability in Boca Raton, Florida

NASA Astrophysics Data System (ADS)

Ziegler, Hannes Moritz

Planners and managers often rely on coarse population distribution data from the census for addressing various social, economic, and environmental problems. In the analysis of physical vulnerabilities to sea-level rise, census units such as blocks or block groups are coarse relative to the required decision-making application. This study explores the benefits offered from integrating image classification and dasymetric mapping at the household level to provide detailed small area population estimates at the scale of residential buildings. In a case study of Boca Raton, FL, a sea-level rise inundation grid based on mapping methods by NOAA is overlaid on the highly detailed population distribution data to identify vulnerable residences and estimate population displacement. The enhanced spatial detail offered through this method has the potential to better guide targeted strategies for future development, mitigation, and adaptation efforts.

Estimation of Population Number via Light Activities on Night-Time Satellite Images

NASA Astrophysics Data System (ADS)

Turan, M. K.; Yücer, E.; Sehirli, E.; Karaş, İ. R.

2017-11-01

Estimation and accurate assessment regarding population gets harder and harder day by day due to growth of world population in a fast manner. Estimating tendencies to settlements in cities and countries, socio-cultural development and population numbers is quite difficult. In addition to them, selection and analysis of parameters such as time, work-force and cost seems like another difficult issue. In this study, population number is guessed by evaluating light activities in İstanbul via night-time images of Turkey. By evaluating light activities between 2000 and 2010, average population per pixel is obtained. Hence, it is used to estimate population numbers in 2011, 2012 and 2013. Mean errors are concluded as 4.14 % for 2011, 3.74 % for 2012 and 3.04 % for 2013 separately. As a result of developed thresholding method, mean error is concluded as 3.64 % to estimate population number in İstanbul for next three years.

Bayesian Small Area Estimates of Diabetes Incidence by United States County, 2009

PubMed Central

Barker, Lawrence E.; Thompson, Theodore J.; Kirtland, Karen A; Boyle, James P; Geiss, Linda S; McCauley, Mary M.; Albright, Ann L.

2015-01-01

In the United States, diabetes is common and costly. Programs to prevent new cases of diabetes are often carried out at the level of the county, a unit of local government. Thus, efficient targeting of such programs requires county-level estimates of diabetes incidence–the fraction of the non-diabetic population who received their diagnosis of diabetes during the past 12 months. Previously, only estimates of prevalence–the overall fraction of population who have the disease–have been available at the county level. Counties with high prevalence might or might not be the same as counties with high incidence, due to spatial variation in mortality and relocation of persons with incident diabetes to another county. Existing methods cannot be used to estimate county-level diabetes incidence, because the fraction of the population who receive a diabetes diagnosis in any year is too small. Here, we extend previously developed methods of Bayesian small-area estimation of prevalence, using diffuse priors, to estimate diabetes incidence for all U.S. counties based on data from a survey designed to yield state-level estimates. We found high incidence in the southeastern United States, the Appalachian region, and in scattered counties throughout the western U.S. Our methods might be applicable in other circumstances in which all cases of a rare condition also must be cases of a more common condition (in this analysis, “newly diagnosed cases of diabetes” and “cases of diabetes”). If appropriate data are available, our methods can be used to estimate proportion of the population with the rare condition at greater geographic specificity than the data source was designed to provide. PMID:26279666

A random spatial sampling method in a rural developing nation

Treesearch

Michelle C. Kondo; Kent D.W. Bream; Frances K. Barg; Charles C. Branas

2014-01-01

Nonrandom sampling of populations in developing nations has limitations and can inaccurately estimate health phenomena, especially among hard-to-reach populations such as rural residents. However, random sampling of rural populations in developing nations can be challenged by incomplete enumeration of the base population. We describe a stratified random sampling method...

Item Response Theory with Estimation of the Latent Population Distribution Using Spline-Based Densities

ERIC Educational Resources Information Center

Woods, Carol M.; Thissen, David

2006-01-01

The purpose of this paper is to introduce a new method for fitting item response theory models with the latent population distribution estimated from the data using splines. A spline-based density estimation system provides a flexible alternative to existing procedures that use a normal distribution, or a different functional form, for the…

Standardizing the double-observer survey method for estimating mountain ungulate prey of the endangered snow leopard.

PubMed

Suryawanshi, Kulbhushansingh R; Bhatnagar, Yash Veer; Mishra, Charudutt

2012-07-01

Mountain ungulates around the world have been threatened by illegal hunting, habitat modification, increased livestock grazing, disease and development. Mountain ungulates play an important functional role in grasslands as primary consumers and as prey for wild carnivores, and monitoring of their populations is important for conservation purposes. However, most of the several currently available methods of estimating wild ungulate abundance are either difficult to implement or too expensive for mountainous terrain. A rigorous method of sampling ungulate abundance in mountainous areas that can allow for some measure of sampling error is therefore much needed. To this end, we used a combination of field data and computer simulations to test the critical assumptions associated with double-observer technique based on capture-recapture theory. The technique was modified and adapted to estimate the populations of bharal (Pseudois nayaur) and ibex (Capra sibirica) at five different sites. Conducting the two double-observer surveys simultaneously led to underestimation of the population by 15%. We therefore recommend separating the surveys in space or time. The overall detection probability for the two observers was 0.74 and 0.79. Our surveys estimated mountain ungulate populations (± 95% confidence interval) of 735 (± 44), 580 (± 46), 509 (± 53), 184 (± 40) and 30 (± 14) individuals at the five sites, respectively. A detection probability of 0.75 was found to be sufficient to detect a change of 20% in populations of >420 individuals. Based on these results, we believe that this method is sufficiently precise for scientific and conservation purposes and therefore recommend the use of the double-observer approach (with the two surveys separated in time or space) for the estimation and monitoring of mountain ungulate populations.

A New Method for Estimating the Effective Population Size from Allele Frequency Changes

PubMed Central

Pollak, Edward

1983-01-01

A new procedure is proposed for estimating the effective population size, given that information is available on changes in frequencies of the alleles at one or more independently segregating loci and the population is observed at two or more separate times. Approximate expressions are obtained for the variances of the new statistic, as well as others, also based on allele frequency changes, that have been discussed in the literature. This analysis indicates that the new statistic will generally have a smaller variance than the others. Estimates of effective population sizes and of the standard errors of the estimates are computed for data on two fly populations that have been discussed in earlier papers. In both cases, there is evidence that the effective population size is very much smaller than the minimum census size of the population. PMID:17246147

Estimating adult sex ratios in nature.

PubMed

Ancona, Sergio; Dénes, Francisco V; Krüger, Oliver; Székely, Tamás; Beissinger, Steven R

2017-09-19

Adult sex ratio (ASR, the proportion of males in the adult population) is a central concept in population and evolutionary biology, and is also emerging as a major factor influencing mate choice, pair bonding and parental cooperation in both human and non-human societies. However, estimating ASR is fraught with difficulties stemming from the effects of spatial and temporal variation in the numbers of males and females, and detection/capture probabilities that differ between the sexes. Here, we critically evaluate methods for estimating ASR in wild animal populations, reviewing how recent statistical advances can be applied to handle some of these challenges. We review methods that directly account for detection differences between the sexes using counts of unmarked individuals (observed, trapped or killed) and counts of marked individuals using mark-recapture models. We review a third class of methods that do not directly sample the number of males and females, but instead estimate the sex ratio indirectly using relationships that emerge from demographic measures, such as survival, age structure, reproduction and assumed dynamics. We recommend that detection-based methods be used for estimating ASR in most situations, and point out that studies are needed that compare different ASR estimation methods and control for sex differences in dispersal.This article is part of the themed issue 'Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies'. © 2017 The Author(s).

Semiparametric methods for estimation of a nonlinear exposure-outcome relationship using instrumental variables with application to Mendelian randomization.

PubMed

Staley, James R; Burgess, Stephen

2017-05-01

Mendelian randomization, the use of genetic variants as instrumental variables (IV), can test for and estimate the causal effect of an exposure on an outcome. Most IV methods assume that the function relating the exposure to the expected value of the outcome (the exposure-outcome relationship) is linear. However, in practice, this assumption may not hold. Indeed, often the primary question of interest is to assess the shape of this relationship. We present two novel IV methods for investigating the shape of the exposure-outcome relationship: a fractional polynomial method and a piecewise linear method. We divide the population into strata using the exposure distribution, and estimate a causal effect, referred to as a localized average causal effect (LACE), in each stratum of population. The fractional polynomial method performs metaregression on these LACE estimates. The piecewise linear method estimates a continuous piecewise linear function, the gradient of which is the LACE estimate in each stratum. Both methods were demonstrated in a simulation study to estimate the true exposure-outcome relationship well, particularly when the relationship was a fractional polynomial (for the fractional polynomial method) or was piecewise linear (for the piecewise linear method). The methods were used to investigate the shape of relationship of body mass index with systolic blood pressure and diastolic blood pressure. © 2017 The Authors Genetic Epidemiology Published by Wiley Periodicals, Inc.

Semiparametric methods for estimation of a nonlinear exposure‐outcome relationship using instrumental variables with application to Mendelian randomization

PubMed Central

Staley, James R.

2017-01-01

ABSTRACT Mendelian randomization, the use of genetic variants as instrumental variables (IV), can test for and estimate the causal effect of an exposure on an outcome. Most IV methods assume that the function relating the exposure to the expected value of the outcome (the exposure‐outcome relationship) is linear. However, in practice, this assumption may not hold. Indeed, often the primary question of interest is to assess the shape of this relationship. We present two novel IV methods for investigating the shape of the exposure‐outcome relationship: a fractional polynomial method and a piecewise linear method. We divide the population into strata using the exposure distribution, and estimate a causal effect, referred to as a localized average causal effect (LACE), in each stratum of population. The fractional polynomial method performs metaregression on these LACE estimates. The piecewise linear method estimates a continuous piecewise linear function, the gradient of which is the LACE estimate in each stratum. Both methods were demonstrated in a simulation study to estimate the true exposure‐outcome relationship well, particularly when the relationship was a fractional polynomial (for the fractional polynomial method) or was piecewise linear (for the piecewise linear method). The methods were used to investigate the shape of relationship of body mass index with systolic blood pressure and diastolic blood pressure. PMID:28317167

A time-lapse photography method for monitoring salmon (Oncorhynchus spp.) passage and abundance in streams

PubMed Central

Leacock, William B.; Eby, Lisa A.; Stanford, Jack A.

2016-01-01

Accurately estimating population sizes is often a critical component of fisheries research and management. Although there is a growing appreciation of the importance of small-scale salmon population dynamics to the stability of salmon stock-complexes, our understanding of these populations is constrained by a lack of efficient and cost-effective monitoring tools for streams. Weirs are expensive, labor intensive, and can disrupt natural fish movements. While conventional video systems avoid some of these shortcomings, they are expensive and require excessive amounts of labor to review footage for data collection. Here, we present a novel method for quantifying salmon in small streams (<15 m wide, <1 m deep) that uses both time-lapse photography and video in a model-based double sampling scheme. This method produces an escapement estimate nearly as accurate as a video-only approach, but with substantially less labor, money, and effort. It requires servicing only every 14 days, detects salmon 24 h/day, is inexpensive, and produces escapement estimates with confidence intervals. In addition to escapement estimation, we present a method for estimating in-stream salmon abundance across time, data needed by researchers interested in predator--prey interactions or nutrient subsidies. We combined daily salmon passage estimates with stream specific estimates of daily mortality developed using previously published data. To demonstrate proof of concept for these methods, we present results from two streams in southwest Kodiak Island, Alaska in which high densities of sockeye salmon spawn. PMID:27326378

Mapping Urban Risk: Flood Hazards, Race, & Environmental Justice In New York”

PubMed Central

Maantay, Juliana; Maroko, Andrew

2009-01-01

This paper demonstrates the importance of disaggregating population data aggregated by census tracts or other units, for more realistic population distribution/location. A newly-developed mapping method, the Cadastral-based Expert Dasymetric System (CEDS), calculates population in hyper-heterogeneous urban areas better than traditional mapping techniques. A case study estimating population potentially impacted by flood hazard in New York City compares the impacted population determined by CEDS with that derived by centroid-containment method and filtered areal weighting interpolation. Compared to CEDS, 37 percent and 72 percent fewer people are estimated to be at risk from floods city-wide, using conventional areal weighting of census data, and centroid-containment selection, respectively. Undercounting of impacted population could have serious implications for emergency management and disaster planning. Ethnic/racial populations are also spatially disaggregated to determine any environmental justice impacts with flood risk. Minorities are disproportionately undercounted using traditional methods. Underestimating more vulnerable sub-populations impairs preparedness and relief efforts. PMID:20047020

Tracking rural-to-urban migration in China: Lessons from the 2005 inter-census population survey.

PubMed

Ebenstein, Avraham; Zhao, Yaohui

2015-01-01

We examined migration in China using the 2005 inter-census population survey, in which migrants were registered at both their place of original (hukou) residence and at their destination. We find evidence that the estimated number of internal migrants in China is extremely sensitive to the enumeration method. We estimate that the traditional destination-based survey method fails to account for more than a third of migrants found using comparable origin-based methods. The 'missing' migrants are disproportionately young, male, and holders of rural hukou. We find that origin-based methods are more effective at capturing migrants who travel short distances for short periods, whereas destination-based methods are more effective when entire households have migrated and no remaining family members are located at the hukou location. We conclude with a set of policy recommendations for the design of population surveys in countries with large migrant populations.

The Petersen-Lincoln estimator and its extension to estimate the size of a shared population.

PubMed

Chao, Anne; Pan, H-Y; Chiang, Shu-Chuan

2008-12-01

The Petersen-Lincoln estimator has been used to estimate the size of a population in a single mark release experiment. However, the estimator is not valid when the capture sample and recapture sample are not independent. We provide an intuitive interpretation for "independence" between samples based on 2 x 2 categorical data formed by capture/non-capture in each of the two samples. From the interpretation, we review a general measure of "dependence" and quantify the correlation bias of the Petersen-Lincoln estimator when two types of dependences (local list dependence and heterogeneity of capture probability) exist. An important implication in the census undercount problem is that instead of using a post enumeration sample to assess the undercount of a census, one should conduct a prior enumeration sample to avoid correlation bias. We extend the Petersen-Lincoln method to the case of two populations. This new estimator of the size of the shared population is proposed and its variance is derived. We discuss a special case where the correlation bias of the proposed estimator due to dependence between samples vanishes. The proposed method is applied to a study of the relapse rate of illicit drug use in Taiwan. ((c) 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim).

Long-term monitoring of endangered Laysan ducks: Index validation and population estimates 1998–2012

USGS Publications Warehouse

Reynolds, Michelle H.; Courtot, Karen; Brinck, Kevin W.; Rehkemper, Cynthia; Hatfield, Jeffrey

2015-01-01

Monitoring endangered wildlife is essential to assessing management or recovery objectives and learning about population status. We tested assumptions of a population index for endangered Laysan duck (or teal; Anas laysanensis) monitored using mark–resight methods on Laysan Island, Hawai’i. We marked 723 Laysan ducks between 1998 and 2009 and identified seasonal surveys through 2012 that met accuracy and precision criteria for estimating population abundance. Our results provide a 15-y time series of seasonal population estimates at Laysan Island. We found differences in detection among seasons and how observed counts related to population estimates. The highest counts and the strongest relationship between count and population estimates occurred in autumn (September–November). The best autumn surveys yielded population abundance estimates that ranged from 674 (95% CI = 619–730) in 2003 to 339 (95% CI = 265–413) in 2012. A population decline of 42% was observed between 2010 and 2012 after consecutive storms and Japan’s To¯hoku earthquake-generated tsunami in 2011. Our results show positive correlations between the seasonal maximum counts and population estimates from the same date, and support the use of standardized bimonthly counts of unmarked birds as a valid index to monitor trends among years within a season at Laysan Island.

Prevalence of rheumatoid arthritis in persons 60 years of age and older in the United States: effect of different methods of case classification.

PubMed

Rasch, Elizabeth K; Hirsch, Rosemarie; Paulose-Ram, Ryne; Hochberg, Marc C

2003-04-01

To determine prevalence estimates for rheumatoid arthritis (RA) in noninstitutionalized older adults in the US. Prevalence estimates were compared using 3 different classification methods based on current classification criteria for RA. Data from the Third National Health and Nutrition Examination Survey (NHANES-III) were used to generate prevalence estimates by 3 classification methods in persons 60 years of age and older (n = 5,302). Method 1 applied the "n of k" rule, such that subjects who met 3 of 6 of the American College of Rheumatology (ACR) 1987 criteria were classified as having RA (data from hand radiographs were not available). In method 2, the ACR classification tree algorithm was applied. For method 3, medication data were used to augment case identification via method 2. Population prevalence estimates and 95% confidence intervals (95% CIs) were determined using the 3 methods on data stratified by sex, race/ethnicity, age, and education. Overall prevalence estimates using the 3 classification methods were 2.03% (95% CI 1.30-2.76), 2.15% (95% CI 1.43-2.87), and 2.34% (95% CI 1.66-3.02), respectively. The prevalence of RA was generally greater in the following groups: women, Mexican Americans, respondents with less education, and respondents who were 70 years of age and older. The prevalence of RA in persons 60 years of age and older is approximately 2%, representing the proportion of the US elderly population who will most likely require medical intervention because of disease activity. Different classification methods yielded similar prevalence estimates, although detection of RA was enhanced by incorporation of data on use of prescription medications, an important consideration in large population surveys.

Mark-recapture using tetracycline and genetics reveal record-high bear density

USGS Publications Warehouse

Peacock, E.; Titus, K.; Garshelis, D.L.; Peacock, M.M.; Kuc, M.

2011-01-01

We used tetracycline biomarking, augmented with genetic methods to estimate the size of an American black bear (Ursus americanus) population on an island in Southeast Alaska. We marked 132 and 189 bears that consumed remote, tetracycline-laced baits in 2 different years, respectively, and observed 39 marks in 692 bone samples subsequently collected from hunters. We genetically analyzed hair samples from bait sites to determine the sex of marked bears, facilitating derivation of sex-specific population estimates. We obtained harvest samples from beyond the study area to correct for emigration. We estimated a density of 155 independent bears/100 km2, which is equivalent to the highest recorded for this species. This high density appears to be maintained by abundant, accessible natural food. Our population estimate (approx. 1,000 bears) could be used as a baseline and to set hunting quotas. The refined biomarking method for abundance estimation is a useful alternative where physical captures or DNA-based estimates are precluded by cost or logistics. Copyright ?? 2011 The Wildlife Society.

Estimation and Partitioning of Heritability in Human Populations using Whole Genome Analysis Methods

PubMed Central

Vinkhuyzen, Anna AE; Wray, Naomi R; Yang, Jian; Goddard, Michael E; Visscher, Peter M

2014-01-01

Understanding genetic variation of complex traits in human populations has moved from the quantification of the resemblance between close relatives to the dissection of genetic variation into the contributions of individual genomic loci. But major questions remain unanswered: how much phenotypic variation is genetic, how much of the genetic variation is additive and what is the joint distribution of effect size and allele frequency at causal variants? We review and compare three whole-genome analysis methods that use mixed linear models (MLM) to estimate genetic variation, using the relationship between close or distant relatives based on pedigree or SNPs. We discuss theory, estimation procedures, bias and precision of each method and review recent advances in the dissection of additive genetic variation of complex traits in human populations that are based upon the application of MLM. Using genome wide data, SNPs account for far more of the genetic variation than the highly significant SNPs associated with a trait, but they do not account for all of the genetic variance estimated by pedigree based methods. We explain possible reasons for this ‘missing’ heritability. PMID:23988118

Estimating population trends with a linear model

USGS Publications Warehouse

Bart, Jonathan; Collins, Brian D.; Morrison, R.I.G.

2003-01-01

We describe a simple and robust method for estimating trends in population size. The method may be used with Breeding Bird Survey data, aerial surveys, point counts, or any other program of repeated surveys at permanent locations. Surveys need not be made at each location during each survey period. The method differs from most existing methods in being design based, rather than model based. The only assumptions are that the nominal sampling plan is followed and that sample size is large enough for use of the t-distribution. Simulations based on two bird data sets from natural populations showed that the point estimate produced by the linear model was essentially unbiased even when counts varied substantially and 25% of the complete data set was missing. The estimating-equation approach, often used to analyze Breeding Bird Survey data, performed similarly on one data set but had substantial bias on the second data set, in which counts were highly variable. The advantages of the linear model are its simplicity, flexibility, and that it is self-weighting. A user-friendly computer program to carry out the calculations is available from the senior author.

IN-RESIDENCE, MULTIPLE ROUTE EXPOSURES TO CHLORPYRIFOS AND DIAZINON ESTIMATED BY INDIRECT METHOD MODELS

EPA Science Inventory

One of the objectives of the National Human Exposure Assessment Survey (NHEXAS) is to estimate exposures to several pollutants in multiple media and determine their distributions for the population of Arizona. This paper presents modeling methods used to estimate exposure dist...

Analysis and Management of Animal Populations: Modeling, Estimation and Decision Making

USGS Publications Warehouse

Williams, B.K.; Nichols, J.D.; Conroy, M.J.

2002-01-01

This book deals with the processes involved in making informed decisions about the management of animal populations. It covers the modeling of population responses to management actions, the estimation of quantities needed in the modeling effort, and the application of these estimates and models to the development of sound management decisions. The book synthesizes and integrates in a single volume the methods associated with these themes, as they apply to ecological assessment and conservation of animal populations. KEY FEATURES * Integrates population modeling, parameter estimation and * decision-theoretic approaches to management in a single, cohesive framework * Provides authoritative, state-of-the-art descriptions of quantitative * approaches to modeling, estimation and decision-making * Emphasizes the role of mathematical modeling in the conduct of science * and management * Utilizes a unifying biological context, consistent mathematical notation, * and numerous biological examples

Genotyping faecal samples of Bengal tiger Panthera tigris tigris for population estimation: a pilot study.

PubMed

Bhagavatula, Jyotsna; Singh, Lalji

2006-10-17

Bengal tiger Panthera tigris tigris the National Animal of India, is an endangered species. Estimating populations for such species is the main objective for designing conservation measures and for evaluating those that are already in place. Due to the tiger's cryptic and secretive behaviour, it is not possible to enumerate and monitor its populations through direct observations; instead indirect methods have always been used for studying tigers in the wild. DNA methods based on non-invasive sampling have not been attempted so far for tiger population studies in India. We describe here a pilot study using DNA extracted from faecal samples of tigers for the purpose of population estimation. In this study, PCR primers were developed based on tiger-specific variations in the mitochondrial cytochrome b for reliably identifying tiger faecal samples from those of sympatric carnivores. Microsatellite markers were developed for the identification of individual tigers with a sibling Probability of Identity of 0.005 that can distinguish even closely related individuals with 99.9% certainty. The effectiveness of using field-collected tiger faecal samples for DNA analysis was evaluated by sampling, identification and subsequently genotyping samples from two protected areas in southern India. Our results demonstrate the feasibility of using tiger faecal matter as a potential source of DNA for population estimation of tigers in protected areas in India in addition to the methods currently in use.

Estimating relative decline in populations of subterranean termites (Isoptera: Rhinotermitidae) due to baiting.

PubMed

Evans, T A

2001-12-01

Although mark-recapture protocols produce inaccurate population estimates of termite colonies, they might be employed to estimate a relative change in colony size. This possibility was tested using two Australian, mound-building, wood-eating, subterranean Coptotermes species. Three different toxicants delivered in baits were used to decrease (but not eliminate) colony size, and a single mark-recapture protocol was used to estimate pre- and postbaiting population sizes. For both species, the numbers of termites retrieved from bait stations varied widely, resulting in no significant differences in the numbers of termites sampled between treatments in either the pre- or postbaiting protocols. There were significantly fewer termites sampled in all treatments, controls included, in the postbaiting protocol compared with the pre-, suggesting a seasonal change in forager numbers. The comparison of population estimates shows a large decrease in toxicant treated colonies compared with little change in control colonies, which suggests that estimating the relative decline in population size using mark-recapture protocols might to be possible. However, the change in population estimate was due entirely to the significantly lower recapture rate in the control colonies relative to the toxicant treated colonies, as numbers of unmarked termites did not change between treatments. The population estimates should be treated with caution because low recapture rates produce dubious population estimates and, in some cases, postbaiting mark-recapture population estimates could be much greater than those at prebaiting, despite consumption of bait in sufficient quantities to cause population decline. A possible interaction between fat-stain markers and toxicants should be investigated if mark-recapture population estimates are used. Alternative methods of population change are advised, along with other indirect measures.

Free-Roaming Dog Population Estimation and Status of the Dog Population Management and Rabies Control Program in Dhaka City, Bangladesh

PubMed Central

Tenzin, Tenzin; Ahmed, Rubaiya; Debnath, Nitish C.; Ahmed, Garba; Yamage, Mat

2015-01-01

Beginning January 2012, a humane method of dog population management using a Catch-Neuter-Vaccinate-Release (CNVR) program was implemented in Dhaka City, Bangladesh as part of the national rabies control program. To enable this program, the size and distribution of the free-roaming dog population needed to be estimated. We present the results of a dog population survey and a pilot assessment of the CNVR program coverage in Dhaka City. Free-roaming dog population surveys were undertaken in 18 wards of Dhaka City on consecutive days using mark-resight methods. Data was analyzed using Lincoln-Petersen index-Chapman correction methods. The CNVR program was assessed over the two years (2012–2013) whilst the coverage of the CNVR program was assessed by estimating the proportion of dogs that were ear-notched (processed dogs) via dog population surveys. The free-roaming dog population was estimated to be 1,242 (95 % CI: 1205–1278) in the 18 sampled wards and 18,585 dogs in Dhaka City (52 dogs/km2) with an estimated human-to-free-roaming dog ratio of 828:1. During the two year CNVR program, a total of 6,665 dogs (3,357 male and 3,308 female) were neutered and vaccinated against rabies in 29 of the 92 city wards. A pilot population survey indicated a mean CNVR coverage of 60.6% (range 19.2–79.3%) with only eight wards achieving > 70% coverage. Given that the coverage in many neighborhoods was below the WHO-recommended threshold level of 70% for rabies eradications and since the CNVR program takes considerable time to implement throughout the entire Dhaka City area, a mass dog vaccination program in the non-CNVR coverage area is recommended to create herd immunity. The findings from this study are expected to guide dog population management and the rabies control program in Dhaka City and elsewhere in Bangladesh. PMID:25978406

Free-roaming dog population estimation and status of the dog population management and rabies control program in Dhaka City, Bangladesh.

PubMed

Tenzin, Tenzin; Ahmed, Rubaiya; Debnath, Nitish C; Ahmed, Garba; Yamage, Mat

2015-05-01

Beginning January 2012, a humane method of dog population management using a Catch-Neuter-Vaccinate-Release (CNVR) program was implemented in Dhaka City, Bangladesh as part of the national rabies control program. To enable this program, the size and distribution of the free-roaming dog population needed to be estimated. We present the results of a dog population survey and a pilot assessment of the CNVR program coverage in Dhaka City. Free-roaming dog population surveys were undertaken in 18 wards of Dhaka City on consecutive days using mark-resight methods. Data was analyzed using Lincoln-Petersen index-Chapman correction methods. The CNVR program was assessed over the two years (2012-2013) whilst the coverage of the CNVR program was assessed by estimating the proportion of dogs that were ear-notched (processed dogs) via dog population surveys. The free-roaming dog population was estimated to be 1,242 (95 % CI: 1205-1278) in the 18 sampled wards and 18,585 dogs in Dhaka City (52 dogs/km2) with an estimated human-to-free-roaming dog ratio of 828:1. During the two year CNVR program, a total of 6,665 dogs (3,357 male and 3,308 female) were neutered and vaccinated against rabies in 29 of the 92 city wards. A pilot population survey indicated a mean CNVR coverage of 60.6% (range 19.2-79.3%) with only eight wards achieving > 70% coverage. Given that the coverage in many neighborhoods was below the WHO-recommended threshold level of 70% for rabies eradications and since the CNVR program takes considerable time to implement throughout the entire Dhaka City area, a mass dog vaccination program in the non-CNVR coverage area is recommended to create herd immunity. The findings from this study are expected to guide dog population management and the rabies control program in Dhaka City and elsewhere in Bangladesh.

Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error

PubMed Central

Liu, Xiaoming; Fu, Yun-Xin; Maxwell, Taylor J.; Boerwinkle, Eric

2010-01-01

It is known that sequencing error can bias estimation of evolutionary or population genetic parameters. This problem is more prominent in deep resequencing studies because of their large sample size n, and a higher probability of error at each nucleotide site. We propose a new method based on the composite likelihood of the observed SNP configurations to infer population mutation rate θ = 4Neμ, population exponential growth rate R, and error rate ɛ, simultaneously. Using simulation, we show the combined effects of the parameters, θ, n, ɛ, and R on the accuracy of parameter estimation. We compared our maximum composite likelihood estimator (MCLE) of θ with other θ estimators that take into account the error. The results show the MCLE performs well when the sample size is large or the error rate is high. Using parametric bootstrap, composite likelihood can also be used as a statistic for testing the model goodness-of-fit of the observed DNA sequences. The MCLE method is applied to sequence data on the ANGPTL4 gene in 1832 African American and 1045 European American individuals. PMID:19952140

A robust measure of HIV-1 population turnover within chronically infected individuals.

PubMed

Achaz, G; Palmer, S; Kearney, M; Maldarelli, F; Mellors, J W; Coffin, J M; Wakeley, J

2004-10-01

A simple nonparameteric test for population structure was applied to temporally spaced samples of HIV-1 sequences from the gag-pol region within two chronically infected individuals. The results show that temporal structure can be detected for samples separated by about 22 months or more. The performance of the method, which was originally proposed to detect geographic structure, was tested for temporally spaced samples using neutral coalescent simulations. Simulations showed that the method is robust to variation in samples sizes and mutation rates, to the presence/absence of recombination, and that the power to detect temporal structure is high. By comparing levels of temporal structure in simulations to the levels observed in real data, we estimate the effective intra-individual population size of HIV-1 to be between 10(3) and 10(4) viruses, which is in agreement with some previous estimates. Using this estimate and a simple measure of sequence diversity, we estimate an effective neutral mutation rate of about 5 x 10(-6) per site per generation in the gag-pol region. The definition and interpretation of estimates of such "effective" population parameters are discussed.

Validation of a physical anthropology methodology using mandibles for gender estimation in a Brazilian population

PubMed Central

CARVALHO, Suzana Papile Maciel; BRITO, Liz Magalhães; de PAIVA, Luiz Airton Saavedra; BICUDO, Lucilene Arilho Ribeiro; CROSATO, Edgard Michel; de OLIVEIRA, Rogério Nogueira

2013-01-01

Validation studies of physical anthropology methods in the different population groups are extremely important, especially in cases in which the population variations may cause problems in the identification of a native individual by the application of norms developed for different communities. Objective This study aimed to estimate the gender of skeletons by application of the method of Oliveira, et al. (1995), previously used in a population sample from Northeast Brazil. Material and Methods The accuracy of this method was assessed for a population from Southeast Brazil and validated by statistical tests. The method used two mandibular measurements, namely the bigonial distance and the mandibular ramus height. The sample was composed of 66 skulls and the method was applied by two examiners. The results were statistically analyzed by the paired t test, logistic discriminant analysis and logistic regression. Results The results demonstrated that the application of the method of Oliveira, et al. (1995) in this population achieved very different outcomes between genders, with 100% for females and only 11% for males, which may be explained by ethnic differences. However, statistical adjustment of measurement data for the population analyzed allowed accuracy of 76.47% for males and 78.13% for females, with the creation of a new discriminant formula. Conclusion It was concluded that methods involving physical anthropology present high rate of accuracy for human identification, easy application, low cost and simplicity; however, the methodologies must be validated for the different populations due to differences in ethnic patterns, which are directly related to the phenotypic aspects. In this specific case, the method of Oliveira, et al. (1995) presented good accuracy and may be used for gender estimation in Brazil in two geographic regions, namely Northeast and Southeast; however, for other regions of the country (North, Central West and South), previous methodological adjustment is recommended as demonstrated in this study. PMID:24037076

Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models

PubMed Central

Boskova, Veronika; Bonhoeffer, Sebastian; Stadler, Tanja

2014-01-01

Quantifying epidemiological dynamics is crucial for understanding and forecasting the spread of an epidemic. The coalescent and the birth-death model are used interchangeably to infer epidemiological parameters from the genealogical relationships of the pathogen population under study, which in turn are inferred from the pathogen genetic sequencing data. To compare the performance of these widely applied models, we performed a simulation study. We simulated phylogenetic trees under the constant rate birth-death model and the coalescent model with a deterministic exponentially growing infected population. For each tree, we re-estimated the epidemiological parameters using both a birth-death and a coalescent based method, implemented as an MCMC procedure in BEAST v2.0. In our analyses that estimate the growth rate of an epidemic based on simulated birth-death trees, the point estimates such as the maximum a posteriori/maximum likelihood estimates are not very different. However, the estimates of uncertainty are very different. The birth-death model had a higher coverage than the coalescent model, i.e. contained the true value in the highest posterior density (HPD) interval more often (2–13% vs. 31–75% error). The coverage of the coalescent decreases with decreasing basic reproductive ratio and increasing sampling probability of infecteds. We hypothesize that the biases in the coalescent are due to the assumption of deterministic rather than stochastic population size changes. Both methods performed reasonably well when analyzing trees simulated under the coalescent. The methods can also identify other key epidemiological parameters as long as one of the parameters is fixed to its true value. In summary, when using genetic data to estimate epidemic dynamics, our results suggest that the birth-death method will be less sensitive to population fluctuations of early outbreaks than the coalescent method that assumes a deterministic exponentially growing infected population. PMID:25375100

Bird population density estimated from acoustic signals

USGS Publications Warehouse

Dawson, D.K.; Efford, M.G.

2009-01-01

Many animal species are detected primarily by sound. Although songs, calls and other sounds are often used for population assessment, as in bird point counts and hydrophone surveys of cetaceans, there are few rigorous methods for estimating population density from acoustic data. 2. The problem has several parts - distinguishing individuals, adjusting for individuals that are missed, and adjusting for the area sampled. Spatially explicit capture-recapture (SECR) is a statistical methodology that addresses jointly the second and third parts of the problem. We have extended SECR to use uncalibrated information from acoustic signals on the distance to each source. 3. We applied this extension of SECR to data from an acoustic survey of ovenbird Seiurus aurocapilla density in an eastern US deciduous forest with multiple four-microphone arrays. We modelled average power from spectrograms of ovenbird songs measured within a window of 0??7 s duration and frequencies between 4200 and 5200 Hz. 4. The resulting estimates of the density of singing males (0??19 ha -1 SE 0??03 ha-1) were consistent with estimates of the adult male population density from mist-netting (0??36 ha-1 SE 0??12 ha-1). The fitted model predicts sound attenuation of 0??11 dB m-1 (SE 0??01 dB m-1) in excess of losses from spherical spreading. 5.Synthesis and applications. Our method for estimating animal population density from acoustic signals fills a gap in the census methods available for visually cryptic but vocal taxa, including many species of bird and cetacean. The necessary equipment is simple and readily available; as few as two microphones may provide adequate estimates, given spatial replication. The method requires that individuals detected at the same place are acoustically distinguishable and all individuals vocalize during the recording interval, or that the per capita rate of vocalization is known. We believe these requirements can be met, with suitable field methods, for a significant number of songbird species. ?? 2009 British Ecological Society.

Population estimation with sparse data: The role of estimators versus indices revisited

Treesearch

Kevin S. McKelvey; Dean E. Pearson

2001-01-01

The use of indices to evaluate small-mammal populations has been heavily criticized, yet a review of small-mammal studies published from 1996 through 2000 indicated that indices are still the primary methods employed for measuring populations. The literature review also found that 98% of the samples collected in these studies were too small for reliable...

A Comparison of Normal and Elliptical Estimation Methods in Structural Equation Models.

ERIC Educational Resources Information Center

Schumacker, Randall E.; Cheevatanarak, Suchittra

Monte Carlo simulation compared chi-square statistics, parameter estimates, and root mean square error of approximation values using normal and elliptical estimation methods. Three research conditions were imposed on the simulated data: sample size, population contamination percent, and kurtosis. A Bentler-Weeks structural model established the…

Use of the superpopulation approach to estimate breeding population size: An example in asynchronously breeding birds

USGS Publications Warehouse

Williams, K.A.; Frederick, P.C.; Nichols, J.D.

2011-01-01

Many populations of animals are fluid in both space and time, making estimation of numbers difficult. Much attention has been devoted to estimation of bias in detection of animals that are present at the time of survey. However, an equally important problem is estimation of population size when all animals are not present on all survey occasions. Here, we showcase use of the superpopulation approach to capture-recapture modeling for estimating populations where group membership is asynchronous, and where considerable overlap in group membership among sampling occasions may occur. We estimate total population size of long-legged wading bird (Great Egret and White Ibis) breeding colonies from aerial observations of individually identifiable nests at various times in the nesting season. Initiation and termination of nests were analogous to entry and departure from a population. Estimates using the superpopulation approach were 47-382% larger than peak aerial counts of the same colonies. Our results indicate that the use of the superpopulation approach to model nesting asynchrony provides a considerably less biased and more efficient estimate of nesting activity than traditional methods. We suggest that this approach may also be used to derive population estimates in a variety of situations where group membership is fluid. ?? 2011 by the Ecological Society of America.

Development and verification of a model for estimating the screening utility in the detection of PCBs in transformer oil.

PubMed

Terakado, Shingo; Glass, Thomas R; Sasaki, Kazuhiro; Ohmura, Naoya

2014-01-01

A simple new model for estimating the screening performance (false positive and false negative rates) of a given test for a specific sample population is presented. The model is shown to give good results on a test population, and is used to estimate the performance on a sampled population. Using the model developed in conjunction with regulatory requirements and the relative costs of the confirmatory and screening tests allows evaluation of the screening test's utility in terms of cost savings. Testers can use the methods developed to estimate the utility of a screening program using available screening tests with their own sample populations.

A cautionary note on Bayesian estimation of population size by removal sampling with diffuse priors.

PubMed

Bord, Séverine; Bioche, Christèle; Druilhet, Pierre

2018-05-01

We consider the problem of estimating a population size by removal sampling when the sampling rate is unknown. Bayesian methods are now widespread and allow to include prior knowledge in the analysis. However, we show that Bayes estimates based on default improper priors lead to improper posteriors or infinite estimates. Similarly, weakly informative priors give unstable estimators that are sensitive to the choice of hyperparameters. By examining the likelihood, we show that population size estimates can be stabilized by penalizing small values of the sampling rate or large value of the population size. Based on theoretical results and simulation studies, we propose some recommendations on the choice of the prior. Then, we applied our results to real datasets. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Worldwide F(ST) estimates relative to five continental-scale populations.

PubMed

Steele, Christopher D; Court, Denise Syndercombe; Balding, David J

2014-11-01

We estimate the population genetics parameter FST (also referred to as the fixation index) from short tandem repeat (STR) allele frequencies, comparing many worldwide human subpopulations at approximately the national level with continental-scale populations. FST is commonly used to measure population differentiation, and is important in forensic DNA analysis to account for remote shared ancestry between a suspect and an alternative source of the DNA. We estimate FST comparing subpopulations with a hypothetical ancestral population, which is the approach most widely used in population genetics, and also compare a subpopulation with a sampled reference population, which is more appropriate for forensic applications. Both estimation methods are likelihood-based, in which FST is related to the variance of the multinomial-Dirichlet distribution for allele counts. Overall, we find low FST values, with posterior 97.5 percentiles < 3% when comparing a subpopulation with the most appropriate population, and even for inter-population comparisons we find FST < 5%. These are much smaller than single nucleotide polymorphism-based inter-continental FST estimates, and are also about half the magnitude of STR-based estimates from population genetics surveys that focus on distinct ethnic groups rather than a general population. Our findings support the use of FST up to 3% in forensic calculations, which corresponds to some current practice.

Problems with sampling desert tortoises: A simulation analysis based on field data

USGS Publications Warehouse

Freilich, J.E.; Camp, R.J.; Duda, J.J.; Karl, A.E.

2005-01-01

The desert tortoise (Gopherus agassizii) was listed as a U.S. threatened species in 1990 based largely on population declines inferred from mark-recapture surveys of 2.59-km2 (1-mi2) plots. Since then, several census methods have been proposed and tested, but all methods still pose logistical or statistical difficulties. We conducted computer simulations using actual tortoise location data from 2 1-mi2 plot surveys in southern California, USA, to identify strengths and weaknesses of current sampling strategies. We considered tortoise population estimates based on these plots as "truth" and then tested various sampling methods based on sampling smaller plots or transect lines passing through the mile squares. Data were analyzed using Schnabel's mark-recapture estimate and program CAPTURE. Experimental subsampling with replacement of the 1-mi2 data using 1-km2 and 0.25-km2 plot boundaries produced data sets of smaller plot sizes, which we compared to estimates from the 1-mi 2 plots. We also tested distance sampling by saturating a 1-mi 2 site with computer simulated transect lines, once again evaluating bias in density estimates. Subsampling estimates from 1-km2 plots did not differ significantly from the estimates derived at 1-mi2. The 0.25-km2 subsamples significantly overestimated population sizes, chiefly because too few recaptures were made. Distance sampling simulations were biased 80% of the time and had high coefficient of variation to density ratios. Furthermore, a prospective power analysis suggested limited ability to detect population declines as high as 50%. We concluded that poor performance and bias of both sampling procedures was driven by insufficient sample size, suggesting that all efforts must be directed to increasing numbers found in order to produce reliable results. Our results suggest that present methods may not be capable of accurately estimating desert tortoise populations.

A Continuous Method for Gene Flow

PubMed Central

Palczewski, Michal; Beerli, Peter

2013-01-01

Most modern population genetics inference methods are based on the coalescence framework. Methods that allow estimating parameters of structured populations commonly insert migration events into the genealogies. For these methods the calculation of the coalescence probability density of a genealogy requires a product over all time periods between events. Data sets that contain populations with high rates of gene flow among them require an enormous number of calculations. A new method, transition probability-structured coalescence (TPSC), replaces the discrete migration events with probability statements. Because the speed of calculation is independent of the amount of gene flow, this method allows calculating the coalescence densities efficiently. The current implementation of TPSC uses an approximation simplifying the interaction among lineages. Simulations and coverage comparisons of TPSC vs. MIGRATE show that TPSC allows estimation of high migration rates more precisely, but because of the approximation the estimation of low migration rates is biased. The implementation of TPSC into programs that calculate quantities on phylogenetic tree structures is straightforward, so the TPSC approach will facilitate more general inferences in many computer programs. PMID:23666937

An empirical Bayes approach to analyzing recurring animal surveys

USGS Publications Warehouse

Johnson, D.H.

1989-01-01

Recurring estimates of the size of animal populations are often required by biologists or wildlife managers. Because of cost or other constraints, estimates frequently lack the accuracy desired but cannot readily be improved by additional sampling. This report proposes a statistical method employing empirical Bayes (EB) estimators as alternatives to those customarily used to estimate population size, and evaluates them by a subsampling experiment on waterfowl surveys. EB estimates, especially a simple limited-translation version, were more accurate and provided shorter confidence intervals with greater coverage probabilities than customary estimates.

A modified approach to estimating sample size for simple logistic regression with one continuous covariate.

PubMed

Novikov, I; Fund, N; Freedman, L S

2010-01-15

Different methods for the calculation of sample size for simple logistic regression (LR) with one normally distributed continuous covariate give different results. Sometimes the difference can be large. Furthermore, some methods require the user to specify the prevalence of cases when the covariate equals its population mean, rather than the more natural population prevalence. We focus on two commonly used methods and show through simulations that the power for a given sample size may differ substantially from the nominal value for one method, especially when the covariate effect is large, while the other method performs poorly if the user provides the population prevalence instead of the required parameter. We propose a modification of the method of Hsieh et al. that requires specification of the population prevalence and that employs Schouten's sample size formula for a t-test with unequal variances and group sizes. This approach appears to increase the accuracy of the sample size estimates for LR with one continuous covariate.

Indirect genetic estimates of breeding population size in the polyploid green sturgeon (Acipenser medirostris).

PubMed

Israel, J A; May, B

2010-03-01

The utility of genetic measures for kinship reconstruction in polysomic species is not well evaluated. We developed a framework to test hypotheses about estimating breeding population size indirectly from collections of outmigrating green sturgeon juveniles. We evaluated a polysomic dataset, in allelic frequency and phenotypic formats, from green sturgeon to describe the relationship among known progeny from experimental families. The distributions of relatedness values for kin classes were used for reconstructing green sturgeon pedigrees from juveniles of unknown relationship. We compared three rarefaction functions that described the relationship between the number of kin groups and number of samples in a pedigree to estimate the annual abundance of spawners contributing to the threatened green sturgeon Southern Distinct Population Segment in the upper Sacramento River. Results suggested the estimated abundance of breeding green sturgeon remained roughly constant in the upper Sacramento River over a 5-year period, ranging from 10 to 28 individuals depending on the year and rarefaction method. These results demonstrate an empirical understanding for the distribution of relatedness values among individuals is a benefit for assessing pedigree reconstruction methods and identifying misclassification rates. Monitoring of rare species using these indirect methods is feasible and can provide insight into breeding and ontogenetic behaviour. While this framework was developed for specific application to studying fish populations in a riverscape, the framework could be advanced to improve genetic estimation of breeding population size and to identify important breeding habitats of rare species when combined with finer-scaled sampling of offspring.

Measurement of admixture proportions and description of admixture structure in different US populations

PubMed Central

Halder, Indrani; Yang, Bao-Zhu; Kranzler, Henry R.; Stein, Murray B.; Shriver, Mark D.; Gelernter, Joel

2010-01-01

Variation in individual admixture proportions leads to heterogeneity within populations. Though novel methods and marker panels have been developed to quantify individual admixture, empirical data describing individual admixture distributions are limited. We investigated variation in individual admixture in four US populations [European American (EA), African American (AA) and Hispanics from Connecticut (EC) and California (WC)] assuming three-way intermixture among Europeans, Africans and Indigenous Americans. Admixture estimates were inferred using a panel of 36 microsatellites and 1 SNP, which have significant allele frequency differences between ancestral populations, and by using both a maximum likelihood (ML) based method and a Bayesian method implemented in the program STRUCTURE. Simulation studies showed that estimates obtained with this marker panel are within 96% of expected values. EAs had the lowest non-European admixture with both methods, but showed greater homogeneity with STRUCTURE than with ML. All other samples showed a high degree of variation in admixture estimates with both methods, were highly concordant and showed evidence of admixture stratification. With both methods, AA subjects had 16% European and <10% Indigenous American admixture on average. EC Hispanics had higher mean African admixture and the WC Hispanics higher mean Indigenous American admixture, possibly reflecting their different continental origins. PMID:19572378

Estimation of the dynamics and rate of transmission of classical swine fever (hog cholera) in wild pigs.

PubMed Central

Hone, J.; Pech, R.; Yip, P.

1992-01-01

Infectious diseases establish in a population of wildlife hosts when the number of secondary infections is greater than or equal to one. To estimate whether establishment will occur requires extensive experience or a mathematical model of disease dynamics and estimates of the parameters of the disease model. The latter approach is explored here. Methods for estimating key model parameters, the transmission coefficient (beta) and the basic reproductive rate (RDRS), are described using classical swine fever (hog cholera) in wild pigs as an example. The tentative results indicate that an acute infection of classical swine fever will establish in a small population of wild pigs. Data required for estimation of disease transmission rates are reviewed and sources of bias and alternative methods discussed. A comprehensive evaluation of the biases and efficiencies of the methods is needed. PMID:1582476

Horvitz-Thompson survey sample methods for estimating large-scale animal abundance

USGS Publications Warehouse

Samuel, M.D.; Garton, E.O.

1994-01-01

Large-scale surveys to estimate animal abundance can be useful for monitoring population status and trends, for measuring responses to management or environmental alterations, and for testing ecological hypotheses about abundance. However, large-scale surveys may be expensive and logistically complex. To ensure resources are not wasted on unattainable targets, the goals and uses of each survey should be specified carefully and alternative methods for addressing these objectives always should be considered. During survey design, the impoflance of each survey error component (spatial design, propofiion of detected animals, precision in detection) should be considered carefully to produce a complete statistically based survey. Failure to address these three survey components may produce population estimates that are inaccurate (biased low), have unrealistic precision (too precise) and do not satisfactorily meet the survey objectives. Optimum survey design requires trade-offs in these sources of error relative to the costs of sampling plots and detecting animals on plots, considerations that are specific to the spatial logistics and survey methods. The Horvitz-Thompson estimators provide a comprehensive framework for considering all three survey components during the design and analysis of large-scale wildlife surveys. Problems of spatial and temporal (especially survey to survey) heterogeneity in detection probabilities have received little consideration, but failure to account for heterogeneity produces biased population estimates. The goal of producing unbiased population estimates is in conflict with the increased variation from heterogeneous detection in the population estimate. One solution to this conflict is to use an MSE-based approach to achieve a balance between bias reduction and increased variation. Further research is needed to develop methods that address spatial heterogeneity in detection, evaluate the effects of temporal heterogeneity on survey objectives and optimize decisions related to survey bias and variance. Finally, managers and researchers involved in the survey design process must realize that obtaining the best survey results requires an interactive and recursive process of survey design, execution, analysis and redesign. Survey refinements will be possible as further knowledge is gained on the actual abundance and distribution of the population and on the most efficient techniques for detection animals.

Validation of a physical anthropology methodology using mandibles for gender estimation in a Brazilian population.

PubMed

Carvalho, Suzana Papile Maciel; Brito, Liz Magalhães; Paiva, Luiz Airton Saavedra de; Bicudo, Lucilene Arilho Ribeiro; Crosato, Edgard Michel; Oliveira, Rogério Nogueira de

2013-01-01

Validation studies of physical anthropology methods in the different population groups are extremely important, especially in cases in which the population variations may cause problems in the identification of a native individual by the application of norms developed for different communities. This study aimed to estimate the gender of skeletons by application of the method of Oliveira, et al. (1995), previously used in a population sample from Northeast Brazil. The accuracy of this method was assessed for a population from Southeast Brazil and validated by statistical tests. The method used two mandibular measurements, namely the bigonial distance and the mandibular ramus height. The sample was composed of 66 skulls and the method was applied by two examiners. The results were statistically analyzed by the paired t test, logistic discriminant analysis and logistic regression. The results demonstrated that the application of the method of Oliveira, et al. (1995) in this population achieved very different outcomes between genders, with 100% for females and only 11% for males, which may be explained by ethnic differences. However, statistical adjustment of measurement data for the population analyzed allowed accuracy of 76.47% for males and 78.13% for females, with the creation of a new discriminant formula. It was concluded that methods involving physical anthropology present high rate of accuracy for human identification, easy application, low cost and simplicity; however, the methodologies must be validated for the different populations due to differences in ethnic patterns, which are directly related to the phenotypic aspects. In this specific case, the method of Oliveira, et al. (1995) presented good accuracy and may be used for gender estimation in Brazil in two geographic regions, namely Northeast and Southeast; however, for other regions of the country (North, Central West and South), previous methodological adjustment is recommended as demonstrated in this study.

Digital radiographic evaluation of mandibular third molar for age estimation in young adults and adolescents of South Indian population using modified Demirjian's method

PubMed Central

Mohammed, Rezwana Begum; Koganti, Ravichandra; Kalyan, Siva V.; Tircouveluri, Saritha; Singh, Johar Rajvinder; Srinivasulu, Enganti

2014-01-01

In recent years, it has become increasingly important to determine the age of living people for a variety of reasons, including identifying criminal and legal responsibility and for many other social events such as birth certificate, marriage, beginning a job, joining the army and retirement Objectives: The aim of this study was to assess the developmental stages of mandibular third molar for estimation of dental age (DA) in different age groups and to evaluate the possible correlation between DA and chronological age (CA) in South Indian population. Materials and Methods: Digital orthopantomography of 330 subjects (165 males, 165 females) who fit the study and the criteria were obtained. Assessment of mandibular third molar development was performed using Demirjian et al., modified method and DA was assessed using tooth specific stages. Results and Discussion: The present study showed a significant correlation between DA and CA in both males and females. Third molar development commenced around 9 years and root completion takes place around 18.9 years in males and in females 9 years and 18.6 years respectively. Demirjian modified method underestimated the mean age of males by 0.8 years and females by 0.5 years and also showed that females mature earlier than males in selected population. Conclusion: Digital radiographic assessment of mandibular third molar development can be used to generate mean DA using Demirjian modified method and also the estimated age range for an individual of unknown CA. Since the Demirjian method is based on French-Canadian population, to enhance the accuracy of forensic age estimates based on third molar development, the use of population-specific standards is recommended. PMID:25177143

The use of resighting data to estimate the rate of population growth of the snail kite in Florida

USGS Publications Warehouse

Dreitz, V.J.; Nichols, J.D.; Hines, J.E.; Bennetts, R.E.; Kitchens, W.M.; DeAngelis, D.L.

2002-01-01

The rate of population growth (lambda) is an important demographic parameter used to assess the viability of a population and to develop management and conservation agendas. We examined the use of resighting data to estimate lambda for the snail kite population in Florida from 1997-2000. The analyses consisted of (1) a robust design approach that derives an estimate of lambda from estimates of population size and (2) the Pradel (1996) temporal symmetry (TSM) approach that directly estimates lambda using an open-population capture-recapture model. Besides resighting data, both approaches required information on the number of unmarked individuals that were sighted during the sampling periods. The point estimates of lambda differed between the robust design and TSM approaches, but the 95% confidence intervals overlapped substantially. We believe the differences may be the result of sparse data and do not indicate the inappropriateness of either modelling technique. We focused on the results of the robust design because this approach provided estimates for all study years. Variation among these estimates was smaller than levels of variation among ad hoc estimates based on previously reported index statistics. We recommend that lambda of snail kites be estimated using capture-resighting methods rather than ad hoc counts.

Estimating the Size of the Methamphetamine-Using Population in New York City Using Network Sampling Techniques.

PubMed

Dombrowski, Kirk; Khan, Bilal; Wendel, Travis; McLean, Katherine; Misshula, Evan; Curtis, Ric

2012-12-01

As part of a recent study of the dynamics of the retail market for methamphetamine use in New York City, we used network sampling methods to estimate the size of the total networked population. This process involved sampling from respondents' list of co-use contacts, which in turn became the basis for capture-recapture estimation. Recapture sampling was based on links to other respondents derived from demographic and "telefunken" matching procedures-the latter being an anonymized version of telephone number matching. This paper describes the matching process used to discover the links between the solicited contacts and project respondents, the capture-recapture calculation, the estimation of "false matches", and the development of confidence intervals for the final population estimates. A final population of 12,229 was estimated, with a range of 8235 - 23,750. The techniques described here have the special virtue of deriving an estimate for a hidden population while retaining respondent anonymity and the anonymity of network alters, but likely require larger sample size than the 132 persons interviewed to attain acceptable confidence levels for the estimate.

A comparison of methods for calculating population exposure estimates of daily weather for health research.

PubMed

Hanigan, Ivan; Hall, Gillian; Dear, Keith B G

2006-09-13

To explain the possible effects of exposure to weather conditions on population health outcomes, weather data need to be calculated at a level in space and time that is appropriate for the health data. There are various ways of estimating exposure values from raw data collected at weather stations but the rationale for using one technique rather than another; the significance of the difference in the values obtained; and the effect these have on a research question are factors often not explicitly considered. In this study we compare different techniques for allocating weather data observations to small geographical areas and different options for weighting averages of these observations when calculating estimates of daily precipitation and temperature for Australian Postal Areas. Options that weight observations based on distance from population centroids and population size are more computationally intensive but give estimates that conceptually are more closely related to the experience of the population. Options based on values derived from sites internal to postal areas, or from nearest neighbour sites--that is, using proximity polygons around weather stations intersected with postal areas--tended to include fewer stations' observations in their estimates, and missing values were common. Options based on observations from stations within 50 kilometres radius of centroids and weighting of data by distance from centroids gave more complete estimates. Using the geographic centroid of the postal area gave estimates that differed slightly from the population weighted centroids and the population weighted average of sub-unit estimates. To calculate daily weather exposure values for analysis of health outcome data for small areas, the use of data from weather stations internal to the area only, or from neighbouring weather stations (allocated by the use of proximity polygons), is too limited. The most appropriate method conceptually is the use of weather data from sites within 50 kilometres radius of the area weighted to population centres, but a simpler acceptable option is to weight to the geographic centroid.

Estimating Kinship in Admixed Populations

PubMed Central

Thornton, Timothy; Tang, Hua; Hoffmann, Thomas J.; Ochs-Balcom, Heather M.; Caan, Bette J.; Risch, Neil

2012-01-01

Genome-wide association studies (GWASs) are commonly used for the mapping of genetic loci that influence complex traits. A problem that is often encountered in both population-based and family-based GWASs is that of identifying cryptic relatedness and population stratification because it is well known that failure to appropriately account for both pedigree and population structure can lead to spurious association. A number of methods have been proposed for identifying relatives in samples from homogeneous populations. A strong assumption of population homogeneity, however, is often untenable, and many GWASs include samples from structured populations. Here, we consider the problem of estimating relatedness in structured populations with admixed ancestry. We propose a method, REAP (relatedness estimation in admixed populations), for robust estimation of identity by descent (IBD)-sharing probabilities and kinship coefficients in admixed populations. REAP appropriately accounts for population structure and ancestry-related assortative mating by using individual-specific allele frequencies at SNPs that are calculated on the basis of ancestry derived from whole-genome analysis. In simulation studies with related individuals and admixture from highly divergent populations, we demonstrate that REAP gives accurate IBD-sharing probabilities and kinship coefficients. We apply REAP to the Mexican Americans in Los Angeles, California (MXL) population sample of release 3 of phase III of the International Haplotype Map Project; in this sample, we identify third- and fourth-degree relatives who have not previously been reported. We also apply REAP to the African American and Hispanic samples from the Women's Health Initiative SNP Health Association Resource (WHI-SHARe) study, in which hundreds of pairs of cryptically related individuals have been identified. PMID:22748210

Accounting for missing data in the estimation of contemporary genetic effective population size (N(e) ).

PubMed

Peel, D; Waples, R S; Macbeth, G M; Do, C; Ovenden, J R

2013-03-01

Theoretical models are often applied to population genetic data sets without fully considering the effect of missing data. Researchers can deal with missing data by removing individuals that have failed to yield genotypes and/or by removing loci that have failed to yield allelic determinations, but despite their best efforts, most data sets still contain some missing data. As a consequence, realized sample size differs among loci, and this poses a problem for unbiased methods that must explicitly account for random sampling error. One commonly used solution for the calculation of contemporary effective population size (N(e) ) is to calculate the effective sample size as an unweighted mean or harmonic mean across loci. This is not ideal because it fails to account for the fact that loci with different numbers of alleles have different information content. Here we consider this problem for genetic estimators of contemporary effective population size (N(e) ). To evaluate bias and precision of several statistical approaches for dealing with missing data, we simulated populations with known N(e) and various degrees of missing data. Across all scenarios, one method of correcting for missing data (fixed-inverse variance-weighted harmonic mean) consistently performed the best for both single-sample and two-sample (temporal) methods of estimating N(e) and outperformed some methods currently in widespread use. The approach adopted here may be a starting point to adjust other population genetics methods that include per-locus sample size components. © 2012 Blackwell Publishing Ltd.

Density estimation in wildlife surveys

Treesearch

Jonathan Bart; Sam Droege; Paul Geissler; Bruce Peterjohn; C. John Ralph

2004-01-01

Several authors have recently discussed the problems with using index methods to estimate trends in population size. Some have expressed the view that index methods should virtually never be used. Others have responded by defending index methods and questioning whether better alternatives exist. We suggest that index methods are often a costeffective component of valid...

Estimating HIV Prevalence in Zimbabwe Using Population-Based Survey Data

PubMed Central

Chinomona, Amos; Mwambi, Henry Godwell

2015-01-01

Estimates of HIV prevalence computed using data obtained from sampling a subgroup of the national population may lack the representativeness of all the relevant domains of the population. These estimates are often computed on the assumption that HIV prevalence is uniform across all domains of the population. Use of appropriate statistical methods together with population-based survey data can enhance better estimation of national and subgroup level HIV prevalence and can provide improved explanations of the variation in HIV prevalence across different domains of the population. In this study we computed design-consistent estimates of HIV prevalence, and their respective 95% confidence intervals at both the national and subgroup levels. In addition, we provided a multivariable survey logistic regression model from a generalized linear modelling perspective for explaining the variation in HIV prevalence using demographic, socio-economic, socio-cultural and behavioural factors. Essentially, this study borrows from the proximate determinants conceptual framework which provides guiding principles upon which socio-economic and socio-cultural variables affect HIV prevalence through biological behavioural factors. We utilize the 2010–11 Zimbabwe Demographic and Health Survey (2010–11 ZDHS) data (which are population based) to estimate HIV prevalence in different categories of the population and for constructing the logistic regression model. It was established that HIV prevalence varies greatly with age, gender, marital status, place of residence, literacy level, belief on whether condom use can reduce the risk of contracting HIV and level of recent sexual activity whereas there was no marked variation in HIV prevalence with social status (measured using a wealth index), method of contraceptive and an individual’s level of education. PMID:26624280

Sex estimation from the patella in an African American population.

PubMed

Peckmann, Tanya R; Fisher, Brooke

2018-02-01

The skull and pelvis have been used for the estimation of sex for unknown human remains. However, in forensic cases where skeletal remains often exhibit postmortem damage and taphonomic changes the patella may be used for the estimation of sex as it is a preservationally favoured bone. The goal of the present research was to derive discriminant function equations from the patella for estimation of sex from an historic African American population. Six parameters were measured on 200 individuals (100 males and 100 females), ranging in age from 20 to 80 years old, from the Robert J. Terry Anatomical Skeleton Collection. The statistical analyses showed that all variables were sexually dimorphic. Discriminant function score equations were generated for use in sex estimation. The overall accuracy of sex classification ranged from 80.0% to 85.0% for the direct method and 80.0%-84.5% for the stepwise method. Overall, when the Spanish and Black South African discriminant functions were applied to the African American population they showed low accuracy rates for sexing the African American sample. However, when the White South African discriminant functions were applied to the African American sample they displayed high accuracy rates for sexing the African American population. The patella was shown to be accurate for sex estimation in the historic African American population. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Instrumental Variable Analysis with a Nonlinear Exposure–Outcome Relationship

PubMed Central

Davies, Neil M.; Thompson, Simon G.

2014-01-01

Background: Instrumental variable methods can estimate the causal effect of an exposure on an outcome using observational data. Many instrumental variable methods assume that the exposure–outcome relation is linear, but in practice this assumption is often in doubt, or perhaps the shape of the relation is a target for investigation. We investigate this issue in the context of Mendelian randomization, the use of genetic variants as instrumental variables. Methods: Using simulations, we demonstrate the performance of a simple linear instrumental variable method when the true shape of the exposure–outcome relation is not linear. We also present a novel method for estimating the effect of the exposure on the outcome within strata of the exposure distribution. This enables the estimation of localized average causal effects within quantile groups of the exposure or as a continuous function of the exposure using a sliding window approach. Results: Our simulations suggest that linear instrumental variable estimates approximate a population-averaged causal effect. This is the average difference in the outcome if the exposure for every individual in the population is increased by a fixed amount. Estimates of localized average causal effects reveal the shape of the exposure–outcome relation for a variety of models. These methods are used to investigate the relations between body mass index and a range of cardiovascular risk factors. Conclusions: Nonlinear exposure–outcome relations should not be a barrier to instrumental variable analyses. When the exposure–outcome relation is not linear, either a population-averaged causal effect or the shape of the exposure–outcome relation can be estimated. PMID:25166881

Assessing Methods for Generalizing Experimental Impact Estimates to Target Populations

ERIC Educational Resources Information Center

Kern, Holger L.; Stuart, Elizabeth A.; Hill, Jennifer; Green, Donald P.

2016-01-01

Randomized experiments are considered the gold standard for causal inference because they can provide unbiased estimates of treatment effects for the experimental participants. However, researchers and policymakers are often interested in using a specific experiment to inform decisions about other target populations. In education research,…

Estimating abundance of mountain lions from unstructured spatial sampling

Treesearch

Robin E. Russell; J. Andrew Royle; Richard Desimone; Michael K. Schwartz; Victoria L. Edwards; Kristy P. Pilgrim; Kevin S. McKelvey

2012-01-01

Mountain lions (Puma concolor) are often difficult to monitor because of their low capture probabilities, extensive movements, and large territories. Methods for estimating the abundance of this species are needed to assess population status, determine harvest levels, evaluate the impacts of management actions on populations, and derive conservation and management...

Software Review: A program for testing capture-recapture data for closure

USGS Publications Warehouse

Stanley, Thomas R.; Richards, Jon D.

2005-01-01

Capture-recapture methods are widely used to estimate population parameters of free-ranging animals. Closed-population capture-recapture models, which assume there are no additions to or losses from the population over the period of study (i.e., the closure assumption), are preferred for population estimation over the open-population models, which do not assume closure, because heterogeneity in detection probabilities can be accounted for and this improves estimates. In this paper we introduce CloseTest, a new Microsoft® Windows-based program that computes the Otis et al. (1978) and Stanley and Burnham (1999) closure tests for capture-recapture data sets. Information on CloseTest features and where to obtain the program are provided.

Comparison of Drive Counts and Mark-Resight As Methods of Population Size Estimation of Highly Dense Sika Deer (Cervus nippon) Populations.

PubMed

Takeshita, Kazutaka; Ikeda, Takashi; Takahashi, Hiroshi; Yoshida, Tsuyoshi; Igota, Hiromasa; Matsuura, Yukiko; Kaji, Koichi

2016-01-01

Assessing temporal changes in abundance indices is an important issue in the management of large herbivore populations. The drive counts method has been frequently used as a deer abundance index in mountainous regions. However, despite an inherent risk for observation errors in drive counts, which increase with deer density, evaluations of the utility of drive counts at a high deer density remain scarce. We compared the drive counts and mark-resight (MR) methods in the evaluation of a highly dense sika deer population (MR estimates ranged between 11 and 53 individuals/km2) on Nakanoshima Island, Hokkaido, Japan, between 1999 and 2006. This deer population experienced two large reductions in density; approximately 200 animals in total were taken from the population through a large-scale population removal and a separate winter mass mortality event. Although the drive counts tracked temporal changes in deer abundance on the island, they overestimated the counts for all years in comparison to the MR method. Increased overestimation in drive count estimates after the winter mass mortality event may be due to a double count derived from increased deer movement and recovery of body condition secondary to the mitigation of density-dependent food limitations. Drive counts are unreliable because they are affected by unfavorable factors such as bad weather, and they are cost-prohibitive to repeat, which precludes the calculation of confidence intervals. Therefore, the use of drive counts to infer the deer abundance needs to be reconsidered.

Monitoring gray wolf populations using multiple survey methods

USGS Publications Warehouse

Ausband, David E.; Rich, Lindsey N.; Glenn, Elizabeth M.; Mitchell, Michael S.; Zager, Pete; Miller, David A.W.; Waits, Lisette P.; Ackerman, Bruce B.; Mack, Curt M.

2013-01-01

The behavioral patterns and large territories of large carnivores make them challenging to monitor. Occupancy modeling provides a framework for monitoring population dynamics and distribution of territorial carnivores. We combined data from hunter surveys, howling and sign surveys conducted at predicted wolf rendezvous sites, and locations of radiocollared wolves to model occupancy and estimate the number of gray wolf (Canis lupus) packs and individuals in Idaho during 2009 and 2010. We explicitly accounted for potential misidentification of occupied cells (i.e., false positives) using an extension of the multi-state occupancy framework. We found agreement between model predictions and distribution and estimates of number of wolf packs and individual wolves reported by Idaho Department of Fish and Game and Nez Perce Tribe from intensive radiotelemetry-based monitoring. Estimates of individual wolves from occupancy models that excluded data from radiocollared wolves were within an average of 12.0% (SD = 6.0) of existing statewide minimum counts. Models using only hunter survey data generally estimated the lowest abundance, whereas models using all data generally provided the highest estimates of abundance, although only marginally higher. Precision across approaches ranged from 14% to 28% of mean estimates and models that used all data streams generally provided the most precise estimates. We demonstrated that an occupancy model based on different survey methods can yield estimates of the number and distribution of wolf packs and individual wolf abundance with reasonable measures of precision. Assumptions of the approach including that average territory size is known, average pack size is known, and territories do not overlap, must be evaluated periodically using independent field data to ensure occupancy estimates remain reliable. Use of multiple survey methods helps to ensure that occupancy estimates are robust to weaknesses or changes in any 1 survey method. Occupancy modeling may be useful for standardizing estimates across large landscapes, even if survey methods differ across regions, allowing for inferences about broad-scale population dynamics of wolves.

Estimating species-specific suvival and movement when species identification is uncertain

USGS Publications Warehouse

Runge, J.P.; Hines, J.E.; Nichols, J.D.

2007-01-01

Incorporating uncertainty in the investigation of ecological studies has been the topic of an increasing body of research. In particular, mark?recapture methodology has shown that incorporating uncertainty in the probability of detecting individuals in populations enables accurate estimation of population-level processes such as survival, reproduction, and dispersal. Recent advances in mark?recapture methodology have included estimating population-level processes for biologically important groups despite the misassignment of individuals to those groups. Examples include estimating rates of apparent survival despite less than perfect accuracy when identifying individuals to gender or breeding state. Here we introduce a method for estimating apparent survival and dispersal in species that co-occur but that are difficult to distinguish. We use data from co-occurring populations of meadow voles (Microtus pennsylvanicus) and montane voles (M. montanus) in addition to simulated data to show that ignoring species uncertainty can lead to biased estimates of population processes. The incorporation of species uncertainty in mark?recapture studies should aid future research investigating ecological concepts such as interspecific competition, niche differentiation, and spatial population dynamics in sibling species.

Using spatial capture–recapture to elucidate population processes and space-use in herpetological studies

USGS Publications Warehouse

Muñoz, David J.; Miller, David A.W.; Sutherland, Chris; Grant, Evan H. Campbell

2016-01-01

The cryptic behavior and ecology of herpetofauna make estimating the impacts of environmental change on demography difficult; yet, the ability to measure demographic relationships is essential for elucidating mechanisms leading to the population declines reported for herpetofauna worldwide. Recently developed spatial capture–recapture (SCR) methods are well suited to standard herpetofauna monitoring approaches. Individually identifying animals and their locations allows accurate estimates of population densities and survival. Spatial capture–recapture methods also allow estimation of parameters describing space-use and movement, which generally are expensive or difficult to obtain using other methods. In this paper, we discuss the basic components of SCR models, the available software for conducting analyses, and the experimental designs based on common herpetological survey methods. We then apply SCR models to Red-backed Salamander (Plethodon cinereus), to determine differences in density, survival, dispersal, and space-use between adult male and female salamanders. By highlighting the capabilities of SCR, and its advantages compared to traditional methods, we hope to give herpetologists the resource they need to apply SCR in their own systems.

Generalizing Observational Study Results: Applying Propensity Score Methods to Complex Surveys

PubMed Central

DuGoff, Eva H; Schuler, Megan; Stuart, Elizabeth A

2014-01-01

ObjectiveTo provide a tutorial for using propensity score methods with complex survey data. Data SourcesSimulated data and the 2008 Medical Expenditure Panel Survey. Study DesignUsing simulation, we compared the following methods for estimating the treatment effect: a naïve estimate (ignoring both survey weights and propensity scores), survey weighting, propensity score methods (nearest neighbor matching, weighting, and subclassification), and propensity score methods in combination with survey weighting. Methods are compared in terms of bias and 95 percent confidence interval coverage. In Example 2, we used these methods to estimate the effect on health care spending of having a generalist versus a specialist as a usual source of care. Principal FindingsIn general, combining a propensity score method and survey weighting is necessary to achieve unbiased treatment effect estimates that are generalizable to the original survey target population. ConclusionsPropensity score methods are an essential tool for addressing confounding in observational studies. Ignoring survey weights may lead to results that are not generalizable to the survey target population. This paper clarifies the appropriate inferences for different propensity score methods and suggests guidelines for selecting an appropriate propensity score method based on a researcher’s goal. PMID:23855598

Generalizing observational study results: applying propensity score methods to complex surveys.

PubMed

Dugoff, Eva H; Schuler, Megan; Stuart, Elizabeth A

2014-02-01

To provide a tutorial for using propensity score methods with complex survey data. Simulated data and the 2008 Medical Expenditure Panel Survey. Using simulation, we compared the following methods for estimating the treatment effect: a naïve estimate (ignoring both survey weights and propensity scores), survey weighting, propensity score methods (nearest neighbor matching, weighting, and subclassification), and propensity score methods in combination with survey weighting. Methods are compared in terms of bias and 95 percent confidence interval coverage. In Example 2, we used these methods to estimate the effect on health care spending of having a generalist versus a specialist as a usual source of care. In general, combining a propensity score method and survey weighting is necessary to achieve unbiased treatment effect estimates that are generalizable to the original survey target population. Propensity score methods are an essential tool for addressing confounding in observational studies. Ignoring survey weights may lead to results that are not generalizable to the survey target population. This paper clarifies the appropriate inferences for different propensity score methods and suggests guidelines for selecting an appropriate propensity score method based on a researcher's goal. © Health Research and Educational Trust.

Generalizing Evidence From Randomized Clinical Trials to Target Populations

PubMed Central

Cole, Stephen R.; Stuart, Elizabeth A.

2010-01-01

Properly planned and conducted randomized clinical trials remain susceptible to a lack of external validity. The authors illustrate a model-based method to standardize observed trial results to a specified target population using a seminal human immunodeficiency virus (HIV) treatment trial, and they provide Monte Carlo simulation evidence supporting the method. The example trial enrolled 1,156 HIV-infected adult men and women in the United States in 1996, randomly assigned 577 to a highly active antiretroviral therapy and 579 to a largely ineffective combination therapy, and followed participants for 52 weeks. The target population was US people infected with HIV in 2006, as estimated by the Centers for Disease Control and Prevention. Results from the trial apply, albeit muted by 12%, to the target population, under the assumption that the authors have measured and correctly modeled the determinants of selection that reflect heterogeneity in the treatment effect. In simulations with a heterogeneous treatment effect, a conventional intent-to-treat estimate was biased with poor confidence limit coverage, but the proposed estimate was largely unbiased with appropriate confidence limit coverage. The proposed method standardizes observed trial results to a specified target population and thereby provides information regarding the generalizability of trial results. PMID:20547574

GONe: Software for estimating effective population size in species with generational overlap

USGS Publications Warehouse

Coombs, J.A.; Letcher, B.H.; Nislow, K.H.

2012-01-01

GONe is a user-friendly, Windows-based program for estimating effective size (N e) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age structure in populations. This method requires estimates of age-specific survival and birth rate and allele frequencies measured in two or more consecutive cohorts. Allele frequencies are acquired by reading in genotypic data from files formatted for either GENEPOP or TEMPOFS. For each interval between consecutive cohorts, N e is estimated at each locus and over all loci. Furthermore, N e estimates are output for three different genetic drift estimators (F s, F c and F k). Confidence intervals are derived from a chi-square distribution with degrees of freedom equal to the number of independent alleles. GONe has been validated over a wide range of N e values, and for scenarios where survival and birth rates differ between sexes, sex ratios are unequal and reproductive variances differ. GONe is freely available for download at. ?? 2011 Blackwell Publishing Ltd.

Global Epidemiology of Amyotrophic Lateral Sclerosis: a Systematic Review of the Published Literature

PubMed Central

Chiò, A; Logroscino, G; Traynor, BJ; Collins, J; Simeone, JC; Goldstein, LA; White, LA

2014-01-01

Background Amyotrophic lateral sclerosis (ALS) is relatively rare, yet the economic and social burden is substantial. Having accurate incidence and prevalence estimates would facilitate efficient allocation of healthcare resources. Objective To provide a comprehensive and critical review of the epidemiologic literature on ALS. Methods MEDLINE and EMBASE (1995–2011) databases of population-based studies on ALS incidence and prevalence reporting quantitative data were analyzed. Data extracted included study location and time, design and data sources, case ascertainment methods, and incidence and/or prevalence rates. Medians and inter-quartile ranges (IQRs) were calculated, and ALS case estimates derived using 2010 population estimates. Results In all, 37 articles met inclusion criteria. In Europe, the median (IQR) incidence rate (/100,000 population) was 2.08 (1.47–2.43), corresponding to an estimated 15,355 (10,852–17,938) cases. Median (IQR) prevalence (/100,000 population) was 5.40 (4.06–7.89), or 39,863 (29,971–58,244) prevalent cases. Conclusions Disparity in rates among ALS incidence and prevalence studies may be due to differences in study design or true variations in population demographics, such as age, and geography, including environmental factors and genetic predisposition. Additional large-scale studies that use standardized case ascertainment methods are needed to more accurately assess the true global burden of ALS. PMID:23860588

Applications of species accumulation curves in large-scale biological data analysis.

PubMed

Deng, Chao; Daley, Timothy; Smith, Andrew D

2015-09-01

The species accumulation curve, or collector's curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non-parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45-63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and k -mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.

Applications of species accumulation curves in large-scale biological data analysis

PubMed Central

Deng, Chao; Daley, Timothy; Smith, Andrew D

2016-01-01

The species accumulation curve, or collector’s curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non-parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45–63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and k-mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible. PMID:27252899

Estimating neural response functions from fMRI

PubMed Central

Kumar, Sukhbinder; Penny, William

2014-01-01

This paper proposes a methodology for estimating Neural Response Functions (NRFs) from fMRI data. These NRFs describe non-linear relationships between experimental stimuli and neuronal population responses. The method is based on a two-stage model comprising an NRF and a Hemodynamic Response Function (HRF) that are simultaneously fitted to fMRI data using a Bayesian optimization algorithm. This algorithm also produces a model evidence score, providing a formal model comparison method for evaluating alternative NRFs. The HRF is characterized using previously established “Balloon” and BOLD signal models. We illustrate the method with two example applications based on fMRI studies of the auditory system. In the first, we estimate the time constants of repetition suppression and facilitation, and in the second we estimate the parameters of population receptive fields in a tonotopic mapping study. PMID:24847246

On estimation of time-dependent attributable fraction from population-based case-control studies.

PubMed

Zhao, Wei; Chen, Ying Qing; Hsu, Li

2017-09-01

Population attributable fraction (PAF) is widely used to quantify the disease burden associated with a modifiable exposure in a population. It has been extended to a time-varying measure that provides additional information on when and how the exposure's impact varies over time for cohort studies. However, there is no estimation procedure for PAF using data that are collected from population-based case-control studies, which, because of time and cost efficiency, are commonly used for studying genetic and environmental risk factors of disease incidences. In this article, we show that time-varying PAF is identifiable from a case-control study and develop a novel estimator of PAF. Our estimator combines odds ratio estimates from logistic regression models and density estimates of the risk factor distribution conditional on failure times in cases from a kernel smoother. The proposed estimator is shown to be consistent and asymptotically normal with asymptotic variance that can be estimated empirically from the data. Simulation studies demonstrate that the proposed estimator performs well in finite sample sizes. Finally, the method is illustrated by a population-based case-control study of colorectal cancer. © 2017, The International Biometric Society.

Inferring invasive species abundance using removal data from management actions

USGS Publications Warehouse

Davis, Amy J.; Hooten, Mevin B.; Miller, Ryan S.; Farnsworth, Matthew L.; Lewis, Jesse S.; Moxcey, Michael; Pepin, Kim M.

2016-01-01

Evaluation of the progress of management programs for invasive species is crucial for demonstrating impacts to stakeholders and strategic planning of resource allocation. Estimates of abundance before and after management activities can serve as a useful metric of population management programs. However, many methods of estimating population size are too labor intensive and costly to implement, posing restrictive levels of burden on operational programs. Removal models are a reliable method for estimating abundance before and after management using data from the removal activities exclusively, thus requiring no work in addition to management. We developed a Bayesian hierarchical model to estimate abundance from removal data accounting for varying levels of effort, and used simulations to assess the conditions under which reliable population estimates are obtained. We applied this model to estimate site-specific abundance of an invasive species, feral swine (Sus scrofa), using removal data from aerial gunning in 59 site/time-frame combinations (480–19,600 acres) throughout Oklahoma and Texas, USA. Simulations showed that abundance estimates were generally accurate when effective removal rates (removal rate accounting for total effort) were above 0.40. However, when abundances were small (<50) the effective removal rate needed to accurately estimates abundances was considerably higher (0.70). Based on our post-validation method, 78% of our site/time frame estimates were accurate. To use this modeling framework it is important to have multiple removals (more than three) within a time frame during which demographic changes are minimized (i.e., a closed population; ≤3 months for feral swine). Our results show that the probability of accurately estimating abundance from this model improves with increased sampling effort (8+ flight hours across the 3-month window is best) and increased removal rate. Based on the inverse relationship between inaccurate abundances and inaccurate removal rates, we suggest auxiliary information that could be collected and included in the model as covariates (e.g., habitat effects, differences between pilots) to improve accuracy of removal rates and hence abundance estimates.

Population entropies estimates of proteins

NASA Astrophysics Data System (ADS)

Low, Wai Yee

2017-05-01

The Shannon entropy equation provides a way to estimate variability of amino acids sequences in a multiple sequence alignment of proteins. Knowledge of protein variability is useful in many areas such as vaccine design, identification of antibody binding sites, and exploration of protein 3D structural properties. In cases where the population entropies of a protein are of interest but only a small sample size can be obtained, a method based on linear regression and random subsampling can be used to estimate the population entropy. This method is useful for comparisons of entropies where the actual sequence counts differ and thus, correction for alignment size bias is needed. In the current work, an R based package named EntropyCorrect that enables estimation of population entropy is presented and an empirical study on how well this new algorithm performs on simulated dataset of various combinations of population and sample sizes is discussed. The package is available at https://github.com/lloydlow/EntropyCorrect. This article, which was originally published online on 12 May 2017, contained an error in Eq. (1), where the summation sign was missing. The corrected equation appears in the Corrigendum attached to the pdf.

A hierarchical model for spatial capture-recapture data

USGS Publications Warehouse

Royle, J. Andrew; Young, K.V.

2008-01-01

Estimating density is a fundamental objective of many animal population studies. Application of methods for estimating population size from ostensibly closed populations is widespread, but ineffective for estimating absolute density because most populations are subject to short-term movements or so-called temporary emigration. This phenomenon invalidates the resulting estimates because the effective sample area is unknown. A number of methods involving the adjustment of estimates based on heuristic considerations are in widespread use. In this paper, a hierarchical model of spatially indexed capture recapture data is proposed for sampling based on area searches of spatial sample units subject to uniform sampling intensity. The hierarchical model contains explicit models for the distribution of individuals and their movements, in addition to an observation model that is conditional on the location of individuals during sampling. Bayesian analysis of the hierarchical model is achieved by the use of data augmentation, which allows for a straightforward implementation in the freely available software WinBUGS. We present results of a simulation study that was carried out to evaluate the operating characteristics of the Bayesian estimator under variable densities and movement patterns of individuals. An application of the model is presented for survey data on the flat-tailed horned lizard (Phrynosoma mcallii) in Arizona, USA.

A method of studying wild bird populations by mist-netting and banding

USGS Publications Warehouse

Stamm, D.D.; Davis, D.E.; Robbins, C.S.

1960-01-01

1. Progress is reported toward development of a method of bird-population study based on mist-netting and banding. A definite pattern of arrangement and schedule of operation are presented. 2. Nets were operated for a total of 4200 net-hours during which 966 captures were made (23.0 birds per 100 net-hours). A total of 431 adult breeding birds were banded and 38 per cent of them were recaptured. 3. A breeding bird census was made simultaneously in the same area by the Williams spot-mapping technique. 4. Estimates of population by recapture agreed closely with the spot-mappmg census. 5. Some birds are demonstrated to have overlapping home-ranges much larger than their singing territories. 6. Recruitment and net-shyness distort recapture estimates of population .but the method allows detection and assessment of their influence in the population dealt with here. 7. The method produced integrated information on population density and dynamics, movement and behavior. 8. The procedure is especially well adapted to studies of disease agents in bird populations. 9. A simple scheme for description of the habitat in terms of relative abundance and frequency of occurrence of tree species was used.

On fixed-area plot sampling for downed coarse woody debris

Treesearch

Jeffrey H. Gove; Paul C. Van Deusen

2011-01-01

The use of fixed-area plots for sampling down coarse woody debris is reviewed. A set of clearly defined protocols for two previously described methods is established and a new method, which we call the 'sausage' method, is developed. All methods (protocols) are shown to be unbiased for volume estimation, but not necessarily for estimation of population...

Estimation of the real population and its impact on the utilisation of healthcare services in Mediterranean resort regions: an ecological study

PubMed Central

Perea-Milla, Emilio; Pons, Sergi Mari; Rivas-Ruiz, Francisco; Gallofre, Anna; Jurado, Enrique Navarro; Ales, Marco A Navarro; Jimenez-Puente, Alberto; Fernandez-Nieto, Fidel; Cerda, Joan C March; Carrasco, Manuel; Martin, Lydia; Cano, Damian Lopez; Gutierrez, Gonzalo E; Macías, Rafael Cortes; Garcia-Ruiz, Jose A

2007-01-01

Background The demographic structure has a significant influence on the use of healthcare services, as does the size of the population denominators. Very few studies have been published on methods for estimating the real population such as tourist resorts. The lack of information about these problems means there is a corresponding lack of information about the behaviour of populational denominators (the floating population or tourist load) and the effect of this on the use of healthcare services. The objectives of the study were: a) To determine the Municipal Solid Waste (MSW) ratio, per person per day, among populations of known size; b) to estimate, by means of this ratio, the real population in an area where tourist numbers are very significant; and c) to determine the impact on the utilisation of hospital emergency healthcare services of the registered population, in comparison to the non-resident population, in two areas where tourist numbers are very significant. Methods An ecological study design was employed. We analysed the Healthcare Districts of the Costa del Sol and the island of Menorca. Both are Spanish territories in the Mediterranean region. Results In the two areas analysed, the correlation coefficient between the MSW ratio and admissions to hospital emergency departments exceeded 0.9, with p < 0.001. On the basis of MSW generation ratios, obtained for a control zone and also measured in neighbouring countries, we estimated the real population. For the summer months, when tourist activity is greatest and demand for emergency healthcare at hospitals is highest, this value was found to be double that of the registered population. Conclusion The MSW indicator, which is both ecological and indirect, can be used to estimate the real population in areas where population levels vary significantly during the year. This parameter is of interest in planning and dimensioning the provision of healthcare services. PMID:17266744

Differences in Movement Pattern and Detectability between Males and Females Influence How Common Sampling Methods Estimate Sex Ratio

PubMed Central

Rodrigues, João Fabrício Mota; Coelho, Marco Túlio Pacheco

2016-01-01

Sampling the biodiversity is an essential step for conservation, and understanding the efficiency of sampling methods allows us to estimate the quality of our biodiversity data. Sex ratio is an important population characteristic, but until now, no study has evaluated how efficient are the sampling methods commonly used in biodiversity surveys in estimating the sex ratio of populations. We used a virtual ecologist approach to investigate whether active and passive capture methods are able to accurately sample a population’s sex ratio and whether differences in movement pattern and detectability between males and females produce biased estimates of sex-ratios when using these methods. Our simulation allowed the recognition of individuals, similar to mark-recapture studies. We found that differences in both movement patterns and detectability between males and females produce biased estimates of sex ratios. However, increasing the sampling effort or the number of sampling days improves the ability of passive or active capture methods to properly sample sex ratio. Thus, prior knowledge regarding movement patterns and detectability for species is important information to guide field studies aiming to understand sex ratio related patterns. PMID:27441554

Minerals Intake Distributions in a Large Sample of Iranian at-Risk Population Using the National Cancer Institute Method: Do They Meet Their Requirements?

PubMed

Heidari, Zahra; Feizi, Awat; Azadbakht, Leila; Sarrafzadegan, Nizal

2015-01-01

Minerals are required for the body's normal function. The current study assessed the intake distribution of minerals and estimated the prevalence of inadequacy and excess among a representative sample of healthy middle aged and elderly Iranian people. In this cross-sectional study, the second follow up to the Isfahan Cohort Study (ICS), 1922 generally healthy people aged 40 and older were investigated. Dietary intakes were collected using 24 hour recalls and two or more consecutive food records. Distribution of minerals intake was estimated using traditional (averaging dietary intake days) and National Cancer Institute (NCI) methods, and the results obtained from the two methods, were compared. The prevalence of minerals intake inadequacy or excess was estimated using the estimated average requirement (EAR) cut-point method, the probability approach and the tolerable upper intake levels (UL). There were remarkable differences between values obtained using traditional and NCI methods, particularly in the lower and upper percentiles of the estimated intake distributions. A high prevalence of inadequacy of magnesium (50 - 100 %), calcium (21 - 93 %) and zinc (30 - 55 % for males > 50 years) was observed. Significant gender differences were found regarding inadequate intakes of calcium (21 - 76 % for males vs. 45 - 93 % for females), magnesium (92 % vs. 100 %), iron (0 vs. 15 % for age group 40 - 50 years) and zinc (29 - 55 % vs. 0 %) (all; p < 0.05). Severely imbalanced intakes of magnesium, calcium and zinc were observed among the middle-aged and elderly Iranian population. Nutritional interventions and population-based education to improve healthy diets among the studied population at risk are needed.

Digital radiographic evaluation of mandibular third molar for age estimation in young adults and adolescents of South Indian population using modified Demirjian's method.

PubMed

Mohammed, Rezwana Begum; Koganti, Ravichandra; Kalyan, Siva V; Tircouveluri, Saritha; Singh, Johar Rajvinder; Srinivasulu, Enganti

2014-09-01

In recent years, it has become increasingly important to determine the age of living people for a variety of reasons, including identifying criminal and legal responsibility and for many other social events such as birth certificate, marriage, beginning a job, joining the army and retirement. The aim of this study was to assess the developmental stages of mandibular third molar for estimation of dental age (DA) in different age groups and to evaluate the possible correlation between DA and chronological age (CA) in South Indian population. Digital orthopantomography of 330 subjects (165 males, 165 females) who fit the study and the criteria were obtained. Assessment of mandibular third molar development was performed using Demirjian et al., modified method and DA was assessed using tooth specific stages. The present study showed a significant correlation between DA and CA in both males and females. Third molar development commenced around 9 years and root completion takes place around 18.9 years in males and in females 9 years and 18.6 years respectively. Demirjian modified method underestimated the mean age of males by 0.8 years and females by 0.5 years and also showed that females mature earlier than males in selected population. Digital radiographic assessment of mandibular third molar development can be used to generate mean DA using Demirjian modified method and also the estimated age range for an individual of unknown CA. Since the Demirjian method is based on French-Canadian population, to enhance the accuracy of forensic age estimates based on third molar development, the use of population-specific standards is recommended.

On Some Confidence Intervals for Estimating the Mean of a Skewed Population

ERIC Educational Resources Information Center

Shi, W.; Kibria, B. M. Golam

2007-01-01

A number of methods are available in the literature to measure confidence intervals. Here, confidence intervals for estimating the population mean of a skewed distribution are considered. This note proposes two alternative confidence intervals, namely, Median t and Mad t, which are simple adjustments to the Student's t confidence interval. In…

Usual Dietary Intakes: Food Intakes, U.S. Population, 2007-10

Cancer.gov

We have applied the NCI Method for estimating distributions of usual intake to data from two recent cycles of the NHANES to estimate means and percentiles of the distributions of food intake and the percentage of persons meeting recommendations for a range of sex-age groups in the US population.

United States Census 2000 Population with Bridged Race Categories. Vital and Health Statistics. Data Evaluation and Methods Research.

ERIC Educational Resources Information Center

Ingram, Deborah D.; Parker, Jennifer D.; Schenker, Nathaniel; Weed, James A.; Hamilton, Brady; Arias, Elizabeth; Madans, Jennifer H.

This report documents the National Center for Health Statistics' (NCHS) methods for bridging the Census 2000 multiple-race resident population to single-race categories and describing bridged race resident population estimates. Data came from the pooled 1997-2000 National Health Interview Surveys. The bridging models included demographic and…

Inferring the demographic history from DNA sequences: An importance sampling approach based on non-homogeneous processes.

PubMed

Ait Kaci Azzou, S; Larribe, F; Froda, S

2016-10-01

In Ait Kaci Azzou et al. (2015) we introduced an Importance Sampling (IS) approach for estimating the demographic history of a sample of DNA sequences, the skywis plot. More precisely, we proposed a new nonparametric estimate of a population size that changes over time. We showed on simulated data that the skywis plot can work well in typical situations where the effective population size does not undergo very steep changes. In this paper, we introduce an iterative procedure which extends the previous method and gives good estimates under such rapid variations. In the iterative calibrated skywis plot we approximate the effective population size by a piecewise constant function, whose values are re-estimated at each step. These piecewise constant functions are used to generate the waiting times of non homogeneous Poisson processes related to a coalescent process with mutation under a variable population size model. Moreover, the present IS procedure is based on a modified version of the Stephens and Donnelly (2000) proposal distribution. Finally, we apply the iterative calibrated skywis plot method to a simulated data set from a rapidly expanding exponential model, and we show that the method based on this new IS strategy correctly reconstructs the demographic history. Copyright © 2016. Published by Elsevier Inc.

Genomic scan as a tool for assessing the genetic component of phenotypic variance in wild populations.

PubMed

Herrera, Carlos M

2012-01-01

Methods for estimating quantitative trait heritability in wild populations have been developed in recent years which take advantage of the increased availability of genetic markers to reconstruct pedigrees or estimate relatedness between individuals, but their application to real-world data is not exempt from difficulties. This chapter describes a recent marker-based technique which, by adopting a genomic scan approach and focusing on the relationship between phenotypes and genotypes at the individual level, avoids the problems inherent to marker-based estimators of relatedness. This method allows the quantification of the genetic component of phenotypic variance ("degree of genetic determination" or "heritability in the broad sense") in wild populations and is applicable whenever phenotypic trait values and multilocus data for a large number of genetic markers (e.g., amplified fragment length polymorphisms, AFLPs) are simultaneously available for a sample of individuals from the same population. The method proceeds by first identifying those markers whose variation across individuals is significantly correlated with individual phenotypic differences ("adaptive loci"). The proportion of phenotypic variance in the sample that is statistically accounted for by individual differences in adaptive loci is then estimated by fitting a linear model to the data, with trait value as the dependent variable and scores of adaptive loci as independent ones. The method can be easily extended to accommodate quantitative or qualitative information on biologically relevant features of the environment experienced by each sampled individual, in which case estimates of the environmental and genotype × environment components of phenotypic variance can also be obtained.

Population estimate of Chinese mystery snail (Bellamya chinensis) in a Nebraska reservoir

USGS Publications Warehouse

Chaine, Noelle M.; Allen, Craig R.; Fricke, Kent A.; Haak, Danielle M.; Hellman, Michelle L.; Kill, Robert A.; Nemec, Kristine T.; Pope, Kevin L.; Smeenk, Nicholas A.; Stephen, Bruce J.; Uden, Daniel R.; Unstad, Kody M.; VanderHam, Ashley E.

2012-01-01

The Chinese mystery snail (Bellamya chinensis) is an aquatic invasive species in North America. Little is known regarding this species' impacts on freshwater ecosystems. It is be lieved that population densities can be high, yet no population estimates have been reported. We utilized a mark-recapture approach to generate a population estimate for Chinese mystery snail in Wild Plum Lake, a 6.47-ha reservoir in southeast Nebraska. We calculated, using bias-adjusted Lincoln-Petersen estimation, that there were approximately 664 adult snails within a 127 m2 transect (5.2 snails/m2). If this density was consistent throughout the littoral zone (<3 m in depth) of the reservoir, then the total adult population in this impoundment is estimated to be 253,570 snails, and the total Chinese mystery snail wet biomass is estimated to be 3,119 kg (643 kg/ha). If this density is confined to the depth sampled in this study (1.46 m), then the adult population is estimated to be 169,400 snails, and wet biomass is estimated to be 2,084 kg (643 kg/ha). Additional research is warranted to further test the utility of mark-recapture methods for aquatic snails and to better understand Chinese mystery snail distributions within reservoirs.

Underwater methods for study of salmonids in the Intermountain West

Treesearch

Russell F. Thurow

1994-01-01

This guide describes underwater methods using snorkeling gear to study fish populations in flowing waters of the Intermountain West. It outlines procedures for estimating salmonid abundance and habitat use and provides criteria for identifying and estimating the size of fish underwater.

An open-population hierarchical distance sampling model

USGS Publications Warehouse

Sollmann, Rachel; Beth Gardner,; Richard B Chandler,; Royle, J. Andrew; T Scott Sillett,

2015-01-01

Modeling population dynamics while accounting for imperfect detection is essential to monitoring programs. Distance sampling allows estimating population size while accounting for imperfect detection, but existing methods do not allow for direct estimation of demographic parameters. We develop a model that uses temporal correlation in abundance arising from underlying population dynamics to estimate demographic parameters from repeated distance sampling surveys. Using a simulation study motivated by designing a monitoring program for island scrub-jays (Aphelocoma insularis), we investigated the power of this model to detect population trends. We generated temporally autocorrelated abundance and distance sampling data over six surveys, using population rates of change of 0.95 and 0.90. We fit the data generating Markovian model and a mis-specified model with a log-linear time effect on abundance, and derived post hoc trend estimates from a model estimating abundance for each survey separately. We performed these analyses for varying number of survey points. Power to detect population changes was consistently greater under the Markov model than under the alternatives, particularly for reduced numbers of survey points. The model can readily be extended to more complex demographic processes than considered in our simulations. This novel framework can be widely adopted for wildlife population monitoring.

An open-population hierarchical distance sampling model.

PubMed

Sollmann, Rahel; Gardner, Beth; Chandler, Richard B; Royle, J Andrew; Sillett, T Scott

2015-02-01

Modeling population dynamics while accounting for imperfect detection is essential to monitoring programs. Distance sampling allows estimating population size while accounting for imperfect detection, but existing methods do not allow for estimation of demographic parameters. We develop a model that uses temporal correlation in abundance arising from underlying population dynamics to estimate demographic parameters from repeated distance sampling surveys. Using a simulation study motivated by designing a monitoring program for Island Scrub-Jays (Aphelocoma insularis), we investigated the power of this model to detect population trends. We generated temporally autocorrelated abundance and distance sampling data over six surveys, using population rates of change of 0.95 and 0.90. We fit the data generating Markovian model and a mis-specified model with a log-linear time effect on abundance, and derived post hoc trend estimates from a model estimating abundance for each survey separately. We performed these analyses for varying numbers of survey points. Power to detect population changes was consistently greater under the Markov model than under the alternatives, particularly for reduced numbers of survey points. The model can readily be extended to more complex demographic processes than considered in our simulations. This novel framework can be widely adopted for wildlife population monitoring.

A Method to Estimate the Size and Characteristics of HIV-positive Populations Using an Individual-based Stochastic Simulation Model.

PubMed

Nakagawa, Fumiyo; van Sighem, Ard; Thiebaut, Rodolphe; Smith, Colette; Ratmann, Oliver; Cambiano, Valentina; Albert, Jan; Amato-Gauci, Andrew; Bezemer, Daniela; Campbell, Colin; Commenges, Daniel; Donoghoe, Martin; Ford, Deborah; Kouyos, Roger; Lodwick, Rebecca; Lundgren, Jens; Pantazis, Nikos; Pharris, Anastasia; Quinten, Chantal; Thorne, Claire; Touloumi, Giota; Delpech, Valerie; Phillips, Andrew

2016-03-01

It is important not only to collect epidemiologic data on HIV but to also fully utilize such information to understand the epidemic over time and to help inform and monitor the impact of policies and interventions. We describe and apply a novel method to estimate the size and characteristics of HIV-positive populations. The method was applied to data on men who have sex with men living in the UK and to a pseudo dataset to assess performance for different data availability. The individual-based simulation model was calibrated using an approximate Bayesian computation-based approach. In 2013, 48,310 (90% plausibility range: 39,900-45,560) men who have sex with men were estimated to be living with HIV in the UK, of whom 10,400 (6,160-17,350) were undiagnosed. There were an estimated 3,210 (1,730-5,350) infections per year on average between 2010 and 2013. Sixty-two percent of the total HIV-positive population are thought to have viral load <500 copies/ml. In the pseudo-epidemic example, HIV estimates have narrower plausibility ranges and are closer to the true number, the greater the data availability to calibrate the model. We demonstrate that our method can be applied to settings with less data, however plausibility ranges for estimates will be wider to reflect greater uncertainty of the data used to fit the model.

Evaluation of the Applicability of Different Age Determination Methods for Estimating Age of the Endangered African Wild Dog (Lycaon Pictus).

PubMed

Mbizah, Moreangels M; Steenkamp, Gerhard; Groom, Rosemary J

2016-01-01

African wild dogs (Lycaon pictus) are endangered and their population continues to decline throughout their range. Given their conservation status, more research focused on their population dynamics, population growth and age specific mortality is needed and this requires reliable estimates of age and age of mortality. Various age determination methods from teeth and skull measurements have been applied in numerous studies and it is fundamental to test the validity of these methods and their applicability to different species. In this study we assessed the accuracy of estimating chronological age and age class of African wild dogs, from dental age measured by (i) counting cementum annuli (ii) pulp cavity/tooth width ratio, (iii) tooth wear (measured by tooth crown height) (iv) tooth wear (measured by tooth crown width/crown height ratio) (v) tooth weight and (vi) skull measurements (length, width and height). A sample of 29 African wild dog skulls, from opportunistically located carcasses was analysed. Linear and ordinal regression analysis was done to investigate the performance of each of the six age determination methods in predicting wild dog chronological age and age class. Counting cementum annuli was the most accurate method for estimating chronological age of wild dogs with a 79% predictive capacity, while pulp cavity/tooth width ratio was also a reliable method with a 68% predictive capacity. Counting cementum annuli and pulp cavity/tooth width ratio were again the most accurate methods for separating wild dogs into three age classes (6-24 months; 25-60 months and > 60 months), with a McFadden's Pseudo-R2 of 0.705 and 0.412 respectively. The use of the cementum annuli method is recommended when estimating age of wild dogs since it is the most reliable method. However, its use is limited as it requires tooth extraction and shipping, is time consuming and expensive, and is not applicable to living individuals. Pulp cavity/tooth width ratio is a moderately reliable method for estimating both chronological age and age class. This method gives a balance between accuracy, cost and practicability, therefore it is recommended when precise age estimations are not paramount.

Evaluation of the Applicability of Different Age Determination Methods for Estimating Age of the Endangered African Wild Dog (Lycaon Pictus)

PubMed Central

Steenkamp, Gerhard; Groom, Rosemary J.

2016-01-01

African wild dogs (Lycaon pictus) are endangered and their population continues to decline throughout their range. Given their conservation status, more research focused on their population dynamics, population growth and age specific mortality is needed and this requires reliable estimates of age and age of mortality. Various age determination methods from teeth and skull measurements have been applied in numerous studies and it is fundamental to test the validity of these methods and their applicability to different species. In this study we assessed the accuracy of estimating chronological age and age class of African wild dogs, from dental age measured by (i) counting cementum annuli (ii) pulp cavity/tooth width ratio, (iii) tooth wear (measured by tooth crown height) (iv) tooth wear (measured by tooth crown width/crown height ratio) (v) tooth weight and (vi) skull measurements (length, width and height). A sample of 29 African wild dog skulls, from opportunistically located carcasses was analysed. Linear and ordinal regression analysis was done to investigate the performance of each of the six age determination methods in predicting wild dog chronological age and age class. Counting cementum annuli was the most accurate method for estimating chronological age of wild dogs with a 79% predictive capacity, while pulp cavity/tooth width ratio was also a reliable method with a 68% predictive capacity. Counting cementum annuli and pulp cavity/tooth width ratio were again the most accurate methods for separating wild dogs into three age classes (6–24 months; 25–60 months and > 60 months), with a McFadden’s Pseudo-R2 of 0.705 and 0.412 respectively. The use of the cementum annuli method is recommended when estimating age of wild dogs since it is the most reliable method. However, its use is limited as it requires tooth extraction and shipping, is time consuming and expensive, and is not applicable to living individuals. Pulp cavity/tooth width ratio is a moderately reliable method for estimating both chronological age and age class. This method gives a balance between accuracy, cost and practicability, therefore it is recommended when precise age estimations are not paramount. PMID:27732663

Estimating site occupancy and detection probability parameters for meso- and large mammals in a coastal eosystem

USGS Publications Warehouse

O'Connell, Allan F.; Talancy, Neil W.; Bailey, Larissa L.; Sauer, John R.; Cook, Robert; Gilbert, Andrew T.

2006-01-01

Large-scale, multispecies monitoring programs are widely used to assess changes in wildlife populations but they often assume constant detectability when documenting species occurrence. This assumption is rarely met in practice because animal populations vary across time and space. As a result, detectability of a species can be influenced by a number of physical, biological, or anthropogenic factors (e.g., weather, seasonality, topography, biological rhythms, sampling methods). To evaluate some of these influences, we estimated site occupancy rates using species-specific detection probabilities for meso- and large terrestrial mammal species on Cape Cod, Massachusetts, USA. We used model selection to assess the influence of different sampling methods and major environmental factors on our ability to detect individual species. Remote cameras detected the most species (9), followed by cubby boxes (7) and hair traps (4) over a 13-month period. Estimated site occupancy rates were similar among sampling methods for most species when detection probabilities exceeded 0.15, but we question estimates obtained from methods with detection probabilities between 0.05 and 0.15, and we consider methods with lower probabilities unacceptable for occupancy estimation and inference. Estimated detection probabilities can be used to accommodate variation in sampling methods, which allows for comparison of monitoring programs using different protocols. Vegetation and seasonality produced species-specific differences in detectability and occupancy, but differences were not consistent within or among species, which suggests that our results should be considered in the context of local habitat features and life history traits for the target species. We believe that site occupancy is a useful state variable and suggest that monitoring programs for mammals using occupancy data consider detectability prior to making inferences about species distributions or population change.

The Game of Contacts: Estimating the Social Visibility of Groups☆

PubMed Central

Salganik, Matthew J.; Mello, Maeve B.; Abdo, Alexandre H.; Bertoni, Neilane; Fazito, Dimitri; Bastos, Francisco I.

2010-01-01

Estimating the sizes of hard-to-count populations is a challenging and important problem that occurs frequently in social science, public health, and public policy. This problem is particularly pressing in HIV/AIDS research because estimates of the sizes of the most at-risk populations—illicit drug users, men who have sex with men, and sex workers—are needed for designing, evaluating, and funding programs to curb the spread of the disease. A promising new approach in this area is the network scale-up method, which uses information about the personal networks of respondents to make population size estimates. However, if the target population has low social visibility, as is likely to be the case in HIV/AIDS research, scale-up estimates will be too low. In this paper we develop a game-like activity that we call the game of contacts in order to estimate the social visibility of groups, and report results from a study of heavy drug users in Curitiba, Brazil (n = 294). The game produced estimates of social visibility that were consistent with qualitative expectations but of surprising magnitude. Further, a number of checks suggest that the data are high-quality. While motivated by the specific problem of population size estimation, our method could be used by researchers more broadly and adds to long-standing efforts to combine the richness of social network analysis with the power and scale of sample surveys. PMID:21318126

A two-stage cluster sampling method using gridded population data, a GIS, and Google Earth(TM) imagery in a population-based mortality survey in Iraq.

PubMed

Galway, Lp; Bell, Nathaniel; Sae, Al Shatari; Hagopian, Amy; Burnham, Gilbert; Flaxman, Abraham; Weiss, Wiliam M; Rajaratnam, Julie; Takaro, Tim K

2012-04-27

Mortality estimates can measure and monitor the impacts of conflict on a population, guide humanitarian efforts, and help to better understand the public health impacts of conflict. Vital statistics registration and surveillance systems are rarely functional in conflict settings, posing a challenge of estimating mortality using retrospective population-based surveys. We present a two-stage cluster sampling method for application in population-based mortality surveys. The sampling method utilizes gridded population data and a geographic information system (GIS) to select clusters in the first sampling stage and Google Earth TM imagery and sampling grids to select households in the second sampling stage. The sampling method is implemented in a household mortality study in Iraq in 2011. Factors affecting feasibility and methodological quality are described. Sampling is a challenge in retrospective population-based mortality studies and alternatives that improve on the conventional approaches are needed. The sampling strategy presented here was designed to generate a representative sample of the Iraqi population while reducing the potential for bias and considering the context specific challenges of the study setting. This sampling strategy, or variations on it, are adaptable and should be considered and tested in other conflict settings.

A two-stage cluster sampling method using gridded population data, a GIS, and Google EarthTM imagery in a population-based mortality survey in Iraq

PubMed Central

2012-01-01

Background Mortality estimates can measure and monitor the impacts of conflict on a population, guide humanitarian efforts, and help to better understand the public health impacts of conflict. Vital statistics registration and surveillance systems are rarely functional in conflict settings, posing a challenge of estimating mortality using retrospective population-based surveys. Results We present a two-stage cluster sampling method for application in population-based mortality surveys. The sampling method utilizes gridded population data and a geographic information system (GIS) to select clusters in the first sampling stage and Google Earth TM imagery and sampling grids to select households in the second sampling stage. The sampling method is implemented in a household mortality study in Iraq in 2011. Factors affecting feasibility and methodological quality are described. Conclusion Sampling is a challenge in retrospective population-based mortality studies and alternatives that improve on the conventional approaches are needed. The sampling strategy presented here was designed to generate a representative sample of the Iraqi population while reducing the potential for bias and considering the context specific challenges of the study setting. This sampling strategy, or variations on it, are adaptable and should be considered and tested in other conflict settings. PMID:22540266

Cetacean Density Estimation from Novel Acoustic Datasets by Acoustic Propagation Modeling

DTIC Science & Technology

2014-09-30

hydrophone, to estimate the population density of false killer whales (Pseudorca crassidens) off of the Kona coast of the Island of Hawai’i... killer whale , suffers from interaction with the fisheries industry and its population has been reported to have declined in the past 20 years. Studies...of abundance estimate of false killer whales in Hawai’i through mark recapture methods will provide comparable results to the ones obtained by this

Diagnostic test accuracy and prevalence inferences based on joint and sequential testing with finite population sampling.

PubMed

Su, Chun-Lung; Gardner, Ian A; Johnson, Wesley O

2004-07-30

The two-test two-population model, originally formulated by Hui and Walter, for estimation of test accuracy and prevalence estimation assumes conditionally independent tests, constant accuracy across populations and binomial sampling. The binomial assumption is incorrect if all individuals in a population e.g. child-care centre, village in Africa, or a cattle herd are sampled or if the sample size is large relative to population size. In this paper, we develop statistical methods for evaluating diagnostic test accuracy and prevalence estimation based on finite sample data in the absence of a gold standard. Moreover, two tests are often applied simultaneously for the purpose of obtaining a 'joint' testing strategy that has either higher overall sensitivity or specificity than either of the two tests considered singly. Sequential versions of such strategies are often applied in order to reduce the cost of testing. We thus discuss joint (simultaneous and sequential) testing strategies and inference for them. Using the developed methods, we analyse two real and one simulated data sets, and we compare 'hypergeometric' and 'binomial-based' inferences. Our findings indicate that the posterior standard deviations for prevalence (but not sensitivity and specificity) based on finite population sampling tend to be smaller than their counterparts for infinite population sampling. Finally, we make recommendations about how small the sample size should be relative to the population size to warrant use of the binomial model for prevalence estimation. Copyright 2004 John Wiley & Sons, Ltd.

Comparison of Drive Counts and Mark-Resight As Methods of Population Size Estimation of Highly Dense Sika Deer (Cervus nippon) Populations

PubMed Central

Takeshita, Kazutaka; Yoshida, Tsuyoshi; Igota, Hiromasa; Matsuura, Yukiko

2016-01-01

Assessing temporal changes in abundance indices is an important issue in the management of large herbivore populations. The drive counts method has been frequently used as a deer abundance index in mountainous regions. However, despite an inherent risk for observation errors in drive counts, which increase with deer density, evaluations of the utility of drive counts at a high deer density remain scarce. We compared the drive counts and mark-resight (MR) methods in the evaluation of a highly dense sika deer population (MR estimates ranged between 11 and 53 individuals/km2) on Nakanoshima Island, Hokkaido, Japan, between 1999 and 2006. This deer population experienced two large reductions in density; approximately 200 animals in total were taken from the population through a large-scale population removal and a separate winter mass mortality event. Although the drive counts tracked temporal changes in deer abundance on the island, they overestimated the counts for all years in comparison to the MR method. Increased overestimation in drive count estimates after the winter mass mortality event may be due to a double count derived from increased deer movement and recovery of body condition secondary to the mitigation of density-dependent food limitations. Drive counts are unreliable because they are affected by unfavorable factors such as bad weather, and they are cost-prohibitive to repeat, which precludes the calculation of confidence intervals. Therefore, the use of drive counts to infer the deer abundance needs to be reconsidered. PMID:27711181

A method for estimating cost savings for population health management programs.

PubMed

Murphy, Shannon M E; McGready, John; Griswold, Michael E; Sylvia, Martha L

2013-04-01

To develop a quasi-experimental method for estimating Population Health Management (PHM) program savings that mitigates common sources of confounding, supports regular updates for continued program monitoring, and estimates model precision. Administrative, program, and claims records from January 2005 through June 2009. Data are aggregated by member and month. Study participants include chronically ill adult commercial health plan members. The intervention group consists of members currently enrolled in PHM, stratified by intensity level. Comparison groups include (1) members never enrolled, and (2) PHM participants not currently enrolled. Mixed model smoothing is employed to regress monthly medical costs on time (in months), a history of PHM enrollment, and monthly program enrollment by intensity level. Comparison group trends are used to estimate expected costs for intervention members. Savings are realized when PHM participants' costs are lower than expected. This method mitigates many of the limitations faced using traditional pre-post models for estimating PHM savings in an observational setting, supports replication for ongoing monitoring, and performs basic statistical inference. This method provides payers with a confident basis for making investment decisions. © Health Research and Educational Trust.

Evaluation of the Current Techniques and Introduction of a Novel Approach for Estimating Maxillary Anterior Teeth Dimensions.

PubMed

Sayed, Mohammed E; Porwal, Amit; Al-Faraj, Nida A; Bajonaid, Amal M; Sumayli, Hassan A

2017-07-01

Several techniques and methods have been proposed to estimate the anterior teeth dimensions in edentulous patients. However, this procedure remains challenging especially when preextraction records are not available. Therefore, the purpose of this study is to evaluate some of the existing extraoral and intraoral methods for estimation of anterior tooth dimensions and to propose a novel method for estimation of central incisor width (CIW) and length (CIL) for Saudi population. Extraoral and intraoral measurements were recorded for a total of 236 subjects. Descriptive statistical analysis and Pearson's correlation tests were performed. Association was evaluated between combined anterior teeth width (CATW) and interalar width (IAW), intercommisural width (ICoW) and interhamular notch distance (IHND) plus 10 mm. Evaluation of the linear relationship between central incisor length (CIL) with facial height (FH) and CIW with bizygomatic width (BZW) was also performed. Significant correlation was found between the CATW and ICoW and IAW (p-values <0.0001); however, no correlation was found relative to IHND plus 10 mm (p-value = 0.456). Further, no correlation was found between the FH and right CIL and BZW and right CIW (p-values = 0.255 and 0.822). The means of CIL, CIW, incisive papillae-fovea palatinae (IP-FP), and IHND were used to estimate the central incisor dimensions: CIL = FP-IP distance/4.45, CIW = IHND/4.49. It was concluded that the ICoW and IAW measurements are the only predictable methods to estimate the initial reference value for CATW. A proposed intraoral approach was hypothesized for estimation of CIW and CIL for the given population. Based on the results of the study, ICoW and IAW measurements can be useful in estimating the initial reference value for CATW, while the proposed novel approach using specific palatal dimensions can be used for estimating the width and length of central incisors. These methods are crucial to obtain esthetic treatment results within the parameters of the given population.

Estimating age-specific reproductive numbers-A comparison of methods.

PubMed

Moser, Carlee B; White, Laura F

2016-01-01

Large outbreaks, such as those caused by influenza, put a strain on resources necessary for their control. In particular, children have been shown to play a key role in influenza transmission during recent outbreaks, and targeted interventions, such as school closures, could positively impact the course of emerging epidemics. As an outbreak is unfolding, it is important to be able to estimate reproductive numbers that incorporate this heterogeneity and to use surveillance data that is routinely collected to more effectively target interventions and obtain an accurate understanding of transmission dynamics. There are a growing number of methods that estimate age-group specific reproductive numbers with limited data that build on methods assuming a homogenously mixing population. In this article, we introduce a new approach that is flexible and improves on many aspects of existing methods. We apply this method to influenza data from two outbreaks, the 2009 H1N1 outbreaks in South Africa and Japan, to estimate age-group specific reproductive numbers and compare it to three other methods that also use existing data from social mixing surveys to quantify contact rates among different age groups. In this exercise, all estimates of the reproductive numbers for children exceeded the critical threshold of one and in most cases exceeded those of adults. We introduce a flexible new method to estimate reproductive numbers that describe heterogeneity in the population.

Sampling considerations for disease surveillance in wildlife populations

USGS Publications Warehouse

Nusser, S.M.; Clark, W.R.; Otis, D.L.; Huang, L.

2008-01-01

Disease surveillance in wildlife populations involves detecting the presence of a disease, characterizing its prevalence and spread, and subsequent monitoring. A probability sample of animals selected from the population and corresponding estimators of disease prevalence and detection provide estimates with quantifiable statistical properties, but this approach is rarely used. Although wildlife scientists often assume probability sampling and random disease distributions to calculate sample sizes, convenience samples (i.e., samples of readily available animals) are typically used, and disease distributions are rarely random. We demonstrate how landscape-based simulation can be used to explore properties of estimators from convenience samples in relation to probability samples. We used simulation methods to model what is known about the habitat preferences of the wildlife population, the disease distribution, and the potential biases of the convenience-sample approach. Using chronic wasting disease in free-ranging deer (Odocoileus virginianus) as a simple illustration, we show that using probability sample designs with appropriate estimators provides unbiased surveillance parameter estimates but that the selection bias and coverage errors associated with convenience samples can lead to biased and misleading results. We also suggest practical alternatives to convenience samples that mix probability and convenience sampling. For example, a sample of land areas can be selected using a probability design that oversamples areas with larger animal populations, followed by harvesting of individual animals within sampled areas using a convenience sampling method.

Performance of Willem's dental age estimation method in children: A systematic review and meta-analysis.

PubMed

Mohd Yusof, Mohd Yusmiaidil Putera; Wan Mokhtar, Ilham; Rajasekharan, Sivaprakash; Overholser, Rosanna; Martens, Luc

2017-11-01

Through numerous validation and method comparison studies on different populations, the Willems method exhibited a superior accuracy. This article aims to systematically examine how accurate the application of Willems dental age method on children of different age groups and its performance based on various populations and regions. A strategic literature search of PubMed, MEDLINE, Web of Science, EMBASE and hand searching were used to identify the studies published up to September 2014 that estimated the dental age using the Willems method (modified Demirjian), with a populations, intervention, comparisons and outcomes (PICO) search strategy using MeSH keywords, focusing on the question: How much Willems method deviates from the chronological age in estimating age in children? Standardized mean differences were calculated for difference of dental age to chronological age by using random effects model. Subgroup analyses were performed to evaluate potential heterogeneity. Of 116 titles retrieved based on the standardized search strategy, only 19 articles fulfilled the inclusion criteria for quantitative analysis. The pooled estimates were separately kept as underestimation (n=7) and overestimation (n=12) of chronological age groups for both genders according to primary studies. On absolute values, females (underestimated by 0.13; 95% CI: 0.09-0.18 and overestimated by 0.27; 95% CI: 0.17-0.36) exhibited better accuracy than males (underestimated by 0.28; 95% CI: 0.14-0.42 and overestimated by 0.33; 95% CI: 0.22-0.44). For comparison purposes, the overall pooled estimate overestimated the age by 0.10 (95% CI: -0.06 to 0.26) and 0.09 (95% CI: -0.09 to 0.19) for males and females, respectively. There was no significant difference between the young and older child in subgroup analysis using omnibus test. The mean age between different regions exhibited no statistically significant. The use of Willems method is appropriate to estimate age in children considering its accuracy among different populations, investigators and age groups. Copyright © 2017 Elsevier B.V. All rights reserved.

Caught Ya! A School-Based Practical Activity to Evaluate the Capture-Mark-Release-Recapture Method

ERIC Educational Resources Information Center

Kingsnorth, Crawford; Cruickshank, Chae; Paterson, David; Diston, Stephen

2017-01-01

The capture-mark-release-recapture method provides a simple way to estimate population size. However, when used as part of ecological sampling, this method does not easily allow an opportunity to evaluate the accuracy of the calculation because the actual population size is unknown. Here, we describe a method that can be used to measure the…

Using satellite radiotelemetry data to delineate and manage wildlife populations

USGS Publications Warehouse

Amstrup, Steven C.; McDonald, T.L.; Durner, George M.

2004-01-01

The greatest promise of radiotelemetry always has been a better understanding of animal movements. Telemetry has helped us know when animals are active, how active they are, how far and how fast they move, the geographic areas they occupy, and whether individuals vary in these traits. Unfortunately, the inability to estimate the error in animals utilization distributions (UDs), has prevented probabilistic linkage of movements data, which are always retrospective, with future management actions. We used the example of the harvested population of polar bears (Ursus maritimus) in the Southern Beaufort Sea to illustrate a method that provides that linkage. We employed a 2-dimensional Gaussian kernel density estimator to smooth and scale frequencies of polar bear radio locations within cells of a grid overlying our study area. True 2-dimensional smoothing allowed us to create accurate descriptions of the UDs of individuals and groups of bears. We used a new method of clustering, based upon the relative use collared bears made of each cell in our grid, to assign individual animals to populations. We applied the fast Fourier transform to make bootstrapped estimates of the error in UDs computationally feasible. Clustering and kernel smoothing identified 3 populations of polar bears in the region between Wrangel Island, Russia, and Banks Island, Canada. The relative probability of occurrence of animals from each population varied significantly among grid cells distributed across the study area. We displayed occurrence probabilities as contour maps wherein each contour line corresponded with a change in relative probability. Only at the edges of our study area and in some offshore regions were bootstrapped estimates of error in occurrence probabilities too high to allow prediction. Error estimates, which also were displayed as contours, allowed us to show that occurrence probabilities did not vary by season. Near Barrow, Alaska, 50% of bears observed are predicted to be from the Chukchi Sea population and 50% from the Southern Beaufort Sea population. At Tuktoyaktuk, Northwest Territories, Canada, 50% are from the Southern Beaufort Sea and 50% from the Northern Beaufort Sea population. The methods described here will aid managers of all wildlife that can be studied by telemetry to allocate harvests and other human perturbations to the appropriate populations, make risk assessments, and predict impacts of human activities. They will aid researchers by providing the refined descriptions of study populations that are necessary for population estimation and other investigative tasks. Arctic, Beaufort Sea, boundaries, clustering, Fourier transform, kernel, management, polar bears, population delineation, radiotelemetry, satellite, smoothing, Ursus maritimus

Dynamics of a low-density tiger population in Southeast Asia in the context of improved law enforcement.

PubMed

Duangchantrasiri, Somphot; Umponjan, Mayuree; Simcharoen, Saksit; Pattanavibool, Anak; Chaiwattana, Soontorn; Maneerat, Sompoch; Kumar, N Samba; Jathanna, Devcharan; Srivathsa, Arjun; Karanth, K Ullas

2016-06-01

Recovering small populations of threatened species is an important global conservation strategy. Monitoring the anticipated recovery, however, often relies on uncertain abundance indices rather than on rigorous demographic estimates. To counter the severe threat from poaching of wild tigers (Panthera tigris), the Government of Thailand established an intensive patrolling system in 2005 to protect and recover its largest source population in Huai Kha Khaeng Wildlife Sanctuary. Concurrently, we assessed the dynamics of this tiger population over the next 8 years with rigorous photographic capture-recapture methods. From 2006 to 2012, we sampled across 624-1026 km(2) with 137-200 camera traps. Cameras deployed for 21,359 trap days yielded photographic records of 90 distinct individuals. We used closed model Bayesian spatial capture-recapture methods to estimate tiger abundances annually. Abundance estimates were integrated with likelihood-based open model analyses to estimate rates of annual and overall rates of survival, recruitment, and changes in abundance. Estimates of demographic parameters fluctuated widely: annual density ranged from 1.25 to 2.01 tigers/100 km(2) , abundance from 35 to 58 tigers, survival from 79.6% to 95.5%, and annual recruitment from 0 to 25 tigers. The number of distinct individuals photographed demonstrates the value of photographic capture-recapture methods for assessments of population dynamics in rare and elusive species that are identifiable from natural markings. Possibly because of poaching pressure, overall tiger densities at Huai Kha Khaeng were 82-90% lower than in ecologically comparable sites in India. However, intensified patrolling after 2006 appeared to reduce poaching and was correlated with marginal improvement in tiger survival and recruitment. Our results suggest that population recovery of low-density tiger populations may be slower than anticipated by current global strategies aimed at doubling the number of wild tigers in a decade. © 2015 Society for Conservation Biology.

Uncertainty in Population Growth Rates: Determining Confidence Intervals from Point Estimates of Parameters

PubMed Central

Devenish Nelson, Eleanor S.; Harris, Stephen; Soulsbury, Carl D.; Richards, Shane A.; Stephens, Philip A.

2010-01-01

Background Demographic models are widely used in conservation and management, and their parameterisation often relies on data collected for other purposes. When underlying data lack clear indications of associated uncertainty, modellers often fail to account for that uncertainty in model outputs, such as estimates of population growth. Methodology/Principal Findings We applied a likelihood approach to infer uncertainty retrospectively from point estimates of vital rates. Combining this with resampling techniques and projection modelling, we show that confidence intervals for population growth estimates are easy to derive. We used similar techniques to examine the effects of sample size on uncertainty. Our approach is illustrated using data on the red fox, Vulpes vulpes, a predator of ecological and cultural importance, and the most widespread extant terrestrial mammal. We show that uncertainty surrounding estimated population growth rates can be high, even for relatively well-studied populations. Halving that uncertainty typically requires a quadrupling of sampling effort. Conclusions/Significance Our results compel caution when comparing demographic trends between populations without accounting for uncertainty. Our methods will be widely applicable to demographic studies of many species. PMID:21049049

A comparison of selection at list time and time-stratified sampling for estimating suspended sediment loads

Treesearch

Robert B. Thomas; Jack Lewis

1993-01-01

Time-stratified sampling of sediment for estimating suspended load is introduced and compared to selection at list time (SALT) sampling. Both methods provide unbiased estimates of load and variance. The magnitude of the variance of the two methods is compared using five storm populations of suspended sediment flux derived from turbidity data. Under like conditions,...

Comparison of Efficiency of Jackknife and Variance Component Estimators of Standard Errors. Program Statistics Research. Technical Report.

ERIC Educational Resources Information Center

Longford, Nicholas T.

Large scale surveys usually employ a complex sampling design and as a consequence, no standard methods for estimation of the standard errors associated with the estimates of population means are available. Resampling methods, such as jackknife or bootstrap, are often used, with reference to their properties of robustness and reduction of bias. A…

Cetacean population density estimation from single fixed sensors using passive acoustics.

PubMed

Küsel, Elizabeth T; Mellinger, David K; Thomas, Len; Marques, Tiago A; Moretti, David; Ward, Jessica

2011-06-01

Passive acoustic methods are increasingly being used to estimate animal population density. Most density estimation methods are based on estimates of the probability of detecting calls as functions of distance. Typically these are obtained using receivers capable of localizing calls or from studies of tagged animals. However, both approaches are expensive to implement. The approach described here uses a MonteCarlo model to estimate the probability of detecting calls from single sensors. The passive sonar equation is used to predict signal-to-noise ratios (SNRs) of received clicks, which are then combined with a detector characterization that predicts probability of detection as a function of SNR. Input distributions for source level, beam pattern, and whale depth are obtained from the literature. Acoustic propagation modeling is used to estimate transmission loss. Other inputs for density estimation are call rate, obtained from the literature, and false positive rate, obtained from manual analysis of a data sample. The method is applied to estimate density of Blainville's beaked whales over a 6-day period around a single hydrophone located in the Tongue of the Ocean, Bahamas. Results are consistent with those from previous analyses, which use additional tag data. © 2011 Acoustical Society of America

Tracking Biases: An Update to the Validity and Reliability of Alcohol Retail Sales Data for Estimating Population Consumption in Scotland

PubMed Central

Henderson, Audrey; Robinson, Mark; McAdams, Rachel; McCartney, Gerry; Beeston, Clare

2016-01-01

Aims To highlight the importance of monitoring biases when using retail sales data to estimate population alcohol consumption. Methods Previously, we identified and where possible quantified sources of bias that may lead to under- or overestimation of alcohol consumption in Scotland. Here, we update findings by using more recent data and by quantifying emergent biases. Results Underestimation resulting from the net effect of biases on population consumption in Scotland increased from −4% in 2010 to −7% in 2013. Conclusion Biases that might impact on the validity and reliability of sales data when estimating population consumption should be routinely monitored and updated. PMID:26419684

Photometric redshifts for the next generation of deep radio continuum surveys - II. Gaussian processes and hybrid estimates

NASA Astrophysics Data System (ADS)

Duncan, Kenneth J.; Jarvis, Matt J.; Brown, Michael J. I.; Röttgering, Huub J. A.

2018-07-01

Building on the first paper in this series (Duncan et al. 2018), we present a study investigating the performance of Gaussian process photometric redshift (photo-z) estimates for galaxies and active galactic nuclei (AGNs) detected in deep radio continuum surveys. A Gaussian process redshift code is used to produce photo-z estimates targeting specific subsets of both the AGN population - infrared (IR), X-ray, and optically selected AGNs - and the general galaxy population. The new estimates for the AGN population are found to perform significantly better at z > 1 than the template-based photo-z estimates presented in our previous study. Our new photo-z estimates are then combined with template estimates through hierarchical Bayesian combination to produce a hybrid consensus estimate that outperforms both of the individual methods across all source types. Photo-z estimates for radio sources that are X-ray sources or optical/IR AGNs are significantly improved in comparison to previous template-only estimates - with outlier fractions and robust scatter reduced by up to a factor of ˜4. The ability of our method to combine the strengths of the two input photo-z techniques and the large improvements we observe illustrate its potential for enabling future exploitation of deep radio continuum surveys for both the study of galaxy and black hole coevolution and for cosmological studies.

Dynamics of a black-capped chickadee population, 1958-1983

USGS Publications Warehouse

Loery, G.; Nichols, J.D.

1985-01-01

The dynamics of a wintering population of Black-capped Chickadees (Parus atricapillus) were studied from 1958-1983 using capture-recapture methods. The Jolly-Seber model was used to obtain annual estimates of population size, survival rate, and recruitment. The average estimated population size over this period was ?160 birds. The average estimated number of new birds entering the population each year and alive at the time of sampling was ?57. The arithmetic mean annual survival rate estimate was ?0.59. We tested hypothesis about possible relationships between these population parameters and (1) the natural introduction of Tufted Titmice (Parus bicolor) to the area, (2) the clear-cutting of portions of nearby red pine (Pinus resinosa) plantations, and (3) natural variations in winter temperatures. The chickadee population exhibited a substantial short-term decline following titmouse establishment, produced by decreases in both survival rate and number of new recruits. Survival rate decline somewhat after the initiation of the pine clear-cutting, but population size was very similar before and after clear-cutting. Weighted least squares analyses provided no evidence of a relationship between survival rate and either of two winter temperature variables.

Change-in-ratio

USGS Publications Warehouse

Udevitz, Mark S.; El-Shaarawi, Abdel H.; Piegorsch, Walter W.

2002-01-01

Change-in-ratio (CIR) methods are used to estimate parameters for ecological populations subject to differential removals from population subclasses. Subclasses can be defined according to criteria such as sex, age, or size of individuals. Removals are generally in the form of closely monitored sport or commercial harvests. Estimation is based on observed changes in subclass proportions caused by the removals.

Change-in-ratio

USGS Publications Warehouse

Udevitz, Mark S.

2014-01-01

Change-in-ratio (CIR) methods are used to estimate parameters for ecological populations subject to differential removals from population subclasses. Subclasses can be defined according to criteria such as sex, age, or size of individuals. Removals are generally in the form of closely monitored sport or commercial harvests. Estimation is based on observed changes in subclass proportions caused by the removals.

Variance Estimation, Design Effects, and Sample Size Calculations for Respondent-Driven Sampling

PubMed Central

2006-01-01

Hidden populations, such as injection drug users and sex workers, are central to a number of public health problems. However, because of the nature of these groups, it is difficult to collect accurate information about them, and this difficulty complicates disease prevention efforts. A recently developed statistical approach called respondent-driven sampling improves our ability to study hidden populations by allowing researchers to make unbiased estimates of the prevalence of certain traits in these populations. Yet, not enough is known about the sample-to-sample variability of these prevalence estimates. In this paper, we present a bootstrap method for constructing confidence intervals around respondent-driven sampling estimates and demonstrate in simulations that it outperforms the naive method currently in use. We also use simulations and real data to estimate the design effects for respondent-driven sampling in a number of situations. We conclude with practical advice about the power calculations that are needed to determine the appropriate sample size for a study using respondent-driven sampling. In general, we recommend a sample size twice as large as would be needed under simple random sampling. PMID:16937083

Inferring modes of colonization for pest species using heterozygosity comparisons and a shared-allele test.

PubMed

Sved, J A; Yu, H; Dominiak, B; Gilchrist, A S

2003-02-01

Long-range dispersal of a species may involve either a single long-distance movement from a core population or spreading via unobserved intermediate populations. Where the new populations originate as small propagules, genetic drift may be extreme and gene frequency or assignment methods may not prove useful in determining the relation between the core population and outbreak samples. We describe computationally simple resampling methods for use in this situation to distinguish between the different modes of dispersal. First, estimates of heterozygosity can be used to test for direct sampling from the core population and to estimate the effective size of intermediate populations. Second, a test of sharing of alleles, particularly rare alleles, can show whether outbreaks are related to each other rather than arriving as independent samples from the core population. The shared-allele statistic also serves as a genetic distance measure that is appropriate for small samples. These methods were applied to data on a fruit fly pest species, Bactrocera tryoni, which is quarantined from some horticultural areas in Australia. We concluded that the outbreaks in the quarantine zone came from a heterogeneous set of genetically differentiated populations, possibly ones that overwinter in the vicinity of the quarantine zone.

Assessing the Generalizability of Randomized Trial Results to Target Populations

PubMed Central

Stuart, Elizabeth A.; Bradshaw, Catherine P.; Leaf, Philip J.

2014-01-01

Recent years have seen increasing interest in and attention to evidence-based practices, where the “evidence” generally comes from well-conducted randomized trials. However, while those trials yield accurate estimates of the effect of the intervention for the participants in the trial (known as “internal validity”), they do not always yield relevant information about the effects in a particular target population (known as “external validity”). This may be due to a lack of specification of a target population when designing the trial, difficulties recruiting a sample that is representative of a pre-specified target population, or to interest in considering a target population somewhat different from the population directly targeted by the trial. This paper first provides an overview of existing design and analysis methods for assessing and enhancing the ability of a randomized trial to estimate treatment effects in a target population. It then provides a case study using one particular method, which weights the subjects in a randomized trial to match the population on a set of observed characteristics. The case study uses data from a randomized trial of School-wide Positive Behavioral Interventions and Supports (PBIS); our interest is in generalizing the results to the state of Maryland. In the case of PBIS, after weighting, estimated effects in the target population were similar to those observed in the randomized trial. The paper illustrates that statistical methods can be used to assess and enhance the external validity of randomized trials, making the results more applicable to policy and clinical questions. However, there are also many open research questions; future research should focus on questions of treatment effect heterogeneity and further developing these methods for enhancing external validity. Researchers should think carefully about the external validity of randomized trials and be cautious about extrapolating results to specific populations unless they are confident of the similarity between the trial sample and that target population. PMID:25307417

Assessing the generalizability of randomized trial results to target populations.

PubMed

Stuart, Elizabeth A; Bradshaw, Catherine P; Leaf, Philip J

2015-04-01

Recent years have seen increasing interest in and attention to evidence-based practices, where the "evidence" generally comes from well-conducted randomized trials. However, while those trials yield accurate estimates of the effect of the intervention for the participants in the trial (known as "internal validity"), they do not always yield relevant information about the effects in a particular target population (known as "external validity"). This may be due to a lack of specification of a target population when designing the trial, difficulties recruiting a sample that is representative of a prespecified target population, or to interest in considering a target population somewhat different from the population directly targeted by the trial. This paper first provides an overview of existing design and analysis methods for assessing and enhancing the ability of a randomized trial to estimate treatment effects in a target population. It then provides a case study using one particular method, which weights the subjects in a randomized trial to match the population on a set of observed characteristics. The case study uses data from a randomized trial of school-wide positive behavioral interventions and supports (PBIS); our interest is in generalizing the results to the state of Maryland. In the case of PBIS, after weighting, estimated effects in the target population were similar to those observed in the randomized trial. The paper illustrates that statistical methods can be used to assess and enhance the external validity of randomized trials, making the results more applicable to policy and clinical questions. However, there are also many open research questions; future research should focus on questions of treatment effect heterogeneity and further developing these methods for enhancing external validity. Researchers should think carefully about the external validity of randomized trials and be cautious about extrapolating results to specific populations unless they are confident of the similarity between the trial sample and that target population.

Pattern and prevalence of substance use and dependence in the Union Territory of Chandigarh: Results of a rapid assessment survey

PubMed Central

Avasthi, Ajit; Basu, Debasish; Subodh, B. N.; Gupta, Pramod K.; Malhotra, Nidhi; Rani, Poonam; Sharma, Sunil

2017-01-01

Background: Substance misuse is a matter of major public health concern in India. House-to-house survey, though an appealing method to generate population-level estimates, has limitations for estimating prevalence rates of use of illicit and rare substances. Materials and Methods: In this rapid assessment survey (RAS), respondent-driven sampling was used to recruit substance-using individuals from the field. Size of the substance-using population was estimated using the “benchmark-multiplier” method. This figure was then projected to the entire population of the Union Territory (U.T) of Chandigarh. Focused group discussions were used to study the perceptions and views of the substance users regarding various aspects of substance use. Results: Prevalence of any substance dependence in the U.T of Chandigarh was estimated to be 4.65%. Dependence rates on opioids, cannabinoids, and sedative hypnotics were found to be 1.53%, 0.52%, and 0.015%, respectively. Prevalence of injectable opioids was calculated to be 0.91%. Injectable buprenorphine was the most commonly used opioid, followed by bhukhi/doda/opium and heroin. A huge gap was found between the prevalence rates of substance-using population and those seeking treatment. Conclusion: RAS can be a useful method to determine the prevalence of illicit and rare substances. Our survey shows that the use of substance including that of opioids is highly prevalent in the U.T of Chandigarh. The findings of this survey can have implications for policymaking. PMID:29085086

Population-based absolute risk estimation with survey data

PubMed Central

Kovalchik, Stephanie A.; Pfeiffer, Ruth M.

2013-01-01

Absolute risk is the probability that a cause-specific event occurs in a given time interval in the presence of competing events. We present methods to estimate population-based absolute risk from a complex survey cohort that can accommodate multiple exposure-specific competing risks. The hazard function for each event type consists of an individualized relative risk multiplied by a baseline hazard function, which is modeled nonparametrically or parametrically with a piecewise exponential model. An influence method is used to derive a Taylor-linearized variance estimate for the absolute risk estimates. We introduce novel measures of the cause-specific influences that can guide modeling choices for the competing event components of the model. To illustrate our methodology, we build and validate cause-specific absolute risk models for cardiovascular and cancer deaths using data from the National Health and Nutrition Examination Survey. Our applications demonstrate the usefulness of survey-based risk prediction models for predicting health outcomes and quantifying the potential impact of disease prevention programs at the population level. PMID:23686614

Population density estimated from locations of individuals on a passive detector array

USGS Publications Warehouse

Efford, Murray G.; Dawson, Deanna K.; Borchers, David L.

2009-01-01

The density of a closed population of animals occupying stable home ranges may be estimated from detections of individuals on an array of detectors, using newly developed methods for spatially explicit capture–recapture. Likelihood-based methods provide estimates for data from multi-catch traps or from devices that record presence without restricting animal movement ("proximity" detectors such as camera traps and hair snags). As originally proposed, these methods require multiple sampling intervals. We show that equally precise and unbiased estimates may be obtained from a single sampling interval, using only the spatial pattern of detections. This considerably extends the range of possible applications, and we illustrate the potential by estimating density from simulated detections of bird vocalizations on a microphone array. Acoustic detection can be defined as occurring when received signal strength exceeds a threshold. We suggest detection models for binary acoustic data, and for continuous data comprising measurements of all signals above the threshold. While binary data are often sufficient for density estimation, modeling signal strength improves precision when the microphone array is small.

Evaluation of a mark-recapture method for estimating mortality and migration rates of stratified populations

USGS Publications Warehouse

Dorazio, R.M.; Rago, P.J.

1991-01-01

We simulated mark–recapture experiments to evaluate a method for estimating fishing mortality and migration rates of populations stratified at release and recovery. When fish released in two or more strata were recovered from different recapture strata in nearly the same proportions, conditional recapture probabilities were estimated outside the [0, 1] interval. The maximum likelihood estimates tended to be biased and imprecise when the patterns of recaptures produced extremely "flat" likelihood surfaces. Absence of bias was not guaranteed, however, in experiments where recapture rates could be estimated within the [0, 1] interval. Inadequate numbers of tag releases and recoveries also produced biased estimates, although the bias was easily detected by the high sampling variability of the estimates. A stratified tag–recapture experiment with sockeye salmon (Oncorhynchus nerka) was used to demonstrate procedures for analyzing data that produce biased estimates of recapture probabilities. An estimator was derived to examine the sensitivity of recapture rate estimates to assumed differences in natural and tagging mortality, tag loss, and incomplete reporting of tag recoveries.

Comparison of flavonoid intake assessment methods.

PubMed

Ivey, Kerry L; Croft, Kevin; Prince, Richard L; Hodgson, Jonathan M

2016-09-14

Flavonoids are a diverse group of polyphenolic compounds found in high concentrations in many plant foods and beverages. High flavonoid intake has been associated with reduced risk of chronic disease. To date, population based studies have used the United States Department of Agriculture (USDA) food content database to determine habitual flavonoid intake. More recently, a new flavonoid food content database, Phenol-Explorer (PE), has been developed. However, the level of agreement between the two databases is yet to be explored. To compare the methods used to create each database, and to explore the level of agreement between the flavonoid intake estimates derived from USDA and PE data. The study population included 1063 randomly selected women aged over 75 years. Two separate intake estimates were determined using food composition data from the USDA and the PE databases. There were many similarities in methods used to create each database; however, there are several methodological differences that manifest themselves in differences in flavonoid intake estimates between the 2 databases. Despite differences in net estimates, there was a strong level of agreement between total-flavonoid, flavanol, flavanone and anthocyanidin intake estimates derived from each database. Intake estimates for flavanol monomers showed greater agreement than flavanol polymers. The level of agreement between the two databases was the weakest for the flavonol and flavone intake estimates. In this population, the application of USDA and PE source data yielded highly correlated intake estimates for total-flavonoids, flavanols, flavanones and anthocyanidins. For these sub-classes, the USDA and PE databases may be used interchangeably in epidemiological investigations. There was poorer correlation between intake estimates for flavonols and flavones due to differences in USDA and PE methodologies. Individual flavonoid compound groups that comprise flavonoid sub-classes had varying levels of agreement. As such, when determining the appropriate database to calculate flavonoid intake variables, it is important to consider methodologies underpinning database creation and which foods are important contributors to dietary intake in the population of interest.

Estimation of selection intensity under overdominance by Bayesian methods.

PubMed

Buzbas, Erkan Ozge; Joyce, Paul; Abdo, Zaid

2009-01-01

A balanced pattern in the allele frequencies of polymorphic loci is a potential sign of selection, particularly of overdominance. Although this type of selection is of some interest in population genetics, there exists no likelihood based approaches specifically tailored to make inference on selection intensity. To fill this gap, we present Bayesian methods to estimate selection intensity under k-allele models with overdominance. Our model allows for an arbitrary number of loci and alleles within a locus. The neutral and selected variability within each locus are modeled with corresponding k-allele models. To estimate the posterior distribution of the mean selection intensity in a multilocus region, a hierarchical setup between loci is used. The methods are demonstrated with data at the Human Leukocyte Antigen loci from world-wide populations.

Population viability analysis with species occurrence data from museum collections.

PubMed

Skarpaas, Olav; Stabbetorp, Odd E

2011-06-01

The most comprehensive data on many species come from scientific collections. Thus, we developed a method of population viability analysis (PVA) in which this type of occurrence data can be used. In contrast to classical PVA, our approach accounts for the inherent observation error in occurrence data and allows the estimation of the population parameters needed for viability analysis. We tested the sensitivity of the approach to spatial resolution of the data, length of the time series, sampling effort, and detection probability with simulated data and conducted PVAs for common, rare, and threatened species. We compared the results of these PVAs with results of standard method PVAs in which observation error is ignored. Our method provided realistic estimates of population growth terms and quasi-extinction risk in cases in which the standard method without observation error could not. For low values of any of the sampling variables we tested, precision decreased, and in some cases biased estimates resulted. The results of our PVAs with the example species were consistent with information in the literature on these species. Our approach may facilitate PVA for a wide range of species of conservation concern for which demographic data are lacking but occurrence data are readily available. ©2011 Society for Conservation Biology.

Hierarchical models and Bayesian analysis of bird survey information

USGS Publications Warehouse

Sauer, J.R.; Link, W.A.; Royle, J. Andrew; Ralph, C. John; Rich, Terrell D.

2005-01-01

Summary of bird survey information is a critical component of conservation activities, but often our summaries rely on statistical methods that do not accommodate the limitations of the information. Prioritization of species requires ranking and analysis of species by magnitude of population trend, but often magnitude of trend is a misleading measure of actual decline when trend is poorly estimated. Aggregation of population information among regions is also complicated by varying quality of estimates among regions. Hierarchical models provide a reasonable means of accommodating concerns about aggregation and ranking of quantities of varying precision. In these models the need to consider multiple scales is accommodated by placing distributional assumptions on collections of parameters. For collections of species trends, this allows probability statements to be made about the collections of species-specific parameters, rather than about the estimates. We define and illustrate hierarchical models for two commonly encountered situations in bird conservation: (1) Estimating attributes of collections of species estimates, including ranking of trends, estimating number of species with increasing populations, and assessing population stability with regard to predefined trend magnitudes; and (2) estimation of regional population change, aggregating information from bird surveys over strata. User-friendly computer software makes hierarchical models readily accessible to scientists.

Estimation of a closed population size of tadpoles in temporary pond.

PubMed

Lima, M S C S; Pederassi, J; Souza, C A S

2018-05-01

The practice of capture-recapture to estimate the diversity is well known to many animal groups, however this practice in the larval phase of anuran amphibians is incipient. We aimed at evaluating the Lincoln estimator, Venn diagram and Bayes theorem in the inference of population size of a larval phase anurocenose from lotic environment. The adherence of results was evaluated using the Kolmogorov-Smirnov test. The marking of tadpoles for later recapture and methods measurement was made with eosin methylene blue. When comparing the results of Lincoln-Petersen estimator corresponding to the Venn diagram and Bayes theorem, we detected percentage differences per sampling, i.e., the proportion of sampled anuran genera is kept among the three methods, although the values are numerically different. By submitting these results to the Kolmogorov-Smirnov test we have found no significant differences. Therefore, no matter the estimator, the measured value is adherent and estimates the total population. Together with the marking methodology, which did not change the behavior of tadpoles, the present study helps to fill the need of more studies on larval phase of amphibians in Brazil, especially in semi-arid northeast.

One-step estimation of networked population size: Respondent-driven capture-recapture with anonymity.

PubMed

Khan, Bilal; Lee, Hsuan-Wei; Fellows, Ian; Dombrowski, Kirk

2018-01-01

Size estimation is particularly important for populations whose members experience disproportionate health issues or pose elevated health risks to the ambient social structures in which they are embedded. Efforts to derive size estimates are often frustrated when the population is hidden or hard-to-reach in ways that preclude conventional survey strategies, as is the case when social stigma is associated with group membership or when group members are involved in illegal activities. This paper extends prior research on the problem of network population size estimation, building on established survey/sampling methodologies commonly used with hard-to-reach groups. Three novel one-step, network-based population size estimators are presented, for use in the context of uniform random sampling, respondent-driven sampling, and when networks exhibit significant clustering effects. We give provably sufficient conditions for the consistency of these estimators in large configuration networks. Simulation experiments across a wide range of synthetic network topologies validate the performance of the estimators, which also perform well on a real-world location-based social networking data set with significant clustering. Finally, the proposed schemes are extended to allow them to be used in settings where participant anonymity is required. Systematic experiments show favorable tradeoffs between anonymity guarantees and estimator performance. Taken together, we demonstrate that reasonable population size estimates are derived from anonymous respondent driven samples of 250-750 individuals, within ambient populations of 5,000-40,000. The method thus represents a novel and cost-effective means for health planners and those agencies concerned with health and disease surveillance to estimate the size of hidden populations. We discuss limitations and future work in the concluding section.

[Chromosome as a chronicler: Genetic dating, historical events, and DNA-genealogic temptation].

PubMed

Balanovsky, O P; Zaporozhchenko, V V

2016-07-01

Nonrecombinant portions of the genome, Y chromosome and mitochondrial DNA, are widely used for research on human population gene pools and reconstruction of their history. These systems allow the genetic dating of clusters of emerging haplotypes. The main method for age estimations is ρ statistics, which is an average number of mutations from founder haplotype to all modern-day haplotypes. A researcher can estimate the age of the cluster by multiplying this number by the mutation rate. The second method of estimation, ASD, is used for STR haplotypes of the Y chromosome and is based on the squared difference in the number of repeats. In addition to the methods of calculation, methods of Bayesian modeling assume a new significance. They have greater computational cost and complexity, but they allow obtaining an a posteriori distribution of the value of interest that is the most consistent with experimental data. The mutation rate must be known for both calculation methods and modeling methods. It can be determined either during the analysis of lineages or by providing calibration points based on populations with known formation time. These two approaches resulted in rate estimations for Y-chromosomal STR haplotypes with threefold difference. This contradiction was only recently refuted through the use of sequence data for the complete Y chromosome; “whole-genomic” rates of single nucleotide mutations obtained by both methods are mutually consistent and mark the area of application for different rates of STR markers. An issue even more crucial than that of the rates is correlation of the reconstructed history of the haplogroup (a cluster of haplotypes) and the history of the population. Although the need for distinguishing “lineage history” and “population history” arose in the earliest days of phylogeographic research, reconstructing the population history using genetic dating requires a number of methods and conditions. It is known that population history events leave distinct traces in the history of haplogroups only under certain demographic conditions. Direct identification of national history with the history of its occurring haplogroups is inappropriate and is avoided in population genetic studies, although because of its simplicity and attractiveness it is a constant temptation for researchers. An example of DNA genealogy, an amateur field that went beyond the borders of even citizen science and is consistently using the principle of equating haplogroup with lineage and population, which leads to absurd results (e.g., Eurasia as an origin of humankind), can serve as a warning against a simplified approach for interpretation of genetic dating results.

Managing Pacific salmon escapements: The gaps between theory and reality

USGS Publications Warehouse

Knudsen, E. Eric; Knudsen, E. Eric; Steward, Cleveland R.; MacDonald, Donald D.; Williams, Jack E.; Reiser, Dudley W.

1999-01-01

There are myriad challenges to estimating intrinsic production capacity for Pacific salmon populations that are heavily exploited and/or suffering from habitat alteration. Likewise, it is difficult to determine whether perceived decreases in production are due to harvest, habitat, or hatchery influences, natural variation, or some combination of all four. There are dramatic gaps between the true nature of the salmon spawner/recruit relationship and the theoretical basis for describing and understanding the relationship. Importantly, there are also extensive practical difficulties associated with gathering and interpreting accurate escapement and run-size information and applying it to population management. Paradoxically, certain aspects of salmon management may well be contributing to losses in abundance and biodiversity, including harvesting salmon in mixed population fisheries, grouping populations into management units subject to a common harvest rate, and fully exploiting all available hatchery fish at the expense of wild fish escapements. Information on U.S. Pacific salmon escapement goal-setting methods, escapement data collection methods and estimation types, and the degree to which stocks are subjected to mixed stock fisheries was summarized and categorized for 1,025 known management units consisting of 9,430 known populations. Using criteria developed in this study, only 1% of U.S. escapement goals are by methods rated as excellent. Escapement goals for 16% of management units were rated as good. Over 60% of escapement goals have been set by methods rated as either fair or poor and 22% of management units have no escapement goals at all. Of the 9,430 populations for which any information was available, 6,614 (70%) had sufficient information to categorize the method by which escapement data are collected. Of those, data collection methods were rated as excellent for 1%, good for 1%, fair for 2%, and poor for 52%. Escapement estimates are not made for 44% of populations. Escapement estimation type (quality of the data resulting from survey methods) was rated as excellent for <1%, good for 30%, fair for 3%, poor for 22%, and nonexistent for 45%. Numerous recommendations for improvements in escapement mangement are made in this chapter. In general, improvements are needed on theoretical escapement management techniques, escapement goal setting methods, and escapement and run size data quality. There is also a need to change managers' and harvesters' expectations to coincide with the natural variation and uncertainty in the abundance of salmon populations. All the recommendations are aimed at optimizing the number of spawners-healthy escapements ensure salmon sustainability by providing eggs for future production, nutrients to the system, and genetic diversity.

Evaluation of yellow sticky traps for monitoring the population of thrips (Thysanoptera) in a mango orchard.

PubMed

Aliakbarpour, Hamaseh; Rawi, Che Salmah Md

2011-08-01

Populations of several thrips species were estimated using yellow sticky traps in an orchard planted with mango, Mangifera indica L. during the dry and wet seasons beginning in late 2008-2009 on Penang Island, Malaysia. To determine the efficacy of using sticky traps to monitor thrips populations, we compared weekly population estimates on yellow sticky traps with thrips population sizes that were determined (using a CO(2) method) directly from mango panicles. Dispersal distance and direction of thrips movement out of the orchard also were studied using yellow sticky traps placed at three distances from the edge of the orchard in four cardinal directions facing into the orchard. The number of thrips associated with the mango panicles was found to be correlated with the number of thrips collected using the sticky trap method. The number of thrips captured by the traps decreased with increasing distance from the mango orchard in all directions. Density of thrips leaving the orchard was related to the surrounding vegetation. Our results demonstrate that sticky traps have the potential to satisfactorily estimate thrips populations in mango orchards and thus they can be effectively employed as a useful tactic for sampling thrips.

Simulated fissioning of uranium and testing of the fission-track dating method

USGS Publications Warehouse

McGee, V.E.; Johnson, N.M.; Naeser, C.W.

1985-01-01

A computer program (FTD-SIM) faithfully simulates the fissioning of 238U with time and 235U with neutron dose. The simulation is based on first principles of physics where the fissioning of 238U with the flux of time is described by Ns = ??f 238Ut and the fissioning of 235U with the fluence of neutrons is described by Ni = ??235U??. The Poisson law is used to set the stochastic variation of fissioning within the uranium population. The life history of a given crystal can thus be traced under an infinite variety of age and irradiation conditions. A single dating attempt or up to 500 dating attempts on a given crystal population can be simulated by specifying the age of the crystal population, the size and variation in the areas to be counted, the amount and distribution of uranium, the neutron dose to be used and its variation, and the desired ratio of 238U to 235U. A variety of probability distributions can be applied to uranium and counting-area. The Price and Walker age equation is used to estimate age. The output of FTD-SIM includes the tabulated results of each individual dating attempt (sample) on demand and/or the summary statistics and histograms for multiple dating attempts (samples) including the sampling age. An analysis of the results from FTD-SIM shows that: (1) The external detector method is intrinsically more precise than the population method. (2) For the external detector method a correlation between spontaneous track count, Ns, and induced track count, Ni, results when the population of grains has a stochastic uranium content and/or when the counting areas between grains are stochastic. For the population method no correlation can exist. (3) In the external detector method the sampling distribution of age is independent of the number of grains counted. In the population method the sampling distribution of age is highly dependent on the number of grains counted. (4) Grains with zero-track counts, either in Ns or Ni, are in integral part of fissioning theory and under certain circumstances must be included in any estimate of age. (5) In estimating standard error of age the standard error of Ns and Ni and ?? must be accurately estimated and propagated through the age equation. Several statistical models are presently available to do so. ?? 1985.

Evaluating abundance and trends in a Hawaiian avian community using state-space analysis

USGS Publications Warehouse

Camp, Richard J.; Brinck, Kevin W.; Gorresen, P.M.; Paxton, Eben H.

2016-01-01

Estimating population abundances and patterns of change over time are important in both ecology and conservation. Trend assessment typically entails fitting a regression to a time series of abundances to estimate population trajectory. However, changes in abundance estimates from year-to-year across time are due to both true variation in population size (process variation) and variation due to imperfect sampling and model fit. State-space models are a relatively new method that can be used to partition the error components and quantify trends based only on process variation. We compare a state-space modelling approach with a more traditional linear regression approach to assess trends in uncorrected raw counts and detection-corrected abundance estimates of forest birds at Hakalau Forest National Wildlife Refuge, Hawai‘i. Most species demonstrated similar trends using either method. In general, evidence for trends using state-space models was less strong than for linear regression, as measured by estimates of precision. However, while the state-space models may sacrifice precision, the expectation is that these estimates provide a better representation of the real world biological processes of interest because they are partitioning process variation (environmental and demographic variation) and observation variation (sampling and model variation). The state-space approach also provides annual estimates of abundance which can be used by managers to set conservation strategies, and can be linked to factors that vary by year, such as climate, to better understand processes that drive population trends.

Population dynamics of HIV-1 inferred from gene sequences.

PubMed Central

Grassly, N C; Harvey, P H; Holmes, E C

1999-01-01

A method for the estimation of population dynamic history from sequence data is described and used to investigate the past population dynamics of HIV-1 subtypes A and B. Using both gag and env gene alignments the effective population size of each subtype is estimated and found to be surprisingly small. This may be a result of the selective sweep of mutations through the population, or may indicate an important role of genetic drift in the fixation of mutations. The implications of these results for the spread of drug-resistant mutations and transmission dynamics, and also the roles of selection and recombination in shaping HIV-1 genetic diversity, are discussed. A larger estimated effective population size for subtype A may be the result of differences in time of origin, transmission dynamics, and/or population structure. To investigate the importance of population structure a model of population subdivision was fitted to each subtype, although the improvement in likelihood was found to be nonsignificant. PMID:9927440

Challenges of DNA-based mark-recapture studies of American black bears

USGS Publications Warehouse

Settlage, K.E.; Van Manen, F.T.; Clark, J.D.; King, T.L.

2008-01-01

We explored whether genetic sampling would be feasible to provide a region-wide population estimate for American black bears (Ursus americanus) in the southern Appalachians, USA. Specifically, we determined whether adequate capture probabilities (p >0.20) and population estimates with a low coefficient of variation (CV <20%) could be achieved given typical agency budget and personnel constraints. We extracted DNA from hair collected from baited barbed-wire enclosures sampled over a 10-week period on 2 study areas: a high-density black bear population in a portion of Great Smoky Mountains National Park and a lower density population on National Forest lands in North Carolina, South Carolina, and Georgia. We identified individual bears by their unique genotypes obtained from 9 microsatellite loci. We sampled 129 and 60 different bears in the National Park and National Forest study areas, respectively, and applied closed mark–recapture models to estimate population abundance. Capture probabilities and precision of the population estimates were acceptable only for sampling scenarios for which we pooled weekly sampling periods. We detected capture heterogeneity biases, probably because of inadequate spatial coverage by the hair-trapping grid. The logistical challenges of establishing and checking a sufficiently high density of hair traps make DNA-based estimates of black bears impractical for the southern Appalachian region. Alternatives are to estimate population size for smaller areas, estimate population growth rates or survival using mark–recapture methods, or use independent marking and recapturing techniques to reduce capture heterogeneity.

The HIV care cascade: a systematic review of data sources, methodology and comparability.

PubMed

Medland, Nicholas A; McMahon, James H; Chow, Eric P F; Elliott, Julian H; Hoy, Jennifer F; Fairley, Christopher K

2015-01-01

The cascade of HIV diagnosis, care and treatment (HIV care cascade) is increasingly used to direct and evaluate interventions to increase population antiretroviral therapy (ART) coverage, a key component of treatment as prevention. The ability to compare cascades over time, sub-population, jurisdiction or country is important. However, differences in data sources and methodology used to construct the HIV care cascade might limit its comparability and ultimately its utility. Our aim was to review systematically the different methods used to estimate and report the HIV care cascade and their comparability. A search of published and unpublished literature through March 2015 was conducted. Cascades that reported the continuum of care from diagnosis to virological suppression in a demographically definable population were included. Data sources and methods of measurement or estimation were extracted. We defined the most comparable cascade elements as those that directly measured diagnosis or care from a population-based data set. Thirteen reports were included after screening 1631 records. The undiagnosed HIV-infected population was reported in seven cascades, each of which used different data sets and methods and could not be considered to be comparable. All 13 used mandatory HIV diagnosis notification systems to measure the diagnosed population. Population-based data sets, derived from clinical data or mandatory reporting of CD4 cell counts and viral load tests from all individuals, were used in 6 of 12 cascades reporting linkage, 6 of 13 reporting retention, 3 of 11 reporting ART and 6 of 13 cascades reporting virological suppression. Cascades with access to population-based data sets were able to directly measure cascade elements and are therefore comparable over time, place and sub-population. Other data sources and methods are less comparable. To ensure comparability, countries wishing to accurately measure the cascade should utilize complete population-based data sets from clinical data from elements of a centralized healthcare setting, where available, or mandatory CD4 cell count and viral load test result reporting. Additionally, virological suppression should be presented both as percentage of diagnosed and percentage of estimated total HIV-infected population, until methods to calculate the latter have been standardized.

Estimating the Parameters of the Beta-Binomial Distribution.

ERIC Educational Resources Information Center

Wilcox, Rand R.

1979-01-01

For some situations the beta-binomial distribution might be used to describe the marginal distribution of test scores for a particular population of examinees. Several different methods of approximating the maximum likelihood estimate were investigated, and it was found that the Newton-Raphson method should be used when it yields admissable…

Ever Enrolled Medicare Population Estimates from the MCBS Access to Care Files

PubMed Central

Petroski, Jason; Ferraro, David; Chu, Adam

2014-01-01

Objective The Medicare Current Beneficiary Survey’s (MCBS) Access to Care (ATC) file is designed to provide timely access to information on the Medicare population, yet because of the survey’s complex sampling design and expedited processing it is difficult to use the file to make both “always-enrolled” and “ever-enrolled” estimates on the Medicare population. In this study, we describe the ATC file and sample design, and we evaluate and review various alternatives for producing “ever-enrolled” estimates. Methods We created “ever enrolled” estimates for key variables in the MCBS using three separate approaches. We tested differences between the alternative approaches for statistical significance and show the relative magnitude of difference between approaches. Results Even when estimates derived from the different approaches were statistically different, the magnitude of the difference was often sufficiently small so as to result in little practical difference among the alternate approaches. However, when considering more than just the estimation method, there are advantages to using certain approaches over others. Conclusion There are several plausible approaches to achieving “ever-enrolled” estimates in the MCBS ATC file; however, the most straightforward approach appears to be implementation and usage of a new set of “ever-enrolled” weights for this file. PMID:24991484

Localised estimates and spatial mapping of poverty incidence in the state of Bihar in India—An application of small area estimation techniques

PubMed Central

Aditya, Kaustav; Sud, U. C.

2018-01-01

Poverty affects many people, but the ramifications and impacts affect all aspects of society. Information about the incidence of poverty is therefore an important parameter of the population for policy analysis and decision making. In order to provide specific, targeted solutions when addressing poverty disadvantage small area statistics are needed. Surveys are typically designed and planned to produce reliable estimates of population characteristics of interest mainly at higher geographic area such as national and state level. Sample sizes are usually not large enough to provide reliable estimates for disaggregated analysis. In many instances estimates are required for areas of the population for which the survey providing the data was unplanned. Then, for areas with small sample sizes, direct survey estimation of population characteristics based only on the data available from the particular area tends to be unreliable. This paper describes an application of small area estimation (SAE) approach to improve the precision of estimates of poverty incidence at district level in the State of Bihar in India by linking data from the Household Consumer Expenditure Survey 2011–12 of NSSO and the Population Census 2011. The results show that the district level estimates generated by SAE method are more precise and representative. In contrast, the direct survey estimates based on survey data alone are less stable. PMID:29879202

Localised estimates and spatial mapping of poverty incidence in the state of Bihar in India-An application of small area estimation techniques.

PubMed

Chandra, Hukum; Aditya, Kaustav; Sud, U C

2018-01-01

Poverty affects many people, but the ramifications and impacts affect all aspects of society. Information about the incidence of poverty is therefore an important parameter of the population for policy analysis and decision making. In order to provide specific, targeted solutions when addressing poverty disadvantage small area statistics are needed. Surveys are typically designed and planned to produce reliable estimates of population characteristics of interest mainly at higher geographic area such as national and state level. Sample sizes are usually not large enough to provide reliable estimates for disaggregated analysis. In many instances estimates are required for areas of the population for which the survey providing the data was unplanned. Then, for areas with small sample sizes, direct survey estimation of population characteristics based only on the data available from the particular area tends to be unreliable. This paper describes an application of small area estimation (SAE) approach to improve the precision of estimates of poverty incidence at district level in the State of Bihar in India by linking data from the Household Consumer Expenditure Survey 2011-12 of NSSO and the Population Census 2011. The results show that the district level estimates generated by SAE method are more precise and representative. In contrast, the direct survey estimates based on survey data alone are less stable.

Estimation of tiger densities in India using photographic captures and recaptures

USGS Publications Warehouse

Karanth, U.; Nichols, J.D.

1998-01-01

Previously applied methods for estimating tiger (Panthera tigris) abundance using total counts based on tracks have proved unreliable. In this paper we use a field method proposed by Karanth (1995), combining camera-trap photography to identify individual tigers based on stripe patterns, with capture-recapture estimators. We developed a sampling design for camera-trapping and used the approach to estimate tiger population size and density in four representative tiger habitats in different parts of India. The field method worked well and provided data suitable for analysis using closed capture-recapture models. The results suggest the potential for applying this methodology for estimating abundances, survival rates and other population parameters in tigers and other low density, secretive animal species with distinctive coat patterns or other external markings. Estimated probabilities of photo-capturing tigers present in the study sites ranged from 0.75 - 1.00. The estimated mean tiger densities ranged from 4.1 (SE hat= 1.31) to 11.7 (SE hat= 1.93) tigers/100 km2. The results support the previous suggestions of Karanth and Sunquist (1995) that densities of tigers and other large felids may be primarily determined by prey community structure at a given site.

Population structure and effective/census population size ratio in threatened three-spined stickleback populations from an isolated river basin in northwest Spain.

PubMed

Pérez-Figueroa, A; Fernández, C; Amaro, R; Hermida, M; San Miguel, E

2015-08-01

Variability at 20 microsatellite loci was examined to assess the population genetic structure, gene flow, and effective population size (N(e)) in three populations of three-spined stickleback (Gasterosteus aculeatus) from the upper basin of the Miño River in Galicia, NW Spain, where this species is threatened. The three populations showed similar levels of genetic diversity. There is a significant genetic differentiation between the three populations, but also significant gene flow. N(e) estimates based on linkage disequilibrium yielded values of 355 for the Miño River population and 241 and 311 for the Rato and Guisande Rivers, respectively, although we expect that these are overestimates. N(e) estimates based on temporal methods, considering gene flow or not, for the tributaries yielded values of 30-56 and 47-56 for the Rato and Guisande Rivers, respectively. Estimated census size (N(c)) for the Rato River was 880 individuals. This yielded a N(e)/N(c) estimate of 3-6 % for temporal estimation of N(e), which is within the empirical range observed in freshwater fishes. We suggest that the three populations analyzed have a sufficient level of genetic diversity with some genetic structure. Additionally, the absence of physical barriers suggests that conservation efforts and monitoring should focus in the whole basin as a unit.

Comparison of an automated Most Probable Number (MPN) technique to traditional plating methods for estimating populations of total aerobes, coliforms and E. coli associated with freshly processed broiler chickens

USDA-ARS?s Scientific Manuscript database

Traditional microbiological techniques for estimating populations of viable bacteria can be laborious and time consuming. The Most Probable Number (MPN) technique is especially tedious as multiple series of tubes must be inoculated at several different dilutions. Recently, an instrument (TEMPOTM) ...

Age estimation standards for a Western Australian population using the coronal pulp cavity index.

PubMed

Karkhanis, Shalmira; Mack, Peter; Franklin, Daniel

2013-09-10

Age estimation is a vital aspect in creating a biological profile and aids investigators by narrowing down potentially matching identities from the available pool. In addition to routine casework, in the present global political scenario, age estimation in living individuals is required in cases of refugees, asylum seekers, human trafficking and to ascertain age of criminal responsibility. Thus robust methods that are simple, non-invasive and ethically viable are required. The aim of the present study is, therefore, to test the reliability and applicability of the coronal pulp cavity index method, for the purpose of developing age estimation standards for an adult Western Australian population. A total of 450 orthopantomograms (220 females and 230 males) of Australian individuals were analyzed. Crown and coronal pulp chamber heights were measured in the mandibular left and right premolars, and the first and second molars. These measurements were then used to calculate the tooth coronal index. Data was analyzed using paired sample t-tests to assess bilateral asymmetry followed by simple linear and multiple regressions to develop age estimation models. The most accurate age estimation based on simple linear regression model was with mandibular right first molar (SEE ±8.271 years). Multiple regression models improved age prediction accuracy considerably and the most accurate model was with bilateral first and second molars (SEE ±6.692 years). This study represents the first investigation of this method in a Western Australian population and our results indicate that the method is suitable for forensic application. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Prevalence of autosomal dominant polycystic kidney disease in the European Union.

PubMed

Willey, Cynthia J; Blais, Jaime D; Hall, Anthony K; Krasa, Holly B; Makin, Andrew J; Czerwiec, Frank S

2017-08-01

Autosomal dominant polycystic kidney disease (ADPKD) is a leading cause of end-stage renal disease, but estimates of its prevalence vary by >10-fold. The objective of this study was to examine the public health impact of ADPKD in the European Union (EU) by estimating minimum prevalence (point prevalence of known cases) and screening prevalence (minimum prevalence plus cases expected after population-based screening). A review of the epidemiology literature from January 1980 to February 2015 identified population-based studies that met criteria for methodological quality. These examined large German and British populations, providing direct estimates of minimum prevalence and screening prevalence. In a second approach, patients from the 2012 European Renal Association‒European Dialysis and Transplant Association (ERA-EDTA) Registry and literature-based inflation factors that adjust for disease severity and screening yield were used to estimate prevalence across 19 EU countries (N = 407 million). Population-based studies yielded minimum prevalences of 2.41 and 3.89/10 000, respectively, and corresponding estimates of screening prevalences of 3.3 and 4.6/10 000. A close correspondence existed between estimates in countries where both direct and registry-derived methods were compared, which supports the validity of the registry-based approach. Using the registry-derived method, the minimum prevalence was 3.29/10 000 (95% confidence interval 3.27-3.30), and if ADPKD screening was implemented in all countries, the expected prevalence was 3.96/10 000 (3.94-3.98). ERA-EDTA-based prevalence estimates and application of a uniform definition of prevalence to population-based studies consistently indicate that the ADPKD point prevalence is <5/10 000, the threshold for rare disease in the EU. © The Author 2016. Published by Oxford University Press on behalf of ERA-EDTA.

Estimating current and future global urban domestic material consumption

NASA Astrophysics Data System (ADS)

Baynes, Timothy Malcolm; Kaviti Musango, Josephine

2018-06-01

Urban material resource requirements are significant at the global level and these are expected to expand with future urban population growth. However, there are no global scale studies on the future material consumption of urban areas. This paper provides estimates of global urban domestic material consumption (DMC) in 2050 using three approaches based on: current gross statistics; a regression model; and a transition theoretic logistic model. All methods use UN urban population projections and assume a simple ‘business-as-usual’ scenario wherein historical aggregate trends in income and material flow continue into the future. A collation of data for 152 cities provided a year 2000 world average DMC/capita estimate, 12 tons/person/year (±22%), which we combined with UN population projections to produce a first-order estimation of urban DMC at 2050 of ~73 billion tons/year (±22%). Urban DMC/capita was found to be significantly correlated (R 2 > 0.9) to urban GDP/capita and area per person through a power law relation used to obtain a second estimate of 106 billion tons (±33%) in 2050. The inelastic exponent of the power law indicates a global tendency for relative decoupling of direct urban material consumption with increasing income. These estimates are global and influenced by the current proportion of developed-world cities in the global population of cities (and in our sample data). A third method employed a logistic model of transitions in urban DMC/capita with regional resolution. This method estimated global urban DMC to rise from approximately 40 billion tons/year in 2010 to ~90 billion tons/year in 2050 (modelled range: 66–111 billion tons/year). DMC/capita across different regions was estimated to converge from a range of 5–27 tons/person/year in the year 2000 to around 8–17 tons/person/year in 2050. The urban population does not increase proportionally during this period and thus the global average DMC/capita increases from ~12 to ~14 tons/person/year, challenging resource decoupling targets.

Estimating the hatchery fraction of a natural population: a Bayesian approach

USGS Publications Warehouse

Barber, Jarrett J.; Gerow, Kenneth G.; Connolly, Patrick J.; Singh, Sarabdeep

2011-01-01

There is strong and growing interest in estimating the proportion of hatchery fish that are in a natural population (the hatchery fraction). In a sample of fish from the relevant population, some are observed to be marked, indicating their origin as hatchery fish. The observed proportion of marked fish is usually less than the actual hatchery fraction, since the observed proportion is determined by the proportion originally marked, differential survival (usually lower) of marked fish relative to unmarked hatchery fish, and rates of mark retention and detection. Bayesian methods can work well in a setting such as this, in which empirical data are limited but for which there may be considerable expert judgment regarding these values. We explored a Bayesian estimation of the hatchery fraction using Monte Carlo–Markov chain methods. Based on our findings, we created an interactive Excel tool to implement the algorithm, which we have made available for free.

Age-structured mark-recapture analysis: A virtual-population-analysis-based model for analyzing age-structured capture-recapture data

USGS Publications Warehouse

Coggins, L.G.; Pine, William E.; Walters, C.J.; Martell, S.J.D.

2006-01-01

We present a new model to estimate capture probabilities, survival, abundance, and recruitment using traditional Jolly-Seber capture-recapture methods within a standard fisheries virtual population analysis framework. This approach compares the numbers of marked and unmarked fish at age captured in each year of sampling with predictions based on estimated vulnerabilities and abundance in a likelihood function. Recruitment to the earliest age at which fish can be tagged is estimated by using a virtual population analysis method to back-calculate the expected numbers of unmarked fish at risk of capture. By using information from both marked and unmarked animals in a standard fisheries age structure framework, this approach is well suited to the sparse data situations common in long-term capture-recapture programs with variable sampling effort. ?? Copyright by the American Fisheries Society 2006.

Are we using the appropriate reference samples to develop juvenile age estimation methods based on bone size? An exploration of growth differences between average children and those who become victims of homicide.

PubMed

Spake, Laure; Cardoso, Hugo F V

2018-01-01

The population on which forensic juvenile skeletal age estimation methods are applied has not been critically considered. Previous research suggests that child victims of homicide tend to be from socioeconomically disadvantaged contexts, and that these contexts impair linear growth. This study investigates whether juvenile skeletal remains examined by forensic anthropologists are short for age compared to their normal healthy peers. Cadaver lengths were obtained from records of autopsies of 1256 individuals, aged birth to eighteen years at death, conducted between 2000 and 2015 in Australia, New Zealand, and the U.S. Growth status of the forensic population, represented by homicide victims, and general population, represented by accident victims, were compared using height for age Z-scores and independent sample t-tests. Cadaver lengths of the accident victims were compared to growth references using one sample t-tests to evaluate whether accident victims reflect the general population. Homicide victims are shorter for age than accident victims in samples from the U.S., but not in Australia and New Zealand. Accident victims are more representative of the general population in Australia and New Zealand. Different results in Australia and New Zealand as opposed to the U.S. may be linked to socioeconomic inequality. These results suggest that physical anthropologists should critically select reference samples when devising forensic juvenile skeletal age estimation methods. Children examined in forensic investigations may be short for age, and thus methods developed on normal healthy children may yield inaccurate results. A healthy reference population may not necessarily constitute an appropriate growth comparison for the forensic anthropology population. Copyright © 2017 Elsevier B.V. All rights reserved.

Sightability adjustment methods for aerial surveys of wildlife populations

USGS Publications Warehouse

Steinhorst, R.K.; Samuel, M.D.

1989-01-01

Aerial surveys are routinely conducted to estimate the abundance of wildlife species and the rate of population change. However, sightability of animal groups is acknowledged as a significant source of bias in these estimates. Recent research has focused on the development of sightability models to predict the probability of sighting groups under various conditions. Given such models, we show how sightability can be incorporated into the estimator of population size as a probability of response using standard results from sample surveys. We develop formulas for the cases where the sighting probability must be estimated. An example, using data from a helicopter survey of moose in Alberta (Jacobson, Alberta Oil Sands Research Project Report, 1976), is given to illustrate the technique.

Estimation of Potential Population Level Effects of Contaminants on Wildlife

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loar, J.M.

2001-06-11

The objective of this project is to provide DOE with improved methods to assess risks from contaminants to wildlife populations. The current approach for wildlife risk assessment consists of comparison of contaminant exposure estimates for individual animals to literature-derived toxicity test endpoints. These test endpoints are assumed to estimate thresholds for population-level effects. Moreover, species sensitivities to contaminants is one of several criteria to be considered when selecting assessment endpoints (EPA 1997 and 1998), yet data on the sensitivities of many birds and mammals are lacking. The uncertainties associated with this approach are considerable. First, because toxicity data are notmore » available for most potential wildlife endpoint species, extrapolation of toxicity data from test species to the species of interest is required. There is no consensus on the most appropriate extrapolation method. Second, toxicity data are represented as statistical measures (e.g., NOAEL s or LOAELs) that provide no information on the nature or magnitude of effects. The level of effect is an artifact of the replication and dosing regime employed, and does not indicate how effects might increase with increasing exposure. Consequently, slight exceedance of a LOAEL is not distinguished from greatly exceeding it. Third, the relationship of toxic effects on individuals to effects on populations is poorly estimated by existing methods. It is assumed that if the exposure of individuals exceeds levels associated with impaired reproduction, then population level effects are likely. Uncertainty associated with this assumption is large because depending on the reproductive strategy of a given species, comparable levels of reproductive impairment may result in dramatically different population-level responses. This project included several tasks to address these problems: (1) investigation of the validity of the current allometric scaling approach for interspecies extrapolation an d development of new scaling models; (2) development of dose-response models for toxicity data presented in the literature; and (3) development of matrix-based population models that were coupled with dose-response models to provide realistic estimation of population-level effects for individual responses.« less

Estimating parasitic sea lamprey abundance in Lake Huron from heterogenous data sources

USGS Publications Warehouse

Young, Robert J.; Jones, Michael L.; Bence, James R.; McDonald, Rodney B.; Mullett, Katherine M.; Bergstedt, Roger A.

2003-01-01

The Great Lakes Fishery Commission uses time series of transformer, parasitic, and spawning population estimates to evaluate the effectiveness of its sea lamprey (Petromyzon marinus) control program. This study used an inverse variance weighting method to integrate Lake Huron sea lamprey population estimates derived from two estimation procedures: 1) prediction of the lake-wide spawning population from a regression model based on stream size and, 2) whole-lake mark and recapture estimates. In addition, we used a re-sampling procedure to evaluate the effect of trading off sampling effort between the regression and mark-recapture models. Population estimates derived from the regression model ranged from 132,000 to 377,000 while mark-recapture estimates of marked recently metamorphosed juveniles and parasitic sea lampreys ranged from 536,000 to 634,000 and 484,000 to 1,608,000, respectively. The precision of the estimates varied greatly among estimation procedures and years. The integrated estimate of the mark-recapture and spawner regression procedures ranged from 252,000 to 702,000 transformers. The re-sampling procedure indicated that the regression model is more sensitive to reduction in sampling effort than the mark-recapture model. Reliance on either the regression or mark-recapture model alone could produce misleading estimates of abundance of sea lampreys and the effect of the control program on sea lamprey abundance. These analyses indicate that the precision of the lakewide population estimate can be maximized by re-allocating sampling effort from marking sea lampreys to trapping additional streams.

Inferring invasive species abundance using removal data from management actions.

PubMed

Davis, Amy J; Hooten, Mevin B; Miller, Ryan S; Farnsworth, Matthew L; Lewis, Jesse; Moxcey, Michael; Pepin, Kim M

2016-10-01

Evaluation of the progress of management programs for invasive species is crucial for demonstrating impacts to stakeholders and strategic planning of resource allocation. Estimates of abundance before and after management activities can serve as a useful metric of population management programs. However, many methods of estimating population size are too labor intensive and costly to implement, posing restrictive levels of burden on operational programs. Removal models are a reliable method for estimating abundance before and after management using data from the removal activities exclusively, thus requiring no work in addition to management. We developed a Bayesian hierarchical model to estimate abundance from removal data accounting for varying levels of effort, and used simulations to assess the conditions under which reliable population estimates are obtained. We applied this model to estimate site-specific abundance of an invasive species, feral swine (Sus scrofa), using removal data from aerial gunning in 59 site/time-frame combinations (480-19,600 acres) throughout Oklahoma and Texas, USA. Simulations showed that abundance estimates were generally accurate when effective removal rates (removal rate accounting for total effort) were above 0.40. However, when abundances were small (<50) the effective removal rate needed to accurately estimates abundances was considerably higher (0.70). Based on our post-validation method, 78% of our site/time frame estimates were accurate. To use this modeling framework it is important to have multiple removals (more than three) within a time frame during which demographic changes are minimized (i.e., a closed population; ≤3 months for feral swine). Our results show that the probability of accurately estimating abundance from this model improves with increased sampling effort (8+ flight hours across the 3-month window is best) and increased removal rate. Based on the inverse relationship between inaccurate abundances and inaccurate removal rates, we suggest auxiliary information that could be collected and included in the model as covariates (e.g., habitat effects, differences between pilots) to improve accuracy of removal rates and hence abundance estimates. © 2016 by the Ecological Society of America.

Estimated abundance of wild burros surveyed on Bureau of Land Management Lands in 2014

USGS Publications Warehouse

Griffin, Paul C.

2015-01-01

The Bureau of Land Management (BLM) requires accurate estimates of the numbers of wild horses (Equus ferus caballus) and burros (Equus asinus) living on the lands it manages. For over ten years, BLM in Arizona has used the simultaneous double-observer method of recording wild burros during aerial surveys and has reported population estimates for those surveys that come from two formulations of a Lincoln-Petersen type of analysis (Graham and Bell, 1989). In this report, I provide those same two types of burro population analysis for 2014 aerial survey data from six herd management areas (HMAs) in Arizona, California, Nevada, and Utah. I also provide burro population estimates based on a different form of simultaneous double-observer analysis, now in widespread use for wild horse surveys that takes into account the potential effects on detection probability of sighting covariates including group size, distance, vegetative cover, and other factors (Huggins, 1989, 1991). The true number of burros present in the six areas surveyed was not known, so population estimates made with these three types of analyses cannot be directly tested for accuracy in this report. I discuss theoretical reasons why the Huggins (1989, 1991) type of analysis should provide less biased estimates of population size than the Lincoln-Petersen analyses and why estimates from all forms of double-observer analyses are likely to be lower than the true number of animals present in the surveyed areas. I note reasons why I suggest using burro observations made at all available distances in analyses, not only those within 200 meters of the flight path. For all analytical methods, small sample sizes of observed groups can be problematic, but that sample size can be increased over time for Huggins (1989, 1991) analyses by pooling observations. I note ways by which burro population estimates could be tested for accuracy when there are radio-collared animals in the population or when there are simultaneous double-observer surveys before and after a burro gather and removal.

Invited review: Inbreeding in the genomics era: Inbreeding, inbreeding depression, and management of genomic variability.

PubMed

Howard, Jeremy T; Pryce, Jennie E; Baes, Christine; Maltecca, Christian

2017-08-01

Traditionally, pedigree-based relationship coefficients have been used to manage the inbreeding and degree of inbreeding depression that exists within a population. The widespread incorporation of genomic information in dairy cattle genetic evaluations allows for the opportunity to develop and implement methods to manage populations at the genomic level. As a result, the realized proportion of the genome that 2 individuals share can be more accurately estimated instead of using pedigree information to estimate the expected proportion of shared alleles. Furthermore, genomic information allows genome-wide relationship or inbreeding estimates to be augmented to characterize relationships for specific regions of the genome. Region-specific stretches can be used to more effectively manage areas of low genetic diversity or areas that, when homozygous, result in reduced performance across economically important traits. The use of region-specific metrics should allow breeders to more precisely manage the trade-off between the genetic value of the progeny and undesirable side effects associated with inbreeding. Methods tailored toward more effectively identifying regions affected by inbreeding and their associated use to manage the genome at the herd level, however, still need to be developed. We have reviewed topics related to inbreeding, measures of relatedness, genetic diversity and methods to manage populations at the genomic level, and we discuss future challenges related to managing populations through implementing genomic methods at the herd and population levels. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Density estimation in wildlife surveys

USGS Publications Warehouse

Bart, Jonathan; Droege, Sam; Geissler, Paul E.; Peterjohn, Bruce G.; Ralph, C. John

2004-01-01

Several authors have recently discussed the problems with using index methods to estimate trends in population size. Some have expressed the view that index methods should virtually never be used. Others have responded by defending index methods and questioning whether better alternatives exist. We suggest that index methods are often a cost-effective component of valid wildlife monitoring but that double-sampling or another procedure that corrects for bias or establishes bounds on bias is essential. The common assertion that index methods require constant detection rates for trend estimation is mathematically incorrect; the requirement is no long-term trend in detection "ratios" (index result/parameter of interest), a requirement that is probably approximately met by many well-designed index surveys. We urge that more attention be given to defining bird density rigorously and in ways useful to managers. Once this is done, 4 sources of bias in density estimates may be distinguished: coverage, closure, surplus birds, and detection rates. Distance, double-observer, and removal methods do not reduce bias due to coverage, closure, or surplus birds. These methods may yield unbiased estimates of the number of birds present at the time of the survey, but only if their required assumptions are met, which we doubt occurs very often in practice. Double-sampling, in contrast, produces unbiased density estimates if the plots are randomly selected and estimates on the intensive surveys are unbiased. More work is needed, however, to determine the feasibility of double-sampling in different populations and habitats. We believe the tension that has developed over appropriate survey methods can best be resolved through increased appreciation of the mathematical aspects of indices, especially the effects of bias, and through studies in which candidate methods are evaluated against known numbers determined through intensive surveys.

Juvenile body mass estimation: A methodological evaluation.

PubMed

Cowgill, Libby

2018-02-01

Two attempts have been made to develop body mass prediction formulae specifically for immature remains: Ruff (Ruff, C.C., 2007, Body size prediction from juvenile skeletal remains. American Journal Physical Anthropology 133, 698-716) and Robbins et al. (Robbins, G., Sciulli, P.W., Blatt, S.H., 2010. Estimating body mass in subadult human skeletons. American Journal Physical Anthropology 143, 146-150). While both were developed from the same reference population, they differ in their independent variable selection: Ruff (2008) used measures of metaphyseal and articular surface size to predict body mass in immature remains, whereas Robbins et al. (2010) relied on cross-sectional properties. Both methods perform well on independent testing samples; however, differences between the two methods exist in the predicted values. This research evaluates the differences in the body mass estimates from these two methods in seven geographically diverse skeletal samples under the age of 18 (n = 461). The purpose of this analysis is not to assess which method performs with greater accuracy or precision; instead, differences between the two methods are used as a heuristic device to focus attention on the unique challenges affecting the prediction of immature body mass estimates in particular. The two methods differ by population only in some cases, which may be a reflection of activity variation or nutritional status. In addition, cross-sectional properties almost always produce higher estimates than metaphyseal surface size across all age categories. This highlights the difficulty in teasing apart information related to body mass from that relevant to loading, particularly when the original reference population is urban/industrial. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sex estimation in a modern American osteological sample using a discriminant function analysis from the calcaneus.

PubMed

DiMichele, Daniel L; Spradley, M Katherine

2012-09-10

Reliable methods for sex estimation during the development of a biological profile are important to the forensic community in instances when the common skeletal elements used to assess sex are absent or damaged. Sex estimation from the calcaneus has potentially significant importance for the forensic community. Specifically, measurements of the calcaneus provide an additional reliable method for sex estimation via discriminant function analysis based on a North American forensic population. Research on a modern American sample was chosen in order to develop up-to-date population specific discriminant functions for sex estimation. The current study addresses this matter, building upon previous research and introduces a new measurement, posterior circumference that promises to advance the accuracy of use of this single, highly resistant bone in future instances of sex determination from partial skeletal remains. Data were collected from The William Bass Skeletal Collection, housed at The University of Tennessee. Sample size includes 320 adult individuals born between the years 1900 and 1985. The sample was comprised of 136 females and 184 males. Skeletons used for measurements were confined to those with fused diaphyses showing no signs of pathology or damage that may have altered measurements, and that also had accompanying records that included information on ancestry, age, and sex. Measurements collected and analyzed include maximum length, load-arm length, load-arm width, and posterior circumference. The sample was used to compute a discriminant function, based on all four variables, and was performed in SAS 9.1.3. The discriminant function obtained an overall cross-validated classification rate of 86.69%. Females were classified correctly in 88.64% of the cases and males were correctly classified in 84.75% of the cases. Due to the increasing heterogeneity of current populations further discussion on this topic will include the importance that the re-evaluation of past studies has on modern forensic populations. Due to secular and micro evolutionary changes among populations, the near future must include additional methods being updated, and new methods being examined, both which should cover a wide population spectrum. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

A Population Pharmacokinetic Model for 51Cr EDTA to Estimate Renal Function.

PubMed

Kuan, Isabelle H S; Duffull, Stephen B; Putt, Tracey L; Schollum, John B W; Walker, Robert J; Wright, Daniel F B

2017-06-01

51 Cr EDTA clearance (CL) from plasma is used to estimate glomerular filtration rate (GFR). We propose that current methods for analysing the raw 51 Cr EDTA measurements over-simplifies the disposition of 51 Cr EDTA and therefore could produce biased GFR estimates. The aim of this study was to develop a population pharmacokinetic model for 51 Cr EDTA disposition and to compare model-predicted GFR to other methods of estimating renal function. Data from 40 individuals who received ~7.4 MBq of 51 Cr EDTA, as an intravenous bolus, were available for analysis. Plasma radioactivity (counts/min) was measured from timed collection points at 2, 4, 6 and 24 h after the dose. A population analysis was conducted using NONMEM ® version 7.2. Model-predicted GFR was compared with other methods for estimating renal function using mean prediction error (MPE). A two-compartment pharmacokinetic model with first-order elimination best fit the data. Compared with the model predictions, creatinine CL from 24 h urine data was unbiased. The commonly used 'slope-intercept' method for estimating isotopic GFR was positively biased compared with the model (MPE 15.5 mL/min/1.73 m 2 [95% confidence interval {CI} 8.9-22.2]. The Cockcroft Gault, Modification of Diet in Renal Disease (MDRD) and Chronic Kidney Disease Epidemiology Collaboration (CKD-Epi) equations led to negatively biased GFR estimates (MPE -19.0 [95% CI -25.4 to -12.7], -20.1 [95% CI -27.2 to -13.1] and -16.5 [95% CI -22.2 to -10.1] mL/min/1.73 m 2 , respectively). The biased GFR estimates were most obvious in patients with relatively normal renal function. This may lead to inaccurate dosing in patients who are receiving drugs with a narrow therapeutic range where dosing is adjusted according to GFR estimates (e.g. carboplatin). The study is registered with the Australian New Zealand Clinical Trials Registry (ANZCTR), number: ACTRN 12611000035921.

Spatial capture-recapture models for jointly estimating population density and landscape connectivity

USGS Publications Warehouse

Royle, J. Andrew; Chandler, Richard B.; Gazenski, Kimberly D.; Graves, Tabitha A.

2013-01-01

Population size and landscape connectivity are key determinants of population viability, yet no methods exist for simultaneously estimating density and connectivity parameters. Recently developed spatial capture–recapture (SCR) models provide a framework for estimating density of animal populations but thus far have not been used to study connectivity. Rather, all applications of SCR models have used encounter probability models based on the Euclidean distance between traps and animal activity centers, which implies that home ranges are stationary, symmetric, and unaffected by landscape structure. In this paper we devise encounter probability models based on “ecological distance,” i.e., the least-cost path between traps and activity centers, which is a function of both Euclidean distance and animal movement behavior in resistant landscapes. We integrate least-cost path models into a likelihood-based estimation scheme for spatial capture–recapture models in order to estimate population density and parameters of the least-cost encounter probability model. Therefore, it is possible to make explicit inferences about animal density, distribution, and landscape connectivity as it relates to animal movement from standard capture–recapture data. Furthermore, a simulation study demonstrated that ignoring landscape connectivity can result in negatively biased density estimators under the naive SCR model.

Spatial capture--recapture models for jointly estimating population density and landscape connectivity.

PubMed

Royle, J Andrew; Chandler, Richard B; Gazenski, Kimberly D; Graves, Tabitha A

2013-02-01

Population size and landscape connectivity are key determinants of population viability, yet no methods exist for simultaneously estimating density and connectivity parameters. Recently developed spatial capture--recapture (SCR) models provide a framework for estimating density of animal populations but thus far have not been used to study connectivity. Rather, all applications of SCR models have used encounter probability models based on the Euclidean distance between traps and animal activity centers, which implies that home ranges are stationary, symmetric, and unaffected by landscape structure. In this paper we devise encounter probability models based on "ecological distance," i.e., the least-cost path between traps and activity centers, which is a function of both Euclidean distance and animal movement behavior in resistant landscapes. We integrate least-cost path models into a likelihood-based estimation scheme for spatial capture-recapture models in order to estimate population density and parameters of the least-cost encounter probability model. Therefore, it is possible to make explicit inferences about animal density, distribution, and landscape connectivity as it relates to animal movement from standard capture-recapture data. Furthermore, a simulation study demonstrated that ignoring landscape connectivity can result in negatively biased density estimators under the naive SCR model.

Guidelines for Measuring Disease Episodes: An Analysis of the Effects on the Components of Expenditure Growth.

PubMed

Dunn, Abe; Liebman, Eli; Rittmueller, Lindsey; Shapiro, Adam Hale

2017-04-01

To provide guidelines to researchers measuring health expenditures by disease and compare these methodologies' implied inflation estimates. A convenience sample of commercially insured individuals over the 2003 to 2007 period from Truven Health. Population weights are applied, based on age, sex, and region, to make the sample of over 4 million enrollees representative of the entire commercially insured population. Different methods are used to allocate medical-care expenditures to distinct condition categories. We compare the estimates of disease-price inflation by method. Across a variety of methods, the compound annual growth rate stays within the range 3.1 to 3.9 percentage points. Disease-specific inflation measures are more sensitive to the selected methodology. The selected allocation method impacts aggregate inflation rates, but considering the variety of methods applied, the differences appear small. Future research is necessary to better understand these differences in other population samples and to connect disease expenditures to measures of quality. © Health Research and Educational Trust.

Measuring geographic access to health care: raster and network-based methods

PubMed Central

2012-01-01

Background Inequalities in geographic access to health care result from the configuration of facilities, population distribution, and the transportation infrastructure. In recent accessibility studies, the traditional distance measure (Euclidean) has been replaced with more plausible measures such as travel distance or time. Both network and raster-based methods are often utilized for estimating travel time in a Geographic Information System. Therefore, exploring the differences in the underlying data models and associated methods and their impact on geographic accessibility estimates is warranted. Methods We examine the assumptions present in population-based travel time models. Conceptual and practical differences between raster and network data models are reviewed, along with methodological implications for service area estimates. Our case study investigates Limited Access Areas defined by Michigan’s Certificate of Need (CON) Program. Geographic accessibility is calculated by identifying the number of people residing more than 30 minutes from an acute care hospital. Both network and raster-based methods are implemented and their results are compared. We also examine sensitivity to changes in travel speed settings and population assignment. Results In both methods, the areas identified as having limited accessibility were similar in their location, configuration, and shape. However, the number of people identified as having limited accessibility varied substantially between methods. Over all permutations, the raster-based method identified more area and people with limited accessibility. The raster-based method was more sensitive to travel speed settings, while the network-based method was more sensitive to the specific population assignment method employed in Michigan. Conclusions Differences between the underlying data models help to explain the variation in results between raster and network-based methods. Considering that the choice of data model/method may substantially alter the outcomes of a geographic accessibility analysis, we advise researchers to use caution in model selection. For policy, we recommend that Michigan adopt the network-based method or reevaluate the travel speed assignment rule in the raster-based method. Additionally, we recommend that the state revisit the population assignment method. PMID:22587023

Effect of distance-related heterogeneity on population size estimates from point counts

USGS Publications Warehouse

Efford, Murray G.; Dawson, Deanna K.

2009-01-01

Point counts are used widely to index bird populations. Variation in the proportion of birds counted is a known source of error, and for robust inference it has been advocated that counts be converted to estimates of absolute population size. We used simulation to assess nine methods for the conduct and analysis of point counts when the data included distance-related heterogeneity of individual detection probability. Distance from the observer is a ubiquitous source of heterogeneity, because nearby birds are more easily detected than distant ones. Several recent methods (dependent double-observer, time of first detection, time of detection, independent multiple-observer, and repeated counts) do not account for distance-related heterogeneity, at least in their simpler forms. We assessed bias in estimates of population size by simulating counts with fixed radius w over four time intervals (occasions). Detection probability per occasion was modeled as a half-normal function of distance with scale parameter sigma and intercept g(0) = 1.0. Bias varied with sigma/w; values of sigma inferred from published studies were often 50% for a 100-m fixed-radius count. More critically, the bias of adjusted counts sometimes varied more than that of unadjusted counts, and inference from adjusted counts would be less robust. The problem was not solved by using mixture models or including distance as a covariate. Conventional distance sampling performed well in simulations, but its assumptions are difficult to meet in the field. We conclude that no existing method allows effective estimation of population size from point counts.

A method to estimate the population level of Aceria litchii (Prostigmata: Eriophyidae) and a study of the population dynamics of this species and its predators on litchi trees in southern Brazil.

PubMed

De Azevedo, Letícia Henrique; Maeda, Enzo Yuji; Inomoto, Mário Massayuki; De Moraes, Gilberto José

2014-02-01

Litchi (Litchi chinensis Sonnerat) is native to Southeast Asia, where most of the world cultivation of this crop is done. Its commercial cultivation in Brazil is recent and concentrated in the state of São Paulo. This crop has been severely damaged in Asia and Brazil by the litchi erineum mite, Aceria litchii (Keifer) (Eriophyidae). The objectives of this study were the adaptation of a method to estimate the density of A. litchii, an evaluation of the population dynamics of this pest and of its associated predators in the state of São Paulo, and an estimation of its injury levels to litchi trees. To estimate the density of A. litchii, an adaptation of a method commonly used to evaluate nematode densities in plant roots was performed. This method was shown to be adequate for the estimation of the number of A. litchii, and it might also be useful for similar evaluations of other erineum forming mites. Field samples to determine the pest population dynamics were collected monthly from August 2011 to July 2012. Sampled leaves were examined under a stereomicroscope for removal of predators and subsequent extraction ofA. litchii by the adapted method. A. litchii reached maximum densities in November 2011 and June 2012, being found at low densities between January and March 2012. The pattern of variation of A. litchii injury levels was similar to that of the density of A. litchii. The main predatory mite co-occurring with A. litchii was the phytoseiid Phytoseius intermedius Evans and McFarlane. However, high injury levels due toA. litchii suggest that the predator was unable to prevent visible damages to the trees, indicating that control activities should be adopted by growers.

Multimethod, multistate Bayesian hierarchical modeling approach for use in regional monitoring of wolves.

PubMed

Jiménez, José; García, Emilio J; Llaneza, Luis; Palacios, Vicente; González, Luis Mariano; García-Domínguez, Francisco; Múñoz-Igualada, Jaime; López-Bao, José Vicente

2016-08-01

In many cases, the first step in large-carnivore management is to obtain objective, reliable, and cost-effective estimates of population parameters through procedures that are reproducible over time. However, monitoring predators over large areas is difficult, and the data have a high level of uncertainty. We devised a practical multimethod and multistate modeling approach based on Bayesian hierarchical-site-occupancy models that combined multiple survey methods to estimate different population states for use in monitoring large predators at a regional scale. We used wolves (Canis lupus) as our model species and generated reliable estimates of the number of sites with wolf reproduction (presence of pups). We used 2 wolf data sets from Spain (Western Galicia in 2013 and Asturias in 2004) to test the approach. Based on howling surveys, the naïve estimation (i.e., estimate based only on observations) of the number of sites with reproduction was 9 and 25 sites in Western Galicia and Asturias, respectively. Our model showed 33.4 (SD 9.6) and 34.4 (3.9) sites with wolf reproduction, respectively. The number of occupied sites with wolf reproduction was 0.67 (SD 0.19) and 0.76 (0.11), respectively. This approach can be used to design more cost-effective monitoring programs (i.e., to define the sampling effort needed per site). Our approach should inspire well-coordinated surveys across multiple administrative borders and populations and lead to improved decision making for management of large carnivores on a landscape level. The use of this Bayesian framework provides a simple way to visualize the degree of uncertainty around population-parameter estimates and thus provides managers and stakeholders an intuitive approach to interpreting monitoring results. Our approach can be widely applied to large spatial scales in wildlife monitoring where detection probabilities differ between population states and where several methods are being used to estimate different population parameters. © 2016 Society for Conservation Biology.

An evaluation of population index and estimation techniques for tadpoles in desert pools

USGS Publications Warehouse

Jung, Robin E.; Dayton, Gage H.; Williamson, Stephen J.; Sauer, John R.; Droege, Sam

2002-01-01

Using visual (VI) and dip net indices (DI) and double-observer (DOE), removal (RE), and neutral red dye capture-recapture (CRE) estimates, we counted, estimated, and censused Couch's spadefoot (Scaphiopus couchii) and canyon treefrog (Hyla arenicolor) tadpole populations in Big Bend National Park, Texas. Initial dye experiments helped us determine appropriate dye concentrations and exposure times to use in mesocosm and field trials. The mesocosm study revealed higher tadpole detection rates, more accurate population estimates, and lower coefficients of variation among pools compared to those from the field study. In both mesocosm and field studies, CRE was the best method for estimating tadpole populations, followed by DOE and RE. In the field, RE, DI, and VI often underestimated populations in pools with higher tadpole numbers. DI improved with increased sampling. Larger pools supported larger tadpole populations, and tadpole detection rates in general decreased with increasing pool volume and surface area. Hence, pool size influenced bias in tadpole sampling. Across all techniques, tadpole detection rates differed among pools, indicating that sampling bias was inherent and techniques did not consistently sample the same proportion of tadpoles in each pool. Estimating bias (i.e., calculating detection rates) therefore was essential in assessing tadpole abundance. Unlike VI and DOE, DI, RE, and CRE could be used in turbid waters in which tadpoles are not visible. The tadpole population estimates we used accommodated differences in detection probabilities in simple desert pool environments but may not work in more complex habitats.

Evaluation of the accuracy of Demirjian method for estimation of dental age among 6-12 years of children in Navi Mumbai: A radiographic study.

PubMed

Hegde, Rahul J; Khare, Sumedh Suhas; Saraf, Tanvi A; Trivedi, Sonal; Naidu, Sonal

2015-01-01

Dental formation is superior to eruption as a method of dental age (DA) assessment. Eruption is only a brief occurrence, whereas formation may be related at different chronologic age levels, thereby providing a precise index for determining DA. The study was designed to determine the nature of inter-relationship between chronologic and DA. Age estimation depending upon tooth formation was done by Demirjian method and accuracy of Demirjian method was also evaluated. The sample for the study consisted of 197 children of Navi Mumbai. Significant positive correlation was found between chronologic age and DA that is, (r = 0.995), (P < 0.0001) for boys and (r = 0.995), (P < 0.0001) for girls. When age estimation was done by Demirjian method, mean the difference between true age (chronologic age) and assessed (DA) was 2 days for boys and 37 days for girls. Demirjian method showed high accuracy when applied to Navi Mumbai (Maharashtra - India) population. Demirjian method showed high accuracy when applied to Navi Mumbai (Maharashtra - India) population.

Inferring modes of colonization for pest species using heterozygosity comparisons and a shared-allele test.

PubMed Central

Sved, J A; Yu, H; Dominiak, B; Gilchrist, A S

2003-01-01

Long-range dispersal of a species may involve either a single long-distance movement from a core population or spreading via unobserved intermediate populations. Where the new populations originate as small propagules, genetic drift may be extreme and gene frequency or assignment methods may not prove useful in determining the relation between the core population and outbreak samples. We describe computationally simple resampling methods for use in this situation to distinguish between the different modes of dispersal. First, estimates of heterozygosity can be used to test for direct sampling from the core population and to estimate the effective size of intermediate populations. Second, a test of sharing of alleles, particularly rare alleles, can show whether outbreaks are related to each other rather than arriving as independent samples from the core population. The shared-allele statistic also serves as a genetic distance measure that is appropriate for small samples. These methods were applied to data on a fruit fly pest species, Bactrocera tryoni, which is quarantined from some horticultural areas in Australia. We concluded that the outbreaks in the quarantine zone came from a heterogeneous set of genetically differentiated populations, possibly ones that overwinter in the vicinity of the quarantine zone. PMID:12618417

Estimation procedures for the combined 1990s periodic forest inventories of California, Oregon, and Washington.

Treesearch

T.M. Barrett

2004-01-01

During the 1990s, forest inventories for California, Oregon, and Washington were conducted by different agencies using different methods. The Pacific Northwest Research Station Forest Inventory and Analysis program recently integrated these inventories into a single database. This document briefly describes potential statistical methods for estimating population totals...

Validation and Assessment of Three Methods to Estimate 24-h Urinary Sodium Excretion from Spot Urine Samples in Chinese Adults

PubMed Central

Peng, Yaguang; Li, Wei; Wang, Yang; Chen, Hui; Bo, Jian; Wang, Xingyu; Liu, Lisheng

2016-01-01

24-h urinary sodium excretion is the gold standard for evaluating dietary sodium intake, but it is often not feasible in large epidemiological studies due to high participant burden and cost. Three methods—Kawasaki, INTERSALT, and Tanaka—have been proposed to estimate 24-h urinary sodium excretion from a spot urine sample, but these methods have not been validated in the general Chinese population. This aim of this study was to assess the validity of three methods for estimating 24-h urinary sodium excretion using spot urine samples against measured 24-h urinary sodium excretion in a Chinese sample population. Data are from a substudy of the Prospective Urban Rural Epidemiology (PURE) study that enrolled 120 participants aged 35 to 70 years and collected their morning fasting urine and 24-h urine specimens. Bias calculations (estimated values minus measured values) and Bland-Altman plots were used to assess the validity of the three estimation methods. 116 participants were included in the final analysis. Mean bias for the Kawasaki method was -740 mg/day (95% CI: -1219, 262 mg/day), and was the lowest among the three methods. Mean bias for the Tanaka method was -2305 mg/day (95% CI: -2735, 1875 mg/day). Mean bias for the INTERSALT method was -2797 mg/day (95% CI: -3245, 2349 mg/day), and was the highest of the three methods. Bland-Altman plots indicated that all three methods underestimated 24-h urinary sodium excretion. The Kawasaki, INTERSALT and Tanaka methods for estimation of 24-h urinary sodium excretion using spot urines all underestimated true 24-h urinary sodium excretion in this sample of Chinese adults. Among the three methods, the Kawasaki method was least biased, but was still relatively inaccurate. A more accurate method is needed to estimate the 24-h urinary sodium excretion from spot urine for assessment of dietary sodium intake in China. PMID:26895296

A Two-Stage Estimation Method for Random Coefficient Differential Equation Models with Application to Longitudinal HIV Dynamic Data.

PubMed

Fang, Yun; Wu, Hulin; Zhu, Li-Xing

2011-07-01

We propose a two-stage estimation method for random coefficient ordinary differential equation (ODE) models. A maximum pseudo-likelihood estimator (MPLE) is derived based on a mixed-effects modeling approach and its asymptotic properties for population parameters are established. The proposed method does not require repeatedly solving ODEs, and is computationally efficient although it does pay a price with the loss of some estimation efficiency. However, the method does offer an alternative approach when the exact likelihood approach fails due to model complexity and high-dimensional parameter space, and it can also serve as a method to obtain the starting estimates for more accurate estimation methods. In addition, the proposed method does not need to specify the initial values of state variables and preserves all the advantages of the mixed-effects modeling approach. The finite sample properties of the proposed estimator are studied via Monte Carlo simulations and the methodology is also illustrated with application to an AIDS clinical data set.

Estimating equations estimates of trends

USGS Publications Warehouse

Link, W.A.; Sauer, J.R.

1994-01-01

The North American Breeding Bird Survey monitors changes in bird populations through time using annual counts at fixed survey sites. The usual method of estimating trends has been to use the logarithm of the counts in a regression analysis. It is contended that this procedure is reasonably satisfactory for more abundant species, but produces biased estimates for less abundant species. An alternative estimation procedure based on estimating equations is presented.

Improving the Navy’s Passive Underwater Acoustic Monitoring of Marine Mammal Populations

DTIC Science & Technology

2013-09-30

passive acoustic monitoring: Correcting humpback whale call detections for site-specific and time-dependent environmental characteristics ,” JASA Exp...marine mammal species using passive acoustic monitoring, with application to obtaining density estimates of transiting humpback whale populations in...minimize the variance of the density estimates, 3) to apply the numerical modeling methods for humpback whale vocalizations to understand distortions

Improving the Navy’s Passive Underwater Acoustic Monitoring of Marine Mammal Populations

DTIC Science & Technology

2014-09-30

species using passive acoustic monitoring, with application to obtaining density estimates of transiting humpback whale populations in the Southern...of the density estimates, 3) to apply the numerical modeling methods for humpback whale vocalizations to understand distortions caused by...obtained. The specific approach being followed to accomplish objectives 1-4 above is listed below. 1) Detailed numerical modeling of humpback whale

Estimating the number of HIV-infected injection drug users in Bangkok: a capture--recapture method.

PubMed

Mastro, T D; Kitayaporn, D; Weniger, B G; Vanichseni, S; Laosunthorn, V; Uneklabh, T; Uneklabh, C; Choopanya, K; Limpakarnjanarat, K

1994-07-01

The purpose of the study was to estimate the number of injection drug users infected with the human immunodeficiency virus (HIV) in Bangkok to allow planning for health services for this population. A two-sample capture-recapture method was used. The first capture listed all persons on methadone treatment for opiate addiction from April 17 through May 17, 1991, at 18 facilities in Bangkok. The second capture involved urine testing of persons held at 72 Bangkok police stations from June 3 through September 30, 1991. Persons whose urine tests were positive for opiate metabolites or methadone were included on the second list. The first capture comprised 4064 persons and the recapture 1540 persons. There were 171 persons included on both lists, yielding an estimate of 36,600 opiate users in Bangkok. Existing data indicate that 89% of opiate users in Bangkok inject drugs and that about one third are infected with HIV, yielding an estimate of approximately 12,000 HIV-infected injection drug users in Bangkok in 1991. During the 1990s the number of cases of acquired immunodeficiency syndrome (AIDS) and other HIV-related diseases, including tuberculosis, in the population of HIV-infected injection drug users in Bangkok will increase dramatically, placing new demands on existing health care facilities. The capture-recapture method may be useful in estimating difficult-to-count populations, including injection drug users.

Estimating Fast Neural Input Using Anatomical and Functional Connectivity

PubMed Central

Eriksson, David

2016-01-01

In the last 20 years there has been an increased interest in estimating signals that are sent between neurons and brain areas. During this time many new methods have appeared for measuring those signals. Here we review a wide range of methods for which connected neurons can be identified anatomically, by tracing axons that run between the cells, or functionally, by detecting if the activity of two neurons are correlated with a short lag. The signals that are sent between the neurons are represented by the activity in the neurons that are connected to the target population or by the activity at the corresponding synapses. The different methods not only differ in the accuracy of the signal measurement but they also differ in the type of signal being measured. For example, unselective recording of all neurons in the source population encompasses more indirect pathways to the target population than if one selectively record from the neurons that project to the target population. Infact, this degree of selectivity is similar to that of optogenetic perturbations; one can perturb selectively or unselectively. Thus it becomes possible to match a given signal measurement method with a signal perturbation method, something that allows for an exact input control to any neuronal population. PMID:28066189

State-space modeling of population sizes and trends in Nihoa Finch and Millerbird

USGS Publications Warehouse

Gorresen, P. Marcos; Brinck, Kevin W.; Camp, Richard J.; Farmer, Chris; Plentovich, Sheldon M.; Banko, Paul C.

2016-01-01

Both of the 2 passerines endemic to Nihoa Island, Hawai‘i, USA—the Nihoa Millerbird (Acrocephalus familiaris kingi) and Nihoa Finch (Telespiza ultima)—are listed as endangered by federal and state agencies. Their abundances have been estimated by irregularly implemented fixed-width strip-transect sampling from 1967 to 2012, from which area-based extrapolation of the raw counts produced highly variable abundance estimates for both species. To evaluate an alternative survey method and improve abundance estimates, we conducted variable-distance point-transect sampling between 2010 and 2014. We compared our results to those obtained from strip-transect samples. In addition, we applied state-space models to derive improved estimates of population size and trends from the legacy time series of strip-transect counts. Both species were fairly evenly distributed across Nihoa and occurred in all or nearly all available habitat. Population trends for Nihoa Millerbird were inconclusive because of high within-year variance. Trends for Nihoa Finch were positive, particularly since the early 1990s. Distance-based analysis of point-transect counts produced mean estimates of abundance similar to those from strip-transects but was generally more precise. However, both survey methods produced biologically unrealistic variability between years. State-space modeling of the long-term time series of abundances obtained from strip-transect counts effectively reduced uncertainty in both within- and between-year estimates of population size, and allowed short-term changes in abundance trajectories to be smoothed into a long-term trend.

Toward accurate and precise estimates of lion density.

PubMed

Elliot, Nicholas B; Gopalaswamy, Arjun M

2017-08-01

Reliable estimates of animal density are fundamental to understanding ecological processes and population dynamics. Furthermore, their accuracy is vital to conservation because wildlife authorities rely on estimates to make decisions. However, it is notoriously difficult to accurately estimate density for wide-ranging carnivores that occur at low densities. In recent years, significant progress has been made in density estimation of Asian carnivores, but the methods have not been widely adapted to African carnivores, such as lions (Panthera leo). Although abundance indices for lions may produce poor inferences, they continue to be used to estimate density and inform management and policy. We used sighting data from a 3-month survey and adapted a Bayesian spatially explicit capture-recapture (SECR) model to estimate spatial lion density in the Maasai Mara National Reserve and surrounding conservancies in Kenya. Our unstructured spatial capture-recapture sampling design incorporated search effort to explicitly estimate detection probability and density on a fine spatial scale, making our approach robust in the context of varying detection probabilities. Overall posterior mean lion density was estimated to be 17.08 (posterior SD 1.310) lions >1 year old/100 km 2 , and the sex ratio was estimated at 2.2 females to 1 male. Our modeling framework and narrow posterior SD demonstrate that SECR methods can produce statistically rigorous and precise estimates of population parameters, and we argue that they should be favored over less reliable abundance indices. Furthermore, our approach is flexible enough to incorporate different data types, which enables robust population estimates over relatively short survey periods in a variety of systems. Trend analyses are essential to guide conservation decisions but are frequently based on surveys of differing reliability. We therefore call for a unified framework to assess lion numbers in key populations to improve management and policy decisions. © 2016 Society for Conservation Biology.

A rapid screening of ancestry for genetic association studies in an admixed population from Pernambuco, Brazil.

PubMed

Coelho, A V C; Moura, R R; Cavalcanti, C A J; Guimarães, R L; Sandrin-Garcia, P; Crovella, S; Brandão, L A C

2015-03-31

Genetic association studies determine how genes influence traits. However, non-detected population substructure may bias the analysis, resulting in spurious results. One method to detect substructure is to genotype ancestry informative markers (AIMs) besides the candidate variants, quantifying how much ancestral populations contribute to the samples' genetic background. The present study aimed to use a minimum quantity of markers, while retaining full potential to estimate ancestries. We tested the feasibility of a subset of the 12 most informative markers from a previously established study to estimate influence from three ancestral populations: European, African and Amerindian. The results showed that in a sample with a diverse ethnicity (N = 822) derived from 1000 Genomes database, the 12 AIMs had the same capacity to estimate ancestries when compared to the original set of 128 AIMs, since estimates from the two panels were closely correlated. Thus, these 12 SNPs were used to estimate ancestry in a new sample (N = 192) from an admixed population in Recife, Northeast Brazil. The ancestry estimates from Recife subjects were in accordance with previous studies, showing that Northeastern Brazilian populations show great influence from European ancestry (59.7%), followed by African (23.0%) and Amerindian (17.3%) ancestries. Ethnicity self-classification according to skin-color was confirmed to be a poor indicator of population substructure in Brazilians, since ancestry estimates overlapped between classifications. Thus, our streamlined panel of 12 markers may substitute panels with more markers, while retaining the capacity to control for population substructure and admixture, thereby reducing sample processing time.

Hierarchical models and the analysis of bird survey information

USGS Publications Warehouse

Sauer, J.R.; Link, W.A.

2003-01-01

Management of birds often requires analysis of collections of estimates. We describe a hierarchical modeling approach to the analysis of these data, in which parameters associated with the individual species estimates are treated as random variables, and probability statements are made about the species parameters conditioned on the data. A Markov-Chain Monte Carlo (MCMC) procedure is used to fit the hierarchical model. This approach is computer intensive, and is based upon simulation. MCMC allows for estimation both of parameters and of derived statistics. To illustrate the application of this method, we use the case in which we are interested in attributes of a collection of estimates of population change. Using data for 28 species of grassland-breeding birds from the North American Breeding Bird Survey, we estimate the number of species with increasing populations, provide precision-adjusted rankings of species trends, and describe a measure of population stability as the probability that the trend for a species is within a certain interval. Hierarchical models can be applied to a variety of bird survey applications, and we are investigating their use in estimation of population change from survey data.

Incorporating parametric uncertainty into population viability analysis models

USGS Publications Warehouse

McGowan, Conor P.; Runge, Michael C.; Larson, Michael A.

2011-01-01

Uncertainty in parameter estimates from sampling variation or expert judgment can introduce substantial uncertainty into ecological predictions based on those estimates. However, in standard population viability analyses, one of the most widely used tools for managing plant, fish and wildlife populations, parametric uncertainty is often ignored in or discarded from model projections. We present a method for explicitly incorporating this source of uncertainty into population models to fully account for risk in management and decision contexts. Our method involves a two-step simulation process where parametric uncertainty is incorporated into the replication loop of the model and temporal variance is incorporated into the loop for time steps in the model. Using the piping plover, a federally threatened shorebird in the USA and Canada, as an example, we compare abundance projections and extinction probabilities from simulations that exclude and include parametric uncertainty. Although final abundance was very low for all sets of simulations, estimated extinction risk was much greater for the simulation that incorporated parametric uncertainty in the replication loop. Decisions about species conservation (e.g., listing, delisting, and jeopardy) might differ greatly depending on the treatment of parametric uncertainty in population models.

Linking data sources for measurement of effective coverage in maternal and newborn health: what do we learn from individual- vs ecological-linking methods?

PubMed

Willey, Barbara; Waiswa, Peter; Kajjo, Darious; Munos, Melinda; Akuze, Joseph; Allen, Elizabeth; Marchant, Tanya

2018-06-01

Improving maternal and newborn health requires improvements in the quality of facility-based care. This is challenging to measure: routine data may be unreliable; respondents in population surveys may be unable to accurately report on quality indicators; and facility assessments lack population level denominators. We explored methods for linking access to skilled birth attendance (SBA) from household surveys to data on provision of care from facility surveys with the aim of estimating population level effective coverage reflecting access to quality care. We used data from Mayuge District, Uganda. Data from household surveys on access to SBA were linked to health facility assessment census data on readiness to provide basic emergency obstetric and newborn care (BEmONC) in the same district. One individual- and two ecological-linking methods were applied. All methods used household survey reports on where care at birth was accessed. The individual-linking method linked this to data about facility readiness from the specific facility where each woman delivered. The first ecological-linking approach used a district-wide mean estimate of facility readiness. The second used an estimate of facility readiness adjusted by level of health facility accessed. Absolute differences between estimates derived from the different linking methods were calculated, and agreement examined using Lin's concordance correlation coefficient. A total of 1177 women resident in Mayuge reported a birth during 2012-13. Of these, 664 took place in facilities within Mayuge, and were eligible for linking to the census of the district's 38 facilities. 55% were assisted by a SBA in a facility. Using the individual-linking method, effective coverage of births that took place with an SBA in a facility ready to provide BEmONC was just 10% (95% confidence interval CI 3-17). The absolute difference between the individual- and ecological-level linking method adjusting for facility level was one percentage point (11%), and tests suggested good agreement. The ecological method using the district-wide estimate demonstrated poor agreement. The proportion of women accessing appropriately equipped facilities for care at birth is far lower than the coverage of facility delivery. To realise the life-saving potential of health services, countries need evidence to inform actions that address gaps in the provision of quality care. Linking household and facility-based information provides a simple but innovative method for estimating quality of care at the population level. These encouraging findings suggest that linking data sets can result in meaningful evidence even when the exact location of care seeking is not known.

A Comparison of Agent-Based Models and the Parametric G-Formula for Causal Inference.

PubMed

Murray, Eleanor J; Robins, James M; Seage, George R; Freedberg, Kenneth A; Hernán, Miguel A

2017-07-15

Decision-making requires choosing from treatments on the basis of correctly estimated outcome distributions under each treatment. In the absence of randomized trials, 2 possible approaches are the parametric g-formula and agent-based models (ABMs). The g-formula has been used exclusively to estimate effects in the population from which data were collected, whereas ABMs are commonly used to estimate effects in multiple populations, necessitating stronger assumptions. Here, we describe potential biases that arise when ABM assumptions do not hold. To do so, we estimated 12-month mortality risk in simulated populations differing in prevalence of an unknown common cause of mortality and a time-varying confounder. The ABM and g-formula correctly estimated mortality and causal effects when all inputs were from the target population. However, whenever any inputs came from another population, the ABM gave biased estimates of mortality-and often of causal effects even when the true effect was null. In the absence of unmeasured confounding and model misspecification, both methods produce valid causal inferences for a given population when all inputs are from that population. However, ABMs may result in bias when extrapolated to populations that differ on the distribution of unmeasured outcome determinants, even when the causal network linking variables is identical. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Percent body fat estimations in college men using field and laboratory methods: A three-compartment model approach

PubMed Central

Moon, Jordan R; Tobkin, Sarah E; Smith, Abbie E; Roberts, Michael D; Ryan, Eric D; Dalbo, Vincent J; Lockwood, Chris M; Walter, Ashley A; Cramer, Joel T; Beck, Travis W; Stout, Jeffrey R

2008-01-01

Background Methods used to estimate percent body fat can be classified as a laboratory or field technique. However, the validity of these methods compared to multiple-compartment models has not been fully established. The purpose of this study was to determine the validity of field and laboratory methods for estimating percent fat (%fat) in healthy college-age men compared to the Siri three-compartment model (3C). Methods Thirty-one Caucasian men (22.5 ± 2.7 yrs; 175.6 ± 6.3 cm; 76.4 ± 10.3 kg) had their %fat estimated by bioelectrical impedance analysis (BIA) using the BodyGram™ computer program (BIA-AK) and population-specific equation (BIA-Lohman), near-infrared interactance (NIR) (Futrex® 6100/XL), four circumference-based military equations [Marine Corps (MC), Navy and Air Force (NAF), Army (A), and Friedl], air-displacement plethysmography (BP), and hydrostatic weighing (HW). Results All circumference-based military equations (MC = 4.7% fat, NAF = 5.2% fat, A = 4.7% fat, Friedl = 4.7% fat) along with NIR (NIR = 5.1% fat) produced an unacceptable total error (TE). Both laboratory methods produced acceptable TE values (HW = 2.5% fat; BP = 2.7% fat). The BIA-AK, and BIA-Lohman field methods produced acceptable TE values (2.1% fat). A significant difference was observed for the MC and NAF equations compared to both the 3C model and HW (p < 0.006). Conclusion Results indicate that the BP and HW are valid laboratory methods when compared to the 3C model to estimate %fat in college-age Caucasian men. When the use of a laboratory method is not feasible, BIA-AK, and BIA-Lohman are acceptable field methods to estimate %fat in this population. PMID:18426582

Modeling Test and Treatment Strategies for Presymptomatic Alzheimer Disease

PubMed Central

Burke, James F.; Langa, Kenneth M.; Hayward, Rodney A.; Albin, Roger L.

2014-01-01

Objectives In this study, we developed a model of presymptomatic treatment of Alzheimer disease (AD) after a screening diagnostic evaluation and explored the circumstances required for an AD prevention treatment to produce aggregate net population benefit. Methods Monte Carlo simulation methods were used to estimate outcomes in a simulated population derived from data on AD incidence and mortality. A wide variety of treatment parameters were explored. Net population benefit was estimated in aggregated QALYs. Sensitivity analyses were performed by individually varying the primary parameters. Findings In the base-case scenario, treatment effects were uniformly positive, and net benefits increased with increasing age at screening. A highly efficacious treatment (i.e. relative risk 0.6) modeled in the base-case is estimated to save 20 QALYs per 1000 patients screened and 221 QALYs per 1000 patients treated. Conclusions Highly efficacious presymptomatic screen and treat strategies for AD are likely to produce substantial aggregate population benefits that are likely greater than the benefits of aspirin in primary prevention of moderate risk cardiovascular disease (28 QALYS per 1000 patients treated), even in the context of an imperfect treatment delivery environment. PMID:25474698

5-Aminouracil treatment. A method for estimating G2.

PubMed

Socher, S H; Davidson, D

1971-02-01

Treatment of Vicia faba lateral roots with a range of concentrations of 5-aminouracil (5-AU) indicate that cells are stopped at a particular point in interphase. The timing of the fall in mitotic index suggests that cells are held at the S - G(2) transition. When cells are held at this point, treatments with 5-AU can be used to estimate the duration of G(2) + mitosis/2 of proliferating cells. Treatment with 5-AU can also be used to demonstrate the presence of subpopulations of dividing cells that differ in their G(2) duration. Using this method, 5-AU-induced inhibition, we have confirmed that in V. faba lateral roots there are two populations of dividing cells: (a) a fast-dividing population, which makes up approximately 85% of the proliferating cell population and has a G(2) + mitosis/2 duration of 3.3 hr, and (b) a slow-dividing population, which makes up approximately 15% of dividing cells and has a G(2) duration in excess of 12 hr. These estimates are similar to those obtained from percentage labeled mitosis (PLM) curves after incorporation of thymidine-(3)H.

Scale Reliability Evaluation with Heterogeneous Populations

ERIC Educational Resources Information Center

Raykov, Tenko; Marcoulides, George A.

2015-01-01

A latent variable modeling approach for scale reliability evaluation in heterogeneous populations is discussed. The method can be used for point and interval estimation of reliability of multicomponent measuring instruments in populations representing mixtures of an unknown number of latent classes or subpopulations. The procedure is helpful also…

A fast least-squares algorithm for population inference

PubMed Central

2013-01-01

Background Population inference is an important problem in genetics used to remove population stratification in genome-wide association studies and to detect migration patterns or shared ancestry. An individual’s genotype can be modeled as a probabilistic function of ancestral population memberships, Q, and the allele frequencies in those populations, P. The parameters, P and Q, of this binomial likelihood model can be inferred using slow sampling methods such as Markov Chain Monte Carlo methods or faster gradient based approaches such as sequential quadratic programming. This paper proposes a least-squares simplification of the binomial likelihood model motivated by a Euclidean interpretation of the genotype feature space. This results in a faster algorithm that easily incorporates the degree of admixture within the sample of individuals and improves estimates without requiring trial-and-error tuning. Results We show that the expected value of the least-squares solution across all possible genotype datasets is equal to the true solution when part of the problem has been solved, and that the variance of the solution approaches zero as its size increases. The Least-squares algorithm performs nearly as well as Admixture for these theoretical scenarios. We compare least-squares, Admixture, and FRAPPE for a variety of problem sizes and difficulties. For particularly hard problems with a large number of populations, small number of samples, or greater degree of admixture, least-squares performs better than the other methods. On simulated mixtures of real population allele frequencies from the HapMap project, Admixture estimates sparsely mixed individuals better than Least-squares. The least-squares approach, however, performs within 1.5% of the Admixture error. On individual genotypes from the HapMap project, Admixture and least-squares perform qualitatively similarly and within 1.2% of each other. Significantly, the least-squares approach nearly always converges 1.5- to 6-times faster. Conclusions The computational advantage of the least-squares approach along with its good estimation performance warrants further research, especially for very large datasets. As problem sizes increase, the difference in estimation performance between all algorithms decreases. In addition, when prior information is known, the least-squares approach easily incorporates the expected degree of admixture to improve the estimate. PMID:23343408

A fast least-squares algorithm for population inference.

PubMed

Parry, R Mitchell; Wang, May D

2013-01-23

Population inference is an important problem in genetics used to remove population stratification in genome-wide association studies and to detect migration patterns or shared ancestry. An individual's genotype can be modeled as a probabilistic function of ancestral population memberships, Q, and the allele frequencies in those populations, P. The parameters, P and Q, of this binomial likelihood model can be inferred using slow sampling methods such as Markov Chain Monte Carlo methods or faster gradient based approaches such as sequential quadratic programming. This paper proposes a least-squares simplification of the binomial likelihood model motivated by a Euclidean interpretation of the genotype feature space. This results in a faster algorithm that easily incorporates the degree of admixture within the sample of individuals and improves estimates without requiring trial-and-error tuning. We show that the expected value of the least-squares solution across all possible genotype datasets is equal to the true solution when part of the problem has been solved, and that the variance of the solution approaches zero as its size increases. The Least-squares algorithm performs nearly as well as Admixture for these theoretical scenarios. We compare least-squares, Admixture, and FRAPPE for a variety of problem sizes and difficulties. For particularly hard problems with a large number of populations, small number of samples, or greater degree of admixture, least-squares performs better than the other methods. On simulated mixtures of real population allele frequencies from the HapMap project, Admixture estimates sparsely mixed individuals better than Least-squares. The least-squares approach, however, performs within 1.5% of the Admixture error. On individual genotypes from the HapMap project, Admixture and least-squares perform qualitatively similarly and within 1.2% of each other. Significantly, the least-squares approach nearly always converges 1.5- to 6-times faster. The computational advantage of the least-squares approach along with its good estimation performance warrants further research, especially for very large datasets. As problem sizes increase, the difference in estimation performance between all algorithms decreases. In addition, when prior information is known, the least-squares approach easily incorporates the expected degree of admixture to improve the estimate.

Prevalence of systolic inter-arm differences in blood pressure for different primary care populations: systematic review and meta-analysis

PubMed Central

Clark, Christopher E; Taylor, Rod S; Shore, Angela C; Campbell, John L

2016-01-01

Background Various prevalence figures have been reported for inter-arm differences in blood pressure (IAD); variation may be explained by differing population vascular risk and by measurement method. Aim To review the literature to derive robust estimates of IAD prevalence relevant to community populations. Design and setting Systematic review and meta-analysis. Method MEDLINE, Embase, and CINAHL were searched for cross-sectional studies likely to represent general or primary care populations, reporting prevalence of IAD and employing a simultaneous method of measurement. Using study-level data, pooled estimates of mean prevalence of systolic IADs were calculated and compared using a random effects model. Results Eighty IAD studies were identified. Sixteen met inclusion criteria: pooled estimates of prevalence for systolic IAD ≥10 mmHg were 11.2% (95% confidence interval [CI] = 9.1 to 13.6) in hypertension, 7.4% (95% CI = 5.8 to 9.2) in diabetes, and 3.6% (95% CI = 2.3 to 5.0) for a general adult population (P<0.001 for subgroup differences). Differences persisted for higher cut-off values. Prevalences were lower for East Asian than for Western populations and were overestimated by sequential measurement where this could be compared with simultaneous measurement within studies (relative risk for IAD: 2.9 [95% CI = 2.1 to 4.1]). Studies with higher mean absolute systolic pressures had higher prevalences for a systolic IAD ≥10 mmHg (P = 0.04). Conclusion Prevalences of IADs rise in relation to underlying cardiovascular comorbidities of the population studied, and are overestimated threefold when sequential measurement is used. Population-specific variation in prevalences of IAD should be taken into account in delivering clinical care and in planning future studies. PMID:27789511

Age estimation of archaeological remains using amino acid racemization in dental enamel: a comparison of morphological, biochemical, and known ages-at-death.

PubMed

Griffin, R C; Chamberlain, A T; Hotz, G; Penkman, K E H; Collins, M J

2009-10-01

The poor accuracy of most current methods for estimating age-at-death in adult human skeletal remains is among the key problems facing palaeodemography. In forensic science, this problem has been solved for unburnt remains by the development of a chemical method for age estimation, using amino acid racemization in collagen extracted from dentine. Previous application of racemization methods to archaeological material has proven problematic. This study presents the application to archaeological human remains of a new age estimation method utilizing amino acid racemization in a potentially closed system-the dental enamel. The amino acid composition and extent of racemization in enamel from two Medieval cemeteries (Newcastle Blackgate and Grantham, England) and from a documented age-at-death sample from a 19th century cemetery (Spitalfriedhof St Johann, Switzerland) were determined. Alterations in the amino acid composition were detected in all populations, indicating that diagenetic change had taken place. However, in the Medieval populations, these changes did not appear to have substantially affected the relationship between racemization and age-at-death, with a strong relationship being retained between aspartic acid racemization and the morphological age estimates. In contrast, there was a poor relationship between racemization and age in the post-medieval documented age-at-death population from Switzerland. This appears to be due to leaching of amino acids post-mortem, indicating that enamel is not functioning as a perfectly closed system. Isolation of amino acids from a fraction of enamel which is less susceptible to leaching may improve the success of amino acid racemization for archaeological age estimation.

Expert elicitation of population-level effects of disturbance

USGS Publications Warehouse

Fleishman, Erica; Burgman, Mark; Runge, Michael C.; Schick, Robert S; Krauss, Scott; Popper, Arthur N.; Hawkins, Anthony

2016-01-01

Expert elicitation is a rigorous method for synthesizing expert knowledge to inform decision making and is reliable and practical when field data are limited. We evaluated the feasibility of applying expert elicitation to estimate population-level effects of disturbance on marine mammals. Diverse experts estimated parameters related to mortality and sublethal injury of North Atlantic right whales (Eubalaena glacialis). We are now eliciting expert knowledge on the movement of right whales among geographic regions to parameterize a spatial model of health. Expert elicitation complements methods such as simulation models or extrapolations from other species, sometimes with greater accuracy and less uncertainty.

Forecasting extinction risk with nonstationary matrix models.

PubMed

Gotelli, Nicholas J; Ellison, Aaron M

2006-02-01

Matrix population growth models are standard tools for forecasting population change and for managing rare species, but they are less useful for predicting extinction risk in the face of changing environmental conditions. Deterministic models provide point estimates of lambda, the finite rate of increase, as well as measures of matrix sensitivity and elasticity. Stationary matrix models can be used to estimate extinction risk in a variable environment, but they assume that the matrix elements are randomly sampled from a stationary (i.e., non-changing) distribution. Here we outline a method for using nonstationary matrix models to construct realistic forecasts of population fluctuation in changing environments. Our method requires three pieces of data: (1) field estimates of transition matrix elements, (2) experimental data on the demographic responses of populations to altered environmental conditions, and (3) forecasting data on environmental drivers. These three pieces of data are combined to generate a series of sequential transition matrices that emulate a pattern of long-term change in environmental drivers. Realistic estimates of population persistence and extinction risk can be derived from stochastic permutations of such a model. We illustrate the steps of this analysis with data from two populations of Sarracenia purpurea growing in northern New England. Sarracenia purpurea is a perennial carnivorous plant that is potentially at risk of local extinction because of increased nitrogen deposition. Long-term monitoring records or models of environmental change can be used to generate time series of driver variables under different scenarios of changing environments. Both manipulative and natural experiments can be used to construct a linking function that describes how matrix parameters change as a function of the environmental driver. This synthetic modeling approach provides quantitative estimates of extinction probability that have an explicit mechanistic basis.

Detecting declines in the abundance of a bull trout (Salvelinus confluentus) population: Understanding the accuracy, precision, and costs of our efforts

USGS Publications Warehouse

Al-Chokhachy, R.; Budy, P.; Conner, M.

2009-01-01

Using empirical field data for bull trout (Salvelinus confluentus), we evaluated the trade-off between power and sampling effort-cost using Monte Carlo simulations of commonly collected mark-recapture-resight and count data, and we estimated the power to detect changes in abundance across different time intervals. We also evaluated the effects of monitoring different components of a population and stratification methods on the precision of each method. Our results illustrate substantial variability in the relative precision, cost, and information gained from each approach. While grouping estimates by age or stage class substantially increased the precision of estimates, spatial stratification of sampling units resulted in limited increases in precision. Although mark-resight methods allowed for estimates of abundance versus indices of abundance, our results suggest snorkel surveys may be a more affordable monitoring approach across large spatial scales. Detecting a 25% decline in abundance after 5 years was not possible, regardless of technique (power = 0.80), without high sampling effort (48% of study site). Detecting a 25% decline was possible after 15 years, but still required high sampling efforts. Our results suggest detecting moderate changes in abundance of freshwater salmonids requires considerable resource and temporal commitments and highlight the difficulties of using abundance measures for monitoring bull trout populations.

A Comparison of Japan and U.K. SF-6D Health-State Valuations Using a Non-Parametric Bayesian Method.

PubMed

Kharroubi, Samer A

2015-08-01

There is interest in the extent to which valuations of health may differ between different countries and cultures, but few studies have compared preference values of health states obtained in different countries. We sought to estimate and compare two directly elicited valuations for SF-6D health states between the Japan and U.K. general adult populations using Bayesian methods. We analysed data from two SF-6D valuation studies where, using similar standard gamble protocols, values for 241 and 249 states were elicited from representative samples of the Japan and U.K. general adult populations, respectively. We estimate a function applicable across both countries that explicitly accounts for the differences between them, and is estimated using data from both countries. The results suggest that differences in SF-6D health-state valuations between the Japan and U.K. general populations are potentially important. The magnitude of these country-specific differences in health-state valuation depended, however, in a complex way on the levels of individual dimensions. The new Bayesian non-parametric method is a powerful approach for analysing data from multiple nationalities or ethnic groups, to understand the differences between them and potentially to estimate the underlying utility functions more efficiently.

On the number of New World founders: a population genetic portrait of the peopling of the Americas.

PubMed

Hey, Jody

2005-06-01

The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.

Abundance trends and status of the Little Colorado River population of humpback chub

USGS Publications Warehouse

Coggins, L.G.; Pine, William E.; Walters, C.J.; Van Haverbeke, D. R.; Ward, D.; Johnstone, H.C.

2006-01-01

The abundance of the Little Colorado River population of federally listed humpback chub Gila cypha in Grand Canyon has been monitored since the late 1980s by means of catch rate indices and capture-recapture-based abundance estimators. Analyses of data from all sources using various methods are consistent and indicate that the adult population has declined since monitoring began. Intensive tagging led to a high proportion (>80%) of the adult population being marked by the mid-1990s. Analysis of these data using both closed and open abundance estimation models yields results that agree with catch rate indices about the extent of the decline. Survival rates for age-2 and older fish are age dependent but apparently not time dependent. Back-calculation of recruitment using the apparent 1990s population age structure implies periods of higher recruitment in the late 1970s to early 1980s than is now the case. Our analyses indicate that the U.S. Fish and Wildlife Service recovery criterion of stable abundance is not being met for this population. Also, there is a critical need to develop new abundance indexing and tagging methods so that early, reliable, and rapid estimates of humpback chub recruitment can be obtained to evaluate population responses to management actions designed to facilitate the restoration of Colorado River native fish communities. ?? Copyright by the American Fisheries Society 2006.

Drifting to oblivion? Rapid genetic differentiation in an endangered lizard following habitat fragmentation and drought

USGS Publications Warehouse

Vandergast, Amy; Wood, Dustin A.; Thompson, Andrew R.; Fisher, Mark; Barrows, Cameron W.; Grant, Tyler J.

2016-01-01

Aim The frequency and severity of habitat alterations and disturbance are predicted to increase in upcoming decades, and understanding how disturbance affects population integrity is paramount for adaptive management. Although rarely is population genetic sampling conducted at multiple time points, pre- and post-disturbance comparisons may provide one of the clearest methods to measure these impacts. We examined how genetic properties of the federally threatened Coachella Valley fringe-toed lizard (Uma inornata) responded to severe drought and habitat fragmentation across its range. Location Coachella Valley, California, USA. Methods We used 11 microsatellites to examine population genetic structure and diversity in 1996 and 2008, before and after a historic drought. We used Bayesian assignment methods and F-statistics to estimate genetic structure. We compared allelic richness across years to measure loss of genetic diversity and employed approximate Bayesian computing methods and heterozygote excess tests to explore the recent demographic history of populations. Finally, we compared effective population size across years and to abundance estimates to determine whether diversity remained low despite post-drought recovery. Results Genetic structure increased between sampling periods, likely as a result of population declines during the historic drought of the late 1990s–early 2000s, and habitat loss and fragmentation that precluded post-drought genetic rescue. Simulations supported recent demographic declines in 3 of 4 main preserves, and in one preserve, we detected significant loss of allelic richness. Effective population sizes were generally low across the range, with estimates ≤100 in most sites. Main conclusions Fragmentation and drought appear to have acted synergistically to induce genetic change over a short time frame. Progressive deterioration of connectivity, low Ne and measurable loss of genetic diversity suggest that conservation efforts have not maintained the genetic integrity of this species. Genetic sampling over time can help evaluate population trends to guide management.

Characterization of a maximum-likelihood nonparametric density estimator of kernel type

NASA Technical Reports Server (NTRS)

Geman, S.; Mcclure, D. E.

1982-01-01

Kernel type density estimators calculated by the method of sieves. Proofs are presented for the characterization theorem: Let x(1), x(2),...x(n) be a random sample from a population with density f(0). Let sigma 0 and consider estimators f of f(0) defined by (1).

A Coalescent-Based Estimator of Admixture From DNA Sequences

PubMed Central

Wang, Jinliang

2006-01-01

A variety of estimators have been developed to use genetic marker information in inferring the admixture proportions (parental contributions) of a hybrid population. The majority of these estimators used allele frequency data, ignored molecular information that is available in markers such as microsatellites and DNA sequences, and assumed that mutations are absent since the admixture event. As a result, these estimators may fail to deliver an estimate or give rather poor estimates when admixture is ancient and thus mutations are not negligible. A previous molecular estimator based its inference of admixture proportions on the average coalescent times between pairs of genes taken from within and between populations. In this article I propose an estimator that considers the entire genealogy of all of the sampled genes and infers admixture proportions from the numbers of segregating sites in DNA sequence samples. By considering the genealogy of all sequences rather than pairs of sequences, this new estimator also allows the joint estimation of other interesting parameters in the admixture model, such as admixture time, divergence time, population size, and mutation rate. Comparative analyses of simulated data indicate that the new coalescent estimator generally yields better estimates of admixture proportions than the previous molecular estimator, especially when the parental populations are not highly differentiated. It also gives reasonably accurate estimates of other admixture parameters. A human mtDNA sequence data set was analyzed to demonstrate the method, and the analysis results are discussed and compared with those from previous studies. PMID:16624918

Hankin and Reeves' approach to estimating fish abundance in small streams: Limitations and alternatives

USGS Publications Warehouse

Thompson, W.L.

2003-01-01

Hankin and Reeves' (1988) approach to estimating fish abundance in small streams has been applied in stream fish studies across North America. However, their population estimator relies on two key assumptions: (1) removal estimates are equal to the true numbers of fish, and (2) removal estimates are highly correlated with snorkel counts within a subset of sampled stream units. Violations of these assumptions may produce suspect results. To determine possible sources of the assumption violations, I used data on the abundance of steelhead Oncorhynchus mykiss from Hankin and Reeves' (1988) in a simulation composed of 50,000 repeated, stratified systematic random samples from a spatially clustered distribution. The simulation was used to investigate effects of a range of removal estimates, from 75% to 100% of true fish abundance, on overall stream fish population estimates. The effects of various categories of removal-estimates-to-snorkel-count correlation levels (r = 0.75-1.0) on fish population estimates were also explored. Simulation results indicated that Hankin and Reeves' approach may produce poor results unless removal estimates exceed at least 85% of the true number of fish within sampled units and unless correlations between removal estimates and snorkel counts are at least 0.90. A potential modification to Hankin and Reeves' approach is the inclusion of environmental covariates that affect detection rates of fish into the removal model or other mark-recapture model. A potential alternative approach is to use snorkeling combined with line transect sampling to estimate fish densities within stream units. As with any method of population estimation, a pilot study should be conducted to evaluate its usefulness, which requires a known (or nearly so) population of fish to serve as a benchmark for evaluating bias and precision of estimators.

Population Estimates, Health Care Characteristics, and Material Hardship Experiences of U.S. Children with Parent-Reported Speech-Language Difficulties: Evidence from Three Nationally Representative Surveys

ERIC Educational Resources Information Center

Sonik, Rajan A.; Parish, Susan L.; Akorbirshoev, Ilhom; Son, Esther; Rosenthal, Eliana

2014-01-01

Purpose: To provide estimates for the prevalence of parent-reported speech-language difficulties in U.S. children, and to describe the levels of health care access and material hardship in this population. Method: We tabulated descriptive and bivariate statistics using cross-sectional data from the 2007 and 2011/2012 iterations of the National…

Comparison of two methods for estimating the number of undocumented Mexican adults in Los Angeles County.

PubMed

Heer, D M; Passel, J F

1987-01-01

This article compares 2 different methods for estimating the number of undocumented Mexican adults in Los Angeles County. The 1st method, the survey-based method, uses a combination of 1980 census data and the results of a survey conducted in Los Angeles County in 1980 and 1981. A sample was selected from babies born in Los Angeles County who had a mother or father of Mexican origin. The survey included questions about the legal status of the baby's parents and certain other relatives. The resulting estimates of undocumented Mexican immigrants are for males aged 18-44 and females aged 18-39. The 2nd method, the residual method, involves comparison of census figures for aliens counted with estimates of legally-resident aliens developed principally with data from the Immigration and Naturalization Service (INS). For this study, estimates by age, sex, and period of entry were produced for persons born in Mexico and living in Los Angeles County. The results of this research indicate that it is possible to measure undocumented immigration with different techniques, yet obtain results that are similar. Both techniques presented here are limited in that they represent estimates of undocumented aliens based on the 1980 census. The number of additional undocumented aliens not counted remains a subject of conjecture. The fact that the proportions undocumented shown in the survey (228,700) are quite similar to the residual estimates (317,800) suggests that the number of undocumented aliens not counted in the census may not be an extremely large fraction of the undocumented population. The survey-based estimates have some significant advantages over the residual estimates. The survey provides tabulations of the undocumented population by characteristics other than the limited demographic information provided by the residual technique. On the other hand, the survey-based estimates require that a survey be conducted and, if national or regional estimates are called for, they may require a number of surveys. The residual technique, however, also requires a data source other than the census. However, the INS discontinued the annual registration of aliens after 1981. Thus, estimates of undocumented aliens based on the residual technique will probably not be possible for subnational areas using the 1990 census unless the registration program is reinstituted. Perhaps the best information on the undocumented population in the 1990 census will come from an improved version of the survey-based technique described here applied in selected local areas.

Percent body fat estimations in college men using field and laboratory methods: a three-compartment model approach.

PubMed

Moon, Jordan R; Tobkin, Sarah E; Smith, Abbie E; Roberts, Michael D; Ryan, Eric D; Dalbo, Vincent J; Lockwood, Chris M; Walter, Ashley A; Cramer, Joel T; Beck, Travis W; Stout, Jeffrey R

2008-04-21

Methods used to estimate percent body fat can be classified as a laboratory or field technique. However, the validity of these methods compared to multiple-compartment models has not been fully established. The purpose of this study was to determine the validity of field and laboratory methods for estimating percent fat (%fat) in healthy college-age men compared to the Siri three-compartment model (3C). Thirty-one Caucasian men (22.5 +/- 2.7 yrs; 175.6 +/- 6.3 cm; 76.4 +/- 10.3 kg) had their %fat estimated by bioelectrical impedance analysis (BIA) using the BodyGram computer program (BIA-AK) and population-specific equation (BIA-Lohman), near-infrared interactance (NIR) (Futrex(R) 6100/XL), four circumference-based military equations [Marine Corps (MC), Navy and Air Force (NAF), Army (A), and Friedl], air-displacement plethysmography (BP), and hydrostatic weighing (HW). All circumference-based military equations (MC = 4.7% fat, NAF = 5.2% fat, A = 4.7% fat, Friedl = 4.7% fat) along with NIR (NIR = 5.1% fat) produced an unacceptable total error (TE). Both laboratory methods produced acceptable TE values (HW = 2.5% fat; BP = 2.7% fat). The BIA-AK, and BIA-Lohman field methods produced acceptable TE values (2.1% fat). A significant difference was observed for the MC and NAF equations compared to both the 3C model and HW (p < 0.006). Results indicate that the BP and HW are valid laboratory methods when compared to the 3C model to estimate %fat in college-age Caucasian men. When the use of a laboratory method is not feasible, BIA-AK, and BIA-Lohman are acceptable field methods to estimate %fat in this population.

A Comparison of Limited-Information and Full-Information Methods in M"plus" for Estimating Item Response Theory Parameters for Nonnormal Populations

ERIC Educational Resources Information Center

DeMars, Christine E.

2012-01-01

In structural equation modeling software, either limited-information (bivariate proportions) or full-information item parameter estimation routines could be used for the 2-parameter item response theory (IRT) model. Limited-information methods assume the continuous variable underlying an item response is normally distributed. For skewed and…

A smoothed residual based goodness-of-fit statistic for nest-survival models

Treesearch

Rodney X. Sturdivant; Jay J. Rotella; Robin E. Russell

2008-01-01

Estimating nest success and identifying important factors related to nest-survival rates is an essential goal for many wildlife researchers interested in understanding avian population dynamics. Advances in statistical methods have led to a number of estimation methods and approaches to modeling this problem. Recently developed models allow researchers to include a...

A Direct Latent Variable Modeling Based Method for Point and Interval Estimation of Coefficient Alpha

ERIC Educational Resources Information Center

Raykov, Tenko; Marcoulides, George A.

2015-01-01

A direct approach to point and interval estimation of Cronbach's coefficient alpha for multiple component measuring instruments is outlined. The procedure is based on a latent variable modeling application with widely circulated software. As a by-product, using sample data the method permits ascertaining whether the population discrepancy…

DS — Software for analyzing data collected using double sampling

USGS Publications Warehouse

Bart, Jonathan; Hartley, Dana

2011-01-01

DS analyzes count data to estimate density or relative density and population size when appropriate. The software is available at http://iwcbm.dev4.fsr.com/IWCBM/default.asp?PageID=126. The software was designed to analyze data collected using double sampling, but it also can be used to analyze index data. DS is not currently configured to apply distance methods or methods based on capture-recapture theory. Double sampling for the purpose of this report means surveying a sample of locations with a rapid method of unknown accuracy and surveying a subset of these locations using a more intensive method assumed to yield unbiased estimates. "Detection ratios" are calculated as the ratio of results from rapid surveys on intensive plots to the number actually present as determined from the intensive surveys. The detection ratios are used to adjust results from the rapid surveys. The formula for density is (results from rapid survey)/(estimated detection ratio from intensive surveys). Population sizes are estimated as (density)(area). Double sampling is well-established in the survey sampling literature—see Cochran (1977) for the basic theory, Smith (1995) for applications of double sampling in waterfowl surveys, Bart and Earnst (2002, 2005) for discussions of its use in wildlife studies, and Bart and others (in press) for a detailed account of how the method was used to survey shorebirds across the arctic region of North America. Indices are surveys that do not involve complete counts of well-defined plots or recording information to estimate detection rates (Thompson and others, 1998). In most cases, such data should not be used to estimate density or population size but, under some circumstances, may be used to compare two densities or estimate how density changes through time or across space (Williams and others, 2005). The Breeding Bird Survey (Sauer and others, 2008) provides a good example of an index survey. Surveyors record all birds detected but do not record any information, such as distance or whether each bird is recorded in subperiods, that could be used to estimate detection rates. Nonetheless, the data are widely used to estimate temporal trends and spatial patterns in abundance (Sauer and others, 2008). DS produces estimates of density (or relative density for indices) by species and stratum. Strata are usually defined using region and habitat but other variables may be used, and the entire study area may be classified as a single stratum. Population size in each stratum and for the entire study area also is estimated for each species. For indices, the estimated totals generally are only useful if (a) plots are surveyed so that densities can be calculated and extrapolated to the entire study area and (b) if the detection rates are close to 1.0. All estimates are accompanied by standard errors (SE) and coefficients of variation (CV, that is, SE/estimate).

Modeling influenza-like illnesses through composite compartmental models

NASA Astrophysics Data System (ADS)

Levy, Nir; , Michael, Iv; Yom-Tov, Elad

2018-03-01

Epidemiological models for the spread of pathogens in a population are usually only able to describe a single pathogen. This makes their application unrealistic in cases where multiple pathogens with similar symptoms are spreading concurrently within the same population. Here we describe a method which makes possible the application of multiple single-strain models under minimal conditions. As such, our method provides a bridge between theoretical models of epidemiology and data-driven approaches for modeling of influenza and other similar viruses. Our model extends the Susceptible-Infected-Recovered model to higher dimensions, allowing the modeling of a population infected by multiple viruses. We further provide a method, based on an overcomplete dictionary of feasible realizations of SIR solutions, to blindly partition the time series representing the number of infected people in a population into individual components, each representing the effect of a single pathogen. We demonstrate the applicability of our proposed method on five years of seasonal influenza-like illness (ILI) rates, estimated from Twitter data. We demonstrate that our method describes, on average, 44% of the variance in the ILI time series. The individual infectious components derived from our model are matched to known viral profiles in the populations, which we demonstrate matches that of independently collected epidemiological data. We further show that the basic reproductive numbers (R 0) of the matched components are in range known for these pathogens. Our results suggest that the proposed method can be applied to other pathogens and geographies, providing a simple method for estimating the parameters of epidemics in a population.

Chronic widespread pain prevalence in the general population: A systematic review.

PubMed

Andrews, P; Steultjens, M; Riskowski, J

2018-01-01

Chronic widespread pain (CWP) is a significant burden in communities. Understanding the impact of population-dependent (e.g., age, gender) and contextual-dependent (e.g. survey method, region, inequality level) factors have on CWP prevalence may provide a foundation for population-based strategies to address CWP. Therefore, the purpose of this study was to estimate the global prevalence of CWP and evaluate the population and contextual factors associated with CWP. A systematic review of CWP prevalence studies (1990-2017) in the general population was undertaken. Meta-analyses were conducted to determine CWP prevalence, and study population data and contextual factors were evaluated using a meta-regression. Thirty-nine manuscripts met the inclusion criteria. Study CWP prevalence ranged from 1.4% to 24.0%, with CWP prevalence in men ranging from 0.8% to 15.3% and 1.7% to 22.1% in women. Estimated overall CWP prevalence was 9.6% (8.0-11.2%). Meta-regression analyses showed gender, United Nations country development status, and human development index (HDI) influenced CWP prevalence, while survey method, region, methodological and reporting quality, and inequality showed no significant effect on the CWP estimate. Globally CWP affects one in ten individuals within the general population, with women more likely to experience CWP than men. HDI was noted to be the socioeconomic factor related to CWP prevalence, with those in more developed countries having a lower CWP prevalence than those in less developed countries. Most CWP estimates were from developed countries, and CWP estimates from countries with a lower socioeconomic position is needed to further refine the global estimate of CWP. This systematic review and meta-analysis updates the current global CWP prevalence by examining the population-level (e.g. age, gender) and contextual (e.g. country development status; survey style; reporting and methodologic quality) factors associated with CWP prevalence. This analyses provides evidence to support higher levels of CWP in countries with a lower socioeconomic position relative to countries with a higher socioeconomic position. © 2017 European Pain Federation - EFIC®.

Parameter estimation techniques based on optimizing goodness-of-fit statistics for structural reliability

NASA Technical Reports Server (NTRS)

Starlinger, Alois; Duffy, Stephen F.; Palko, Joseph L.

1993-01-01

New methods are presented that utilize the optimization of goodness-of-fit statistics in order to estimate Weibull parameters from failure data. It is assumed that the underlying population is characterized by a three-parameter Weibull distribution. Goodness-of-fit tests are based on the empirical distribution function (EDF). The EDF is a step function, calculated using failure data, and represents an approximation of the cumulative distribution function for the underlying population. Statistics (such as the Kolmogorov-Smirnov statistic and the Anderson-Darling statistic) measure the discrepancy between the EDF and the cumulative distribution function (CDF). These statistics are minimized with respect to the three Weibull parameters. Due to nonlinearities encountered in the minimization process, Powell's numerical optimization procedure is applied to obtain the optimum value of the EDF. Numerical examples show the applicability of these new estimation methods. The results are compared to the estimates obtained with Cooper's nonlinear regression algorithm.

Design and Weighting Methods for a Nationally Representative Sample of HIV-infected Adults Receiving Medical Care in the United States-Medical Monitoring Project

PubMed Central

Iachan, Ronaldo; H. Johnson, Christopher; L. Harding, Richard; Kyle, Tonja; Saavedra, Pedro; L. Frazier, Emma; Beer, Linda; L. Mattson, Christine; Skarbinski, Jacek

2016-01-01

Background: Health surveys of the general US population are inadequate for monitoring human immunodeficiency virus (HIV) infection because the relatively low prevalence of the disease (<0.5%) leads to small subpopulation sample sizes. Objective: To collect a nationally and locally representative probability sample of HIV-infected adults receiving medical care to monitor clinical and behavioral outcomes, supplementing the data in the National HIV Surveillance System. This paper describes the sample design and weighting methods for the Medical Monitoring Project (MMP) and provides estimates of the size and characteristics of this population. Methods: To develop a method for obtaining valid, representative estimates of the in-care population, we implemented a cross-sectional, three-stage design that sampled 23 jurisdictions, then 691 facilities, then 9,344 HIV patients receiving medical care, using probability-proportional-to-size methods. The data weighting process followed standard methods, accounting for the probabilities of selection at each stage and adjusting for nonresponse and multiplicity. Nonresponse adjustments accounted for differing response at both facility and patient levels. Multiplicity adjustments accounted for visits to more than one HIV care facility. Results: MMP used a multistage stratified probability sampling design that was approximately self-weighting in each of the 23 project areas and nationally. The probability sample represents the estimated 421,186 HIV-infected adults receiving medical care during January through April 2009. Methods were efficient (i.e., induced small, unequal weighting effects and small standard errors for a range of weighted estimates). Conclusion: The information collected through MMP allows monitoring trends in clinical and behavioral outcomes and informs resource allocation for treatment and prevention activities. PMID:27651851

The Beta-Geometric Model Applied to Fecundability in a Sample of Married Women

NASA Astrophysics Data System (ADS)

Adekanmbi, D. B.; Bamiduro, T. A.

2006-10-01

The time required to achieve pregnancy among married couples termed fecundability has been proposed to follow a beta-geometric distribution. The accuracy of the method used in estimating the parameters of the model has an implication on the goodness of fit of the model. In this study, the parameters of the model are estimated using the Method of Moments and Newton-Raphson estimation procedure. The goodness of fit of the model was considered, using estimates from the two methods of estimation, as well as the asymptotic relative efficiency of the estimates. A noticeable improvement in the fit of the model to the data on time to conception was observed, when the parameters are estimated by Newton-Raphson procedure, and thereby estimating reasonable expectations of fecundability for married female population in the country.

Using the Kernel Method of Test Equating for Estimating the Standard Errors of Population Invariance Measures. Research Report. ETS RR-06-20

ERIC Educational Resources Information Center

Moses, Tim

2006-01-01

Population invariance is an important requirement of test equating. An equating function is said to be population invariant when the choice of (sub)population used to compute the equating function does not matter. In recent studies, the extent to which equating functions are population invariant is typically addressed in terms of practical…

Comparison of estimation methods for creating small area rates of acute myocardial infarction among Medicare beneficiaries in California.

PubMed

Yasaitis, Laura C; Arcaya, Mariana C; Subramanian, S V

2015-09-01

Creating local population health measures from administrative data would be useful for health policy and public health monitoring purposes. While a wide range of options--from simple spatial smoothers to model-based methods--for estimating such rates exists, there are relatively few side-by-side comparisons, especially not with real-world data. In this paper, we compare methods for creating local estimates of acute myocardial infarction rates from Medicare claims data. A Bayesian Monte Carlo Markov Chain estimator that incorporated spatial and local random effects performed best, followed by a method-of-moments spatial Empirical Bayes estimator. As the former is more complicated and time-consuming, spatial linear Empirical Bayes methods may represent a good alternative for non-specialist investigators. Copyright © 2015 Elsevier Ltd. All rights reserved.

Double sampling to estimate density and population trends in birds

USGS Publications Warehouse

Bart, Jonathan; Earnst, Susan L.

2002-01-01

We present a method for estimating density of nesting birds based on double sampling. The approach involves surveying a large sample of plots using a rapid method such as uncorrected point counts, variable circular plot counts, or the recently suggested double-observer method. A subsample of those plots is also surveyed using intensive methods to determine actual density. The ratio of the mean count on those plots (using the rapid method) to the mean actual density (as determined by the intensive searches) is used to adjust results from the rapid method. The approach works well when results from the rapid method are highly correlated with actual density. We illustrate the method with three years of shorebird surveys from the tundra in northern Alaska. In the rapid method, surveyors covered ~10 ha h-1 and surveyed each plot a single time. The intensive surveys involved three thorough searches, required ~3 h ha-1, and took 20% of the study effort. Surveyors using the rapid method detected an average of 79% of birds present. That detection ratio was used to convert the index obtained in the rapid method into an essentially unbiased estimate of density. Trends estimated from several years of data would also be essentially unbiased. Other advantages of double sampling are that (1) the rapid method can be changed as new methods become available, (2) domains can be compared even if detection rates differ, (3) total population size can be estimated, and (4) valuable ancillary information (e.g. nest success) can be obtained on intensive plots with little additional effort. We suggest that double sampling be used to test the assumption that rapid methods, such as variable circular plot and double-observer methods, yield density estimates that are essentially unbiased. The feasibility of implementing double sampling in a range of habitats needs to be evaluated.

Mountain goat abundance and population trends in the Olympic Mountains, Washington, 2011

USGS Publications Warehouse

Jenkins, Kurt; Happe, Patricia; Griffin, Paul C.; Beirne, Katherine; Hoffman, Roger; Baccus, William

2011-01-01

We conducted an aerial helicopter survey between July 18 and July 25, 2011, to estimate abundance and trends of introduced mountain goats (Oreamnos americanus) in the Olympic Mountains. The survey was the first since we developed a sightability correction model in 2008, which provided the means to estimate the number of mountain goats present in the surveyed areas and not seen during the aerial surveys, and to adjust for undercounting biases. Additionally, the count was the first since recent telemetry studies revealed that the previously defined survey zone, which was delineated at lower elevations by the 1,520-meter elevation contour, did not encompass all lands used by mountain goats during summer. We redefined the lower elevation boundary of survey units before conducting the 2011 surveys in an effort to more accurately estimate the entire mountain goat population. We surveyed 39 survey units, comprising 39 percent of the 59,615-hectare survey area. We estimated a mountain goat population of 344±44 (standard error, SE) in the expanded survey area. Based on this level of estimation uncertainty, the 95-percent confidence interval ranged from 258 to 430 mountain goats at the time of the survey. To permit comparisons of mountain goat populations between the 2004 and 2011 surveys, we recomputed population estimates derived from the 2004 survey using the newly developed bias correction methods, and we computed the 2004 and 2011 surveys based on comparable survey zone definitions (for example, using the boundaries of the 2004 survey). The recomputed estimates of mountain goat populations were 217±19 (SE) in 2004 and 303±41(SE) in 2011. The difference between the current 2011 population estimate (344±44[SE]) and the recomputed 2011 estimate (303±41[SE]) reflects the number of mountain goats counted in the expanded lower elevation portions of the survey zone added in 2011. We conclude that the population of mountain goats has increased in the Olympic Mountains at an average rate of 4.9±2.2(SE) percent annually since 2004. We caution that the estimated rate of population growth may be conservative if severe spring weather deterred some mountain goats from reaching the high-elevation survey areas during the 2011 surveys. If the estimated average rate of population growth were to remain constant in the future, then the population would double in approximately 14-15 years.

Estimating population diversity with CatchAll

PubMed Central

Bunge, John; Woodard, Linda; Böhning, Dankmar; Foster, James A.; Connolly, Sean; Allen, Heather K.

2012-01-01

Motivation: The massive data produced by next-generation sequencing require advanced statistical tools. We address estimating the total diversity or species richness in a population. To date, only relatively simple methods have been implemented in available software. There is a need for software employing modern, computationally intensive statistical analyses including error, goodness-of-fit and robustness assessments. Results: We present CatchAll, a fast, easy-to-use, platform-independent program that computes maximum likelihood estimates for finite-mixture models, weighted linear regression-based analyses and coverage-based non-parametric methods, along with outlier diagnostics. Given sample ‘frequency count’ data, CatchAll computes 12 different diversity estimates and applies a model-selection algorithm. CatchAll also derives discounted diversity estimates to adjust for possibly uncertain low-frequency counts. It is accompanied by an Excel-based graphics program. Availability: Free executable downloads for Linux, Windows and Mac OS, with manual and source code, at www.northeastern.edu/catchall. Contact: jab18@cornell.edu PMID:22333246

Estimating the number of injecting drug users in Scotland's HCV-diagnosed population using capture-recapture methods.

PubMed

McDonald, S A; Hutchinson, S J; Schnier, C; McLeod, A; Goldberg, D J

2014-01-01

In countries maintaining national hepatitis C virus (HCV) surveillance systems, a substantial proportion of individuals report no risk factors for infection. Our goal was to estimate the proportion of diagnosed HCV antibody-positive persons in Scotland (1991-2010) who probably acquired infection through injecting drug use (IDU), by combining data on IDU risk from four linked data sources using log-linear capture-recapture methods. Of 25,521 HCV-diagnosed individuals, 14,836 (58%) reported IDU risk with their HCV diagnosis. Log-linear modelling estimated a further 2484 HCV-diagnosed individuals with IDU risk, giving an estimated prevalence of 83. Stratified analyses indicated variation across birth cohort, with estimated prevalence as low as 49% in persons born before 1960 and greater than 90% for those born since 1960. These findings provide public-health professionals with a more complete profile of Scotland's HCV-infected population in terms of transmission route, which is essential for targeting educational, prevention and treatment interventions.

Uncertainty Quantification Techniques for Population Density Estimates Derived from Sparse Open Source Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stewart, Robert N; White, Devin A; Urban, Marie L

2013-01-01

The Population Density Tables (PDT) project at the Oak Ridge National Laboratory (www.ornl.gov) is developing population density estimates for specific human activities under normal patterns of life based largely on information available in open source. Currently, activity based density estimates are based on simple summary data statistics such as range and mean. Researchers are interested in improving activity estimation and uncertainty quantification by adopting a Bayesian framework that considers both data and sociocultural knowledge. Under a Bayesian approach knowledge about population density may be encoded through the process of expert elicitation. Due to the scale of the PDT effort whichmore » considers over 250 countries, spans 40 human activity categories, and includes numerous contributors, an elicitation tool is required that can be operationalized within an enterprise data collection and reporting system. Such a method would ideally require that the contributor have minimal statistical knowledge, require minimal input by a statistician or facilitator, consider human difficulties in expressing qualitative knowledge in a quantitative setting, and provide methods by which the contributor can appraise whether their understanding and associated uncertainty was well captured. This paper introduces an algorithm that transforms answers to simple, non-statistical questions into a bivariate Gaussian distribution as the prior for the Beta distribution. Based on geometric properties of the Beta distribution parameter feasibility space and the bivariate Gaussian distribution, an automated method for encoding is developed that responds to these challenging enterprise requirements. Though created within the context of population density, this approach may be applicable to a wide array of problem domains requiring informative priors for the Beta distribution.« less

A review of population-based prevalence studies of physical activity in adults in the Asia-Pacific region

PubMed Central

2012-01-01

Background Physical activity (PA) surveillance is an important component of non-communicable disease risk factor monitoring, and occurs through national and international surveillance systems. This review identifies population PA estimates for adults in the Asia-Pacific region, and examines variation in trends and prevalence rates obtained using different PA measures. Methods Data were obtained from a MEDLINE search; World Health Organization's Global Health Infobase; Government websites and reference lists of relevant papers. Inclusion criteria included: national studies or those reporting large scale population-level data; data published from 2000 to 2010 and trend data prior; sample sizes over n = 1000, or fewer subjects in small nations. Results In total, 56 population surveys from 29 Asia-Pacific countries were identified. Data on 'sufficient physical activity' amongst adults were available from 45 studies (80%), with estimates ranging from 7% to 93% (median 62%, inter-quartile range 40%-85%). For 14 countries, estimates of 'sufficient activity' were documented in multiple surveys using different methods, with the largest variation from 18% to 92% in Nepal. Median or mean MET-minutes/day, reported in 20 studies, ranged from 6 to 1356. Serial trend data were available for 11 countries (22%), for periods spanning 2-10 years. Of these, five countries demonstrated increases in physical activity over time, four demonstrated decreases and three showed no changes. Conclusions Many countries in the Asia-Pacific region collect population-level PA data. This review highlights differences in estimates within and between countries. Some differences may be real, others due to variation in the PA questions asked and survey methods used. Use of standardized protocols and measures, and combined reporting of data are essential goals of improved international PA surveillance. PMID:22251660

Marine bird and sea otter population abundance of Prince william sound, Alaska: Trends following the t/v Exxon Valdez oil spill, 1989-93. Restoration project 93045. Exxon Valdez oil spill restoration project final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agler, B.A.; Seiser, P.E.; Kendall, S.J.

1994-05-01

We conducted small boat surveys to estimate marine bird and sea otter (Enhdra lutris) populations in Prince William Sound, Alaska during March and July 1993, using methods developed for the 1989-91 surveys (Klosiewski and Laing 1994). During 1993, we recorded 65 birds and 13 mammal species. We estimated that 402,760 + or - 167,697 marine birds were in the Sound during March 1993, an increase of >200,000 birds over 1990 and 1991. To examine trends in our marine bird population estimates from 1989-93, we assumed that in the absence of oil spill effects, population estimates in the oiled zone wouldmore » change at the same rate as those in the unoiled zone. For Prince William Sound as a whole, we examined population trends from 1989-1993, using regression analyses. We also examined the relative abundance of the species groups seen in Prince William Sound from 1972 to 1993. Sea otter populations in 1993 were estimated at 6,813 + or - 1,861 for March and 8,216 + or - 2,435 for July. We found no difference in the rate of change between the oiled and unoiled zones from 1989-93 for either the March or July population estimates. There was no significant trend in the total number of sea otters in Prince William Sound from 1989-93.« less

How many people in Canada use prescription opioids non-medically in general and street drug using populations?

PubMed

Popova, Svetlana; Patra, Jayadeep; Mohapatra, Satya; Fischer, Benedikt; Rehm, Jürgen

2009-01-01

Medical prescriptions for opioids as well as their non-medical use have increased in Canada in recent years. This study aimed to estimate the number of non-medical prescription opioid (PO) users in the general and street drug using populations in Canada. The number of non-medical PO users among the general population and the number of non-medical PO users, heroin users, or both among the street drug using population was estimated for Canada and for the most populous Canadian provinces. Different estimation methods were used: 1) the number of non-medical PO users in the Canadian general population was estimated based on Canadian availability data, and the ratio of US availability to non-medical PO use from US survey data; 2) numbers within the street drug using population were indirectly estimated based on overdose death data, and a key informants survey. Distribution and trends by usage of opioids were determined by using the multi-site Canadian OPICAN cohort data. Between 321,000 to 914,000 non-medical PO users were estimated to exist among the general population in Canada in 2003. The estimated number of non-medical PO users, heroin users, or both among the street drug using population was about 72,000, with more individuals using nonmedical PO than heroin in 2003. Based on data from the OPICAN survey, in 2005 the majority of the street drug using population in main Canadian cities was non-medical PO users, with the exception of Vancouver and Montreal. A relative increase of 24% was observed from 2002 to 2005 in the proportion of the street drug using population who used non-medical POs only. There is an urgent need to further assess the extent and patterns of non-medical prescription opioid use, related problems and drug distribution channels in Canada.

A New Population Estimate for the Florida Scrub Jay on Merritt Island National Wildlife Refuge

NASA Technical Reports Server (NTRS)

Breininger, David R.

1989-01-01

The variable circular plot method was used to sample avifauna within different vegetation types determined from aerial imagery. The Florida Scrub Jay (Aphelocoma coerulescens coerulescens) population was estimated to range between 1,415 and 3,603 birds. Approximately half of the scrub and slash pine habitat appeared to be unused by Florida Scrub Jay, probably because the slash pine cover was too dense or the oak cover was too sparse. Results from the study suggest that the entire state population may be much lower than believed because the size of two of the three largest populations may have been overestimated.

[Estimation with the capture-recapture method of the number of economic immigrants in Mallorca].

PubMed

Ramos Monserrat, M; March Cerdá, J C

2002-05-15

estimate the number of irregular economic immigrants in Mallorca. We used the capture-recapture method, an indirect method based on contrasts of data from two or more sources. Data were obtained from the Delegación de Gobierno (police and immigration authority), Comisiones Obreras (labor union), and institutions that provide health-related services to immigrants. Individuals were identified by birth date and country of origin. The total number of economic immigrants estimated with this method was 39 392. According to the Delegación de Gobierno data, the number of regular immigrants on the date of our inquiry was 9000. With the capture-recapture method, the number of irregular immigrants in Mallorca was therefore estimated at 30 000. The capture-recapture method can be useful to estimate the population of irregular immigrants in a given area at a given time, if sufficiently precise information on the identity of each individual can be obtained.

Differential Estimates of Southern Flying Squirrel (Glaucomys volans) Population Structure Based on Capture Method.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laves, Kevin S.; Loeb, Susan C.

2006-01-01

ABSTRACT.—It is commonly assumed that population estimates derived from trapping small mammals are accurate and unbiased or that estimates derived from different capture methods are comparable. We captured southern flying squirrels (Glaucomys volans) using two methods to study their effect on red-cockaded woodpecker (Picoides borealis) reproductive success. Southern flying squirrels were captured at and removed from 30 red-cockaded woodpecker cluster sites during March to July 1994 and 1995 using Sherman traps placed in a grid encompassing a red-cockaded woodpecker nest tree and by hand from red-cockaded woodpecker cavities. Totals of 195 (1994) and 190 (1995) red-cockaded woodpecker cavities were examinedmore » at least three times each year. Trappability of southern flying squirrels in Sherman traps was significantly greater in 1995 (1.18%; 22,384 trap nights) than in 1994 (0.42%; 20,384 trap nights), and capture rate of southern flying squirrels in cavities was significantly greater in 1994 (22.7%; 502 cavity inspections) than in 1995 (10.8%; 555 cavity inspections). However, more southern flying squirrels were captured per cavity inspection than per Sherman trap night in both years. Male southern flying squirrels were more likely to be captured from cavities than in Sherman traps in 1994, but not in 1995. Both male and female juveniles were more likely to be captured in cavities than in traps in both years. In 1994 males in reproductive condition were more likely to be captured in cavities than in traps and in 1995 we captured significantly more reproductive females in cavities than in traps. Our data suggest that population estimates based solely on one trapping method may not represent true population size or structure of southern flying squirrels.« less

[Progress on Individual Stature Estimation in Forensic Medicine].

PubMed

Wu, Rong-qi; Huang, Li-na; Chen, Xin

2015-12-01

Individual stature estimation is one of the most important contents of forensic anthropology. Currently, it has been used that the regression equations established by the data collected by direct measurement or radiological techniques in a certain group of limbs, irregular bones, and anatomic landmarks. Due to the impact of population mobility, human physical improvement, racial and geographic differences, estimation of individual stature should be a regular study. This paper reviews the different methods of stature estimation, briefly describes the advantages and disadvantages of each method, and prospects a new research direction.

Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

PubMed

Sawaya, Michael A; Stetz, Jeffrey B; Clevenger, Anthony P; Gibeau, Michael L; Kalinowski, Steven T

2012-01-01

We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008) and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17) and females (λ= 0.90, 95% CI = 0.67-1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains.

Estimating Grizzly and Black Bear Population Abundance and Trend in Banff National Park Using Noninvasive Genetic Sampling

PubMed Central

Sawaya, Michael A.; Stetz, Jeffrey B.; Clevenger, Anthony P.; Gibeau, Michael L.; Kalinowski, Steven T.

2012-01-01

We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears ( = 73.5, 95% CI = 64–94 in 2006;  = 50.4, 95% CI = 49–59 in 2008) and black bears ( = 62.6, 95% CI = 51–89 in 2006;  = 81.8, 95% CI = 72–102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males ( = 0.93, 95% CI = 0.74–1.17) and females ( = 0.90, 95% CI = 0.67–1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains. PMID:22567089

Population annealing with weighted averages: A Monte Carlo method for rough free-energy landscapes

NASA Astrophysics Data System (ADS)

Machta, J.

2010-08-01

The population annealing algorithm introduced by Hukushima and Iba is described. Population annealing combines simulated annealing and Boltzmann weighted differential reproduction within a population of replicas to sample equilibrium states. Population annealing gives direct access to the free energy. It is shown that unbiased measurements of observables can be obtained by weighted averages over many runs with weight factors related to the free-energy estimate from the run. Population annealing is well suited to parallelization and may be a useful alternative to parallel tempering for systems with rough free-energy landscapes such as spin glasses. The method is demonstrated for spin glasses.

A universal approximation to grain size from images of non-cohesive sediment

USGS Publications Warehouse

Buscombe, D.; Rubin, D.M.; Warrick, J.A.

2010-01-01

The two-dimensional spectral decomposition of an image of sediment provides a direct statistical estimate, grid-by-number style, of the mean of all intermediate axes of all single particles within the image. We develop and test this new method which, unlike existing techniques, requires neither image processing algorithms for detection and measurement of individual grains, nor calibration. The only information required of the operator is the spatial resolution of the image. The method is tested with images of bed sediment from nine different sedimentary environments (five beaches, three rivers, and one continental shelf), across the range 0.1 mm to 150 mm, taken in air and underwater. Each population was photographed using a different camera and lighting conditions. We term it a “universal approximation” because it has produced accurate estimates for all populations we have tested it with, without calibration. We use three approaches (theory, computational experiments, and physical experiments) to both understand and explore the sensitivities and limits of this new method. Based on 443 samples, the root-mean-squared (RMS) error between size estimates from the new method and known mean grain size (obtained from point counts on the image) was found to be ±≈16%, with a 95% probability of estimates within ±31% of the true mean grain size (measured in a linear scale). The RMS error reduces to ≈11%, with a 95% probability of estimates within ±20% of the true mean grain size if point counts from a few images are used to correct bias for a specific population of sediment images. It thus appears it is transferable between sedimentary populations with different grain size, but factors such as particle shape and packing may introduce bias which may need to be calibrated for. For the first time, an attempt has been made to mathematically relate the spatial distribution of pixel intensity within the image of sediment to the grain size.

A universal approximation of grain size from images of noncohesive sediment

NASA Astrophysics Data System (ADS)

Buscombe, D.; Rubin, D. M.; Warrick, J. A.

2010-06-01

The two-dimensional spectral decomposition of an image of sediment provides a direct statistical estimate, grid-by-number style, of the mean of all intermediate axes of all single particles within the image. We develop and test this new method which, unlike existing techniques, requires neither image processing algorithms for detection and measurement of individual grains, nor calibration. The only information required of the operator is the spatial resolution of the image. The method is tested with images of bed sediment from nine different sedimentary environments (five beaches, three rivers, and one continental shelf), across the range 0.1 mm to 150 mm, taken in air and underwater. Each population was photographed using a different camera and lighting conditions. We term it a "universal approximation" because it has produced accurate estimates for all populations we have tested it with, without calibration. We use three approaches (theory, computational experiments, and physical experiments) to both understand and explore the sensitivities and limits of this new method. Based on 443 samples, the root-mean-squared (RMS) error between size estimates from the new method and known mean grain size (obtained from point counts on the image) was found to be ±≈16%, with a 95% probability of estimates within ±31% of the true mean grain size (measured in a linear scale). The RMS error reduces to ≈11%, with a 95% probability of estimates within ±20% of the true mean grain size if point counts from a few images are used to correct bias for a specific population of sediment images. It thus appears it is transferable between sedimentary populations with different grain size, but factors such as particle shape and packing may introduce bias which may need to be calibrated for. For the first time, an attempt has been made to mathematically relate the spatial distribution of pixel intensity within the image of sediment to the grain size.

Adaptive kernel function using line transect sampling

NASA Astrophysics Data System (ADS)

Albadareen, Baker; Ismail, Noriszura

2018-04-01

The estimation of f(0) is crucial in the line transect method which is used for estimating population abundance in wildlife survey's. The classical kernel estimator of f(0) has a high negative bias. Our study proposes an adaptation in the kernel function which is shown to be more efficient than the usual kernel estimator. A simulation study is adopted to compare the performance of the proposed estimators with the classical kernel estimators.

Near-Earth-object survey progress and population of small near-Earth asteroids

NASA Astrophysics Data System (ADS)

Harris, A.

2014-07-01

Estimating the total population vs. size of NEAs and the completion of surveys is the same thing since the total population is just the number discovered divided by the estimated completion. I review the method of completion estimation based on ratio of re-detected objects to total detections (known plus new discoveries). The method is quite general and can be used for population estimations of all sorts, from wildlife to various classes of solar system bodies. Since 2001, I have been making estimates of population and survey progress approximately every two years. Plotted below, left, is my latest estimate, including NEA discoveries up to August, 2012. I plan to present an update at the meeting. All asteroids of a given size are not equally easy to detect because of specific orbital geometries. Thus a model of the orbital distribution is necessary, and computer simulations using those orbits need to establish the relation between the raw re-detection ratio and the actual completion fraction. This can be done for any sub-group population, allowing to estimate the population of a subgroup and the expected current completion. Once a reliable survey computer model has been developed and ''calibrated'' with respect to actual survey re-detections versus size, it can be extrapolated to smaller sizes to estimate completion even at very small size where re-detections are rare or even zero. I have recently investigated the subgroup of extremely low encounter velocity NEAs, the class of interest for the Asteroid Redirect Mission (ARM), recently proposed by NASA. I found that asteroids of diameter ˜ 10 m with encounter velocity with the Earth lower than 2.5 km/sec are detected by current surveys nearly 1,000 times more efficiently than the general background of NEAs of that size. Thus the current completion of these slow relative velocity objects may be around 1%, compared to 10^{-6} for that size objects of the general velocity distribution. Current surveys are nowhere near complete, but there may be fewer such objects than have been suggested. This conclusion is reinforced by the fact that at least a couple such discovered objects are known to be not real asteroids but spent rocket bodies in heliocentric orbit, of which there are only of the order of a hundred. Brown et al. (Nature 503, 238-241, 2013, below right, green squares are a re-plot of my blue circles on left plot) recently suggested that the population of small NEAs in the size range from roughly 5 to 50 meters in diameter may have been substantially under-estimated. To be sure, the greatest uncertainty in population estimates is in that range, since there are very few bolide events to use for estimation, and the surveys are extremely incomplete in that size range, so a factor of 3 or so discrepancy is not significant. However, the population estimated from surveys carried still smaller, where the bolide frequency becomes more secure, disagrees from the bolide estimate by even less than a factor of 3 and in fact intersects at about 3 m diameter. On the other hand, the shallow-sloping size-frequency distribution derived from the sparse large bolide data diverges badly from the survey estimates, in sizes where the survey estimates become ever-increasingly reliable, even by 100-200 m diameter. It appears that the bolide data provides a good "anchor" of the population in the size range up to about 5 m diameter, but above that one might do better just connecting that population with a straight line (on a log-log plot) with the survey-determined population at larger size, 50-100 m diameter or so.

Regional analysis of population trajectories from the North American Breeding Bird Survey

USGS Publications Warehouse

Sauer, J.R.; Link, W.A.; Helbig, Andreas J.; Flade, Martin

1999-01-01

The North American Breeding Bird Survey (BBS) was started in 1966, and provides information on population change and distribution for most of the birds in North America. The geographic extent of the survey, and the logistical compromises needed to survey such a large area, present many challenges for estimation from BBS data. In this paper, we describe the survey and discuss some of the limitations of the survey design and implementation. Analysis of the survey has evolved over time as new statistical methods and insights into the analysis of count data are developed. Survey results and analysis tools for the BBS are now available over intemet; we present new methods that use generalized linear models for estimation of population change and empirical Bayes procedures for regional summaries.

Spatially explicit population estimates for black bears based on cluster sampling

USGS Publications Warehouse

Humm, J.; McCown, J. Walter; Scheick, B.K.; Clark, Joseph D.

2017-01-01

We estimated abundance and density of the 5 major black bear (Ursus americanus) subpopulations (i.e., Eglin, Apalachicola, Osceola, Ocala-St. Johns, Big Cypress) in Florida, USA with spatially explicit capture-mark-recapture (SCR) by extracting DNA from hair samples collected at barbed-wire hair sampling sites. We employed a clustered sampling configuration with sampling sites arranged in 3 × 3 clusters spaced 2 km apart within each cluster and cluster centers spaced 16 km apart (center to center). We surveyed all 5 subpopulations encompassing 38,960 km2 during 2014 and 2015. Several landscape variables, most associated with forest cover, helped refine density estimates for the 5 subpopulations we sampled. Detection probabilities were affected by site-specific behavioral responses coupled with individual capture heterogeneity associated with sex. Model-averaged bear population estimates ranged from 120 (95% CI = 59–276) bears or a mean 0.025 bears/km2 (95% CI = 0.011–0.44) for the Eglin subpopulation to 1,198 bears (95% CI = 949–1,537) or 0.127 bears/km2 (95% CI = 0.101–0.163) for the Ocala-St. Johns subpopulation. The total population estimate for our 5 study areas was 3,916 bears (95% CI = 2,914–5,451). The clustered sampling method coupled with information on land cover was efficient and allowed us to estimate abundance across extensive areas that would not have been possible otherwise. Clustered sampling combined with spatially explicit capture-recapture methods has the potential to provide rigorous population estimates for a wide array of species that are extensive and heterogeneous in their distribution.

The applicability of dental wear in age estimation for a modern American population.

PubMed

Faillace, Katie E; Bethard, Jonathan D; Marks, Murray K

2017-12-01

Though applied in bioarchaeology, dental wear is an underexplored age indicator in the biological anthropology of contemporary populations, although research has been conducted on dental attrition in forensic contexts (Kim et al., , Journal of Forensic Sciences, 45, 303; Prince et al., , Journal of Forensic Sciences, 53, 588; Yun et al., , Journal of Forensic Sciences, 52, 678). The purpose of this study is to apply and adapt existing techniques for age estimation based on dental wear to a modern American population, with the aim of producing accurate age range estimates for individuals from an industrialized context. Methodologies following Yun and Prince were applied to a random sample from the University of New Mexico (n = 583) and Universidade de Coimbra (n = 50) cast and skeletal collections. Analysis of variance (ANOVA) and linear regression analyses were conducted to examine the relationship between tooth wear scores and age. Application of both Yun et al. () and Prince et al. () methodologies resulted in inaccurate age estimates. Recalibrated sectioning points correctly classified individuals as over or under 50 years for 88% of the sample. Linear regression demonstrated 60% of age estimates fell within ±10 years of the actual age, and accuracy improved for individuals under 45 years, with 74% of predictions within ±10 years. This study demonstrates age estimation from dental wear is possible for modern populations, with comparable age intervals to other established methods. It provides a quantifiable method of seriation into "older" and "younger" adult categories, and provides more reliable age interval estimates than cranial sutures in instances where only the skull is available. © 2017 Wiley Periodicals, Inc.

Estimating Brownian motion dispersal rate, longevity and population density from spatially explicit mark-recapture data on tropical butterflies.

PubMed

Tufto, Jarle; Lande, Russell; Ringsby, Thor-Harald; Engen, Steinar; Saether, Bernt-Erik; Walla, Thomas R; DeVries, Philip J

2012-07-01

1. We develop a Bayesian method for analysing mark-recapture data in continuous habitat using a model in which individuals movement paths are Brownian motions, life spans are exponentially distributed and capture events occur at given instants in time if individuals are within a certain attractive distance of the traps. 2. The joint posterior distribution of the dispersal rate, longevity, trap attraction distances and a number of latent variables representing the unobserved movement paths and time of death of all individuals is computed using Gibbs sampling. 3. An estimate of absolute local population density is obtained simply by dividing the Poisson counts of individuals captured at given points in time by the estimated total attraction area of all traps. Our approach for estimating population density in continuous habitat avoids the need to define an arbitrary effective trapping area that characterized previous mark-recapture methods in continuous habitat. 4. We applied our method to estimate spatial demography parameters in nine species of neotropical butterflies. Path analysis of interspecific variation in demographic parameters and mean wing length revealed a simple network of strong causation. Larger wing length increases dispersal rate, which in turn increases trap attraction distance. However, higher dispersal rate also decreases longevity, thus explaining the surprising observation of a negative correlation between wing length and longevity. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

A method for estimating Dekkera/Brettanomyces populations in wines.

PubMed

Benito, S; Palomero, F; Morata, A; Calderón, F; Suárez-Lepe, J A

2009-05-01

The formation of ethylphenols in wines, a consequence of Dekkera/Brettanomyces metabolism, can affect their quality. The main aims of this work were to further our knowledge of Dekkera/Brettanomyces with respect to ethylphenol production, and to develop a methodology for detecting this spoilage yeast and for estimating its population size in wines using differential-selective media and high performance liquid chromatography (HPLC). This work examines the reduction of p-coumaric acid and the formation of 4-vinylphenol and 4-ethylphenol (recorded by HPLC-DAD) in a prepared medium because of the activities of different yeast species and populations. A regression model was constructed for estimating the population of Dekkera/Brettanomyces at the beginning of fermentation via the conversion of hydroxycinnamic acids into ethylphenols. The proposed methodology allows the populations of Dekkera/Brettanomyces at the beginning of fermentation to be estimated in problem wines. Moreover, it avoids false positives because of yeasts resistant to the effects of the selective elements of the medium. This may help prevent the appearance of organoleptic anomalies in wines at the winery level.

Using Population-Size Estimation and Cross-sectional Survey Methods to Evaluate HIV Service Coverage Among Key Populations in Burkina Faso and Togo.

PubMed

Holland, Claire E; Kouanda, Seni; Lougué, Marcel; Pitche, Vincent Palokinam; Schwartz, Sheree; Anato, Simplice; Ouedraogo, Henri Gautier; Tchalla, Jules; Yah, Clarence S; Kapesa, Laurent; Ketende, Sosthenes; Beyrer, Chris; Baral, Stefan

2016-11-01

The objective of our study was to measure progress toward the UNAIDS 90-90-90 HIV care targets among key populations in urban areas of 2 countries in West Africa: Burkina Faso and Togo. We recruited female sex workers (FSWs) and men who have sex with men (MSM) through respondent-driven sampling. From January to July 2013, 2738 participants were enrolled, tested for HIV, and completed interviewer-administered surveys. We used population-size estimation methods to calculate the number of people who were engaged in the HIV continuum of care. HIV prevalence ranged from 0.6% (2 of 329) of MSM in Kara, Togo, to 32.9% (115 of 350) of FSWs in Bobo Dioulasso, Burkina Faso. Of those confirmed to be HIV infected, a range of 0.0% (0 of 2) of MSM in Kara to 55.7% (64 of 115) of FSWs in Bobo Dioulasso were using ART. Based on population estimates, the percentage gap between HIV-infected people who should be using ART (per the 90-90-90 targets) and those who reported using ART ranged from 31.5% among FSWs in Bobo Dioulasso to 100.0% among MSM in Kara. HIV service coverage among MSM and FSWs in Burkina Faso and Togo was low in 2013. Interventions for improving engagement of these at-risk populations in the HIV continuum of care should include frequent, routine HIV testing and linkage to evidence-based HIV treatment services. Population-size estimates can be used to inform governments, policy makers, and funding agencies about where elements of HIV service coverage are most needed.

Forest-dweller demographics in West Kalimantan, Indonesia.

PubMed

Fox, J; Atok, K

1997-03-01

This study sought to ascertain, from census and other data, the number of people living on state-claimed forest land (SCFL) in West Kalimantan in the outer islands of Indonesia. One aim was to determine why data collection is problematic. In 1990 the outer islands accounted for 38% of total population, 93% of its land mass, and 98% of its forests. 72% of the land mass of the outer islands was designated SCFL. Kalimantan has 38.5 million hectares of SCFL, while West Kalimantan has 9.2 million hectares, or 63% of the land area of the province. In 1990, 3.2 million people lived in West Kalimantan. Two sets of forest cover maps and census statistics at the village level were integrated into the geographic information system (GIS) technology by district and regency boundaries and the location of villages. The fieldwork was conducted in Sengah Temila District in Pontianak Regency and Simpang Hulu District in Ketapang Regency. Four methods were used to estimate forest populations: 1) estimating gross population density, 2) mapping forest villages, 3) adjusting density to account for uneven population distribution, and 4) estimating population densities for specific villages and generalizing to the province level. Methods 3 and 4 gave the most reasonable estimates. Population varied from 650,000 to 1 million. Government census statistics proved to be accurate representations of human population. The 1:50,000 scale of topological maps of West Kalimantan correctly identified the location of villages listed in the census. The Indonesian Ministry of Forestry's forest-planning maps and the RePPProT maps both reported similar SCFL. The GIS technology was useful in integrating data from several sources. The lack of knowledge was not due to political or institutional interests.

Simulation-Extrapolation for Estimating Means and Causal Effects with Mismeasured Covariates

ERIC Educational Resources Information Center

Lockwood, J. R.; McCaffrey, Daniel F.

2015-01-01

Regression, weighting and related approaches to estimating a population mean from a sample with nonrandom missing data often rely on the assumption that conditional on covariates, observed samples can be treated as random. Standard methods using this assumption generally will fail to yield consistent estimators when covariates are measured with…

What to Do about Zero Frequency Cells when Estimating Polychoric Correlations

ERIC Educational Resources Information Center

Savalei, Victoria

2011-01-01

Categorical structural equation modeling (SEM) methods that fit the model to estimated polychoric correlations have become popular in the social sciences. When population thresholds are high in absolute value, contingency tables in small samples are likely to contain zero frequency cells. Such cells make the estimation of the polychoric…

45 CFR 284.11 - What definitions apply to this part?

Code of Federal Regulations, 2010 CFR

2010-10-01

... METHODOLOGY FOR DETERMINING WHETHER AN INCREASE IN A STATE OR TERRITORY'S CHILD POVERTY RATE IS THE RESULT OF... estimating the number and percentage of children in poverty in each State. These methods may include national estimates based on the Current Population Survey; the Small Area Income and Poverty Estimates; the annual...

A comparison of turtle sampling methods in a small lake in Standing Stone State Park, Overton County, Tennessee

USGS Publications Warehouse

Weber, A.; Layzer, James B.

2011-01-01

We used basking traps and hoop nets to sample turtles in Standing Stone Lake at 2-week intervals from May to November 2006. In alternate weeks, we conducted visual basking surveys. We collected and observed four species of turtles: spiny softshell (Apalone spinifera), northern map turtle (Graptemys geographica), pond slider (Trachernys scripta), and snapping turtle (Chelydra serpentina). Relative abundances varied greatly among sampling methods. To varying degrees, all methods were species selective. Population estimates from mark and recaptures of three species, basking counts, and hoop net catches indicated that pond sliders were the most abundant species, but northern map turtles were 8× more abundant than pond sliders in basking trap catches. We saw relatively few snapping turtles basking even though population estimates indicated they were the second most abundant species. Populations of all species were dominated by adult individuals. Sex ratios of three species differed significantly from 1:1. Visual surveys were the most efficient method for determining the presence of species, but capture methods were necessary to obtain size and sex data.

Integration of manatee life-history data and population modeling

USGS Publications Warehouse

Eberhardt, L.L.; O'Shea, Thomas J.; O'Shea, Thomas J.; Ackerman, B.B.; Percival, H. Franklin

1995-01-01

Aerial counts and the number of deaths have been a major focus of attention in attempts to understand the population status of the Florida manatee (Trichechus manatus latirostris). Uncertainties associated with these data have made interpretation difficult. However, knowledge of manatee life-history attributes increased and now permits the development of a population model. We describe a provisional model based on the classical approach of Lotka. Parameters in the model are based on data from'other papers in this volume and draw primarily on observations from the Crystal River, Blue Spring, and Adantic Coast areas. The model estimates X (the finite rate ofincrease) at each study area, and application ofthe delta method provides estimates of variance components and partial derivatives ofX with respectto key input parameters (reproduction, adult survival, and early survival). In some study areas, only approximations of some parameters are available. Estimates of X and coefficients of variation (in parentheses) of manatees were 1.07 (0.009) in the Crystal River, 1.06 (0.012) at Blue Spring, and 1.01 (0.012) on the Atlantic Coast. Changing adult survival has a major effect on X. Early-age survival has the smallest effect. Bootstrap comparisons of population growth estimates from trend counts in the Crystal River and at Blue Spring and the reproduction and survival data suggest that the higher, observed rates from counts are probably not due to chance. Bootstrapping for variance estimates based on reproduction and survival data from manatees at Blue Spring and in the Crystal River provided estimates of X, adult survival, and rates of reproduction that were similar to those obtained by other methods. Our estimates are preliminary and suggestimprovements for future data collection and analysis. However, results support efforts to reduce mortality as the most effective means to promote the increased growth necessary for the eventual recovery of the Florida manatee population.

A comparison of small-area estimation techniques to estimate selected stand attributes using LiDAR-derived auxiliary variables

Treesearch

Michael E. Goerndt; Vicente J. Monleon; Hailemariam Temesgen

2011-01-01

One of the challenges often faced in forestry is the estimation of forest attributes for smaller areas of interest within a larger population. Small-area estimation (SAE) is a set of techniques well suited to estimation of forest attributes for small areas in which the existing sample size is small and auxiliary information is available. Selected SAE methods were...

[Diabetes mellitus in an adult population of the IMSS (Mexican Institute of Social Security). Results of the National Health Survey 2000].

PubMed

Vázquez-Martínez, José Luis; Gómez-Dantés, Héctor; Fernández-Cantón, Sonia

2006-01-01

To describe the prevalence and control of diabetes in the adult population served by the Instituto Mexicano del Seguro Social according to data from the National Health Survey 2000 (ENSA-2000). The data for adults from the National Health Survey 2000 was used to estimate and describe the prevalence of diabetes in the population that belongs to the social security system in Mexico. Criteria used to define diabetes mellitus were the medical diagnosis of the disease (MDDM) and the glucose measurement from capillary blood (>126 mg/dL fasting sample and 200 mg/dL in casual blood sample). If diabetes was confirmed only through blood sample, the diabetes case was define as survey finding (SF). Prevalences were estimated for both groups, while means and medians were estimated for the four possible combination groups (SF+, MDDM+, SF+, MDDM-, SF-, MDDM+, SF-, MDDM-). Sampling results were adjusted for population estimates according to the methods established in the ENSA-2000. Diabetes is described according to age, sex, education level, geographic region, background of diabetes in the family, body mass index (BMI), abdominal perimeter. A logistic regression method was used to estimate potential associations with different risk factors. Overall prevalence was 8.7%; for MDDM, it was 7.1%, and for SF, only 1.5%. Glycemia was highest in SF+ and MDDM-, median 292 mg/dL and in MDDM+ but SF-, median 289 mg/dL. Major risk factors were background of diabetes in both parents, abdominal obesity, low educational level age (coef. = 0.5943 per decade) and BMI (coef. = 0.0133). Diabetes in social security population is higher than in the rest of the population, while genetic background, age, educational level, high BMI and abdominal perimeter have important influences in diabetes prevalence in this population. Glucose control is suboptimal even in patients under medical supervision.

Can the prevalence of high blood drug concentrations in a population be estimated by analysing oral fluid? A study of tetrahydrocannabinol and amphetamine.

PubMed

Gjerde, Hallvard; Verstraete, Alain

2010-02-25

To study several methods for estimating the prevalence of high blood concentrations of tetrahydrocannabinol and amphetamine in a population of drug users by analysing oral fluid (saliva). Five methods were compared, including simple calculation procedures dividing the drug concentrations in oral fluid by average or median oral fluid/blood (OF/B) drug concentration ratios or linear regression coefficients, and more complex Monte Carlo simulations. Populations of 311 cannabis users and 197 amphetamine users from the Rosita-2 Project were studied. The results of a feasibility study suggested that the Monte Carlo simulations might give better accuracies than simple calculations if good data on OF/B ratios is available. If using only 20 randomly selected OF/B ratios, a Monte Carlo simulation gave the best accuracy but not the best precision. Dividing by the OF/B regression coefficient gave acceptable accuracy and precision, and was therefore the best method. None of the methods gave acceptable accuracy if the prevalence of high blood drug concentrations was less than 15%. Dividing the drug concentration in oral fluid by the OF/B regression coefficient gave an acceptable estimation of high blood drug concentrations in a population, and may therefore give valuable additional information on possible drug impairment, e.g. in roadside surveys of drugs and driving. If good data on the distribution of OF/B ratios are available, a Monte Carlo simulation may give better accuracy. 2009 Elsevier Ireland Ltd. All rights reserved.

Mourning dove population trend estimates from Call-Count and North American Breeding Bird Surveys

USGS Publications Warehouse

Sauer, J.R.; Dolton, D.D.; Droege, S.

1994-01-01

The mourning dove (Zenaida macroura) Callcount Survey and the North American Breeding Bird Survey provide information on population trends of mourning doves throughout the continental United States. Because surveys are an integral part of the development of hunting regulations, a need exists to determine which survey provides precise information. We estimated population trends from 1966 to 1988 by state and dove management unit, and assessed the relative efficiency of each survey. Estimates of population trend differ (P lt 0.05) between surveys in 11 of 48 states; 9 of 11 states with divergent results occur in the Eastern Management Unit. Differences were probably a consequence of smaller sample sizes in the Callcount Survey. The Breeding Bird Survey generally provided trend estimates with smaller variances than did the Callcount Survey. Although the Callcount Survey probably provides more withinroute accuracy because of survey methods and timing, the Breeding Bird Survey has a larger sample size of survey routes and greater consistency of coverage in the Eastern Unit.

Estimated collective effective dose to the population from nuclear medicine examinations in Slovenia

PubMed Central

Skrk, Damijan; Zontar, Dejan

2013-01-01

Background A national survey of patient exposure from nuclear medicine diagnostic procedures was performed by Slovenian Radiation Protection Administration in order to estimate their contribution to the collective effective dose to the population of Slovenia. Methods A set of 36 examinations with the highest contributions to the collective effective dose was identified. Data about frequencies and average administered activities of radioisotopes used for those examinations were collected from all nuclear medicine departments in Slovenia. A collective effective dose to the population and an effective dose per capita were estimated from the collected data using dose conversion factors. Results The total collective effective dose to the population from nuclear medicine diagnostic procedures in 2011 was estimated to 102 manSv, giving an effective dose per capita of 0.05 mSv. Conclusions The comparison of results of this study with studies performed in other countries indicates that the nuclear medicine providers in Slovenia are well aware of the importance of patient protection measures and of optimisation of procedures. PMID:24133396

A method for estimating 2D Wrinkle Ridge Strain from application of fault displacement scaling to the Yakima Folds, Washington

NASA Astrophysics Data System (ADS)

Mège, Daniel; Reidel, Stephen P.

The Yakima folds on the central Columbia Plateau are a succession of thrusted anticlines thought to be analogs of planetary wrinkle ridges. They provide a unique opportunity to understand wrinkle ridge structure. Field data and length-displacement scaling are used to demonstrate a method for estimating two-dimensional horizontal contractional strain at wrinkle ridges. Strain is given as a function of ridge length, and depends on other parameters that can be inferred from the Yakima folds and fault population displacement studies. Because ridge length can be readily obtained from orbital imagery, the method can be applied to any wrinkle ridge population, and helps constrain quantitative tectonic models on other planets.

Estimation of Standard Error of Regression Effects in Latent Regression Models Using Binder's Linearization. Research Report. ETS RR-07-09

ERIC Educational Resources Information Center

Li, Deping; Oranje, Andreas

2007-01-01

Two versions of a general method for approximating standard error of regression effect estimates within an IRT-based latent regression model are compared. The general method is based on Binder's (1983) approach, accounting for complex samples and finite populations by Taylor series linearization. In contrast, the current National Assessment of…

Sampling methods to detect and estimate populations of Tyrophagus putrescentiae (Schrank) (Sarcoptiformes: Acaridae) infesting dry-cured hams

USDA-ARS?s Scientific Manuscript database

Spatial and temporal dynamics of pest populations is an important aspect of effective pest management. However, absolute sampling of some pest populations such as the ham mite, Tyrophagus putrescentiae (Schrank) (Sarcoptiformes: Acaridae), a serious pest of dry-cured ham, can be difficult. Sampling ...

Estimating changes in urban land and urban population using refined areal interpolation techniques

NASA Astrophysics Data System (ADS)

Zoraghein, Hamidreza; Leyk, Stefan

2018-05-01

The analysis of changes in urban land and population is important because the majority of future population growth will take place in urban areas. U.S. Census historically classifies urban land using population density and various land-use criteria. This study analyzes the reliability of census-defined urban lands for delineating the spatial distribution of urban population and estimating its changes over time. To overcome the problem of incompatible enumeration units between censuses, regular areal interpolation methods including Areal Weighting (AW) and Target Density Weighting (TDW), with and without spatial refinement, are implemented. The goal in this study is to estimate urban population in Massachusetts in 1990 and 2000 (source zones), within tract boundaries of the 2010 census (target zones), respectively, to create a consistent time series of comparable urban population estimates from 1990 to 2010. Spatial refinement is done using ancillary variables such as census-defined urban areas, the National Land Cover Database (NLCD) and the Global Human Settlement Layer (GHSL) as well as different combinations of them. The study results suggest that census-defined urban areas alone are not necessarily the most meaningful delineation of urban land. Instead, it appears that alternative combinations of the above-mentioned ancillary variables can better depict the spatial distribution of urban land, and thus make it possible to reduce the estimation error in transferring the urban population from source zones to target zones when running spatially-refined temporal areal interpolation.

Changing Urbania: Estimating Changes in Urban Land and Urban Population Using Refined Areal Interpolation Techniques

NASA Astrophysics Data System (ADS)

Zoraghein, H.; Leyk, S.; Balk, D.

2017-12-01

The analysis of changes in urban land and population is important because the majority of future population growth will take place in urban areas. The U.S. Census historically classifies urban land using population density and various land-use criteria. This study analyzes the reliability of census-defined urban lands for delineating the spatial distribution of urban population and estimating its changes over time. To overcome the problem of incompatible enumeration units between censuses, regular areal interpolation methods including Areal Weighting (AW) and Target Density Weighting (TDW), with and without spatial refinement, are implemented. The goal in this study is to estimate urban population in Massachusetts in 1990 and 2000 (source zones), within tract boundaries of the 2010 census (target zones), respectively, to create a consistent time series of comparable urban population estimates from 1990 to 2010. Spatial refinement is done using ancillary variables such as census-defined urban areas, the National Land Cover Database (NLCD) and the Global Human Settlement Layer (GHSL) as well as different combinations of them. The study results suggest that census-defined urban areas alone are not necessarily the most meaningful delineation of urban land. Instead it appears that alternative combinations of the above-mentioned ancillary variables can better depict the spatial distribution of urban land, and thus make it possible to reduce the estimation error in transferring the urban population from source zones to target zones when running spatially-refined temporal areal interpolation.

Incorporating precision, accuracy and alternative sampling designs into a continental monitoring program for colonial waterbirds

USGS Publications Warehouse

Steinkamp, Melanie J.; Peterjohn, B.G.; Keisman, J.L.

2003-01-01

A comprehensive monitoring program for colonial waterbirds in North America has never existed. At smaller geographic scales, many states and provinces conduct surveys of colonial waterbird populations. Periodic regional surveys are conducted at varying times during the breeding season using a variety of survey methods, which complicates attempts to estimate population trends for most species. The US Geological Survey Patuxent Wildlife Research Center has recently started to coordinate colonial waterbird monitoring efforts throughout North America. A centralized database has been developed with an Internet-based data entry and retrieval page. The extent of existing colonial waterbird surveys has been defined, allowing gaps in coverage to be identified and basic inventories completed where desirable. To enable analyses of comparable data at regional or larger geographic scales, sampling populations through statistically sound sampling designs should supersede obtaining counts at every colony. Standardized breeding season survey techniques have been agreed upon and documented in a monitoring manual. Each survey in the manual has associated with it recommendations for bias estimation, and includes specific instructions on measuring detectability. The methods proposed in the manual are for developing reliable, comparable indices of population size to establish trend information at multiple spatial and temporal scales, but they will not result in robust estimates of total population numbers.

A new approach to estimate parameters of speciation models with application to apes.

PubMed

Becquet, Celine; Przeworski, Molly

2007-10-01

How populations diverge and give rise to distinct species remains a fundamental question in evolutionary biology, with important implications for a wide range of fields, from conservation genetics to human evolution. A promising approach is to estimate parameters of simple speciation models using polymorphism data from multiple loci. Existing methods, however, make a number of assumptions that severely limit their applicability, notably, no gene flow after the populations split and no intralocus recombination. To overcome these limitations, we developed a new Markov chain Monte Carlo method to estimate parameters of an isolation-migration model. The approach uses summaries of polymorphism data at multiple loci surveyed in a pair of diverging populations or closely related species and, importantly, allows for intralocus recombination. To illustrate its potential, we applied it to extensive polymorphism data from populations and species of apes, whose demographic histories are largely unknown. The isolation-migration model appears to provide a reasonable fit to the data. It suggests that the two chimpanzee species became reproductively isolated in allopatry approximately 850 Kya, while Western and Central chimpanzee populations split approximately 440 Kya but continued to exchange migrants. Similarly, Eastern and Western gorillas and Sumatran and Bornean orangutans appear to have experienced gene flow since their splits approximately 90 and over 250 Kya, respectively.

More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure.

PubMed

Stone, Anne C; Battistuzzi, Fabia U; Kubatko, Laura S; Perry, George H; Trudeau, Evan; Lin, Hsiuman; Kumar, Sudhir

2010-10-27

Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees (Pan troglodytes) from each of the three established subspecies (P. t. troglodytes, P. t. schweinfurthii and P. t. verus) and the proposed fourth subspecies (P. t. ellioti). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human-chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1-1.5, 1.1-0.76 and 0.25-0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.

Indicator Species Population Monitoring in Antarctica with Uav

NASA Astrophysics Data System (ADS)

Zmarz, A.; Korczak-Abshire, M.; Storvold, R.; Rodzewicz, M.; Kędzierska, I.

2015-08-01

A program to monitor bird and pinniped species in the vicinity of Arctowski Station, King George Island, South Shetlands, Antarctica, has been conducted over the past 38 years. Annual monitoring of these indicator species includes estimations of breeding population sizes of three Pygoscelis penguin species: Adélie, gentoo and chinstrap. Six penguin colonies situated on the western shores of two bays: Admiralty and King George are investigated. To study changes in penguin populations Unmanned Aerial Vehicles were used for the first time in the 2014/15 austral summer season. During photogrammetric flights the high-resolution images of eight penguin breeding colonies were taken. Obtained high resolution images were used for estimation of breeding population size and compared with the results of measurements taken at the same time from the ground. During this Antarctic expedition eight successful photogrammetry missions (total distance 1500 km) were performed. Images were taken with digital SLR Canon 700D, Nikon D5300, Nikon D5100 with a 35mm objective lens. Flights altitude at 350 - 400 AGL, allowed images to be taken with a resolution GSD (ground sample distance) less than 5 cm. The Image J software analysis method was tested to provide automatic population estimates from obtained images. The use of UAV for monitoring of indicator species, enabled data acquisition from areas inaccessible by ground methods.

Estimating abundance

USGS Publications Warehouse

Sutherland, Chris; Royle, Andy

2016-01-01

This chapter provides a non-technical overview of ‘closed population capture–recapture’ models, a class of well-established models that are widely applied in ecology, such as removal sampling, covariate models, and distance sampling. These methods are regularly adopted for studies of reptiles, in order to estimate abundance from counts of marked individuals while accounting for imperfect detection. Thus, the chapter describes some classic closed population models for estimating abundance, with considerations for some recent extensions that provide a spatial context for the estimation of abundance, and therefore density. Finally, the chapter suggests some software for use in data analysis, such as the Windows-based program MARK, and provides an example of estimating abundance and density of reptiles using an artificial cover object survey of Slow Worms (Anguis fragilis).

Estimating abundance: Chapter 27

USGS Publications Warehouse

Royle, J. Andrew

2016-01-01

This chapter provides a non-technical overview of ‘closed population capture–recapture’ models, a class of well-established models that are widely applied in ecology, such as removal sampling, covariate models, and distance sampling. These methods are regularly adopted for studies of reptiles, in order to estimate abundance from counts of marked individuals while accounting for imperfect detection. Thus, the chapter describes some classic closed population models for estimating abundance, with considerations for some recent extensions that provide a spatial context for the estimation of abundance, and therefore density. Finally, the chapter suggests some software for use in data analysis, such as the Windows-based program MARK, and provides an example of estimating abundance and density of reptiles using an artificial cover object survey of Slow Worms (Anguis fragilis).

Assessing tiger population dynamics using photographic capture-recapture sampling

USGS Publications Warehouse

Karanth, K.U.; Nichols, J.D.; Kumar, N.S.; Hines, J.E.

2006-01-01

Although wide-ranging, elusive, large carnivore species, such as the tiger, are of scientific and conservation interest, rigorous inferences about their population dynamics are scarce because of methodological problems of sampling populations at the required spatial and temporal scales. We report the application of a rigorous, noninvasive method for assessing tiger population dynamics to test model-based predictions about population viability. We obtained photographic capture histories for 74 individual tigers during a nine-year study involving 5725 trap-nights of effort. These data were modeled under a likelihood-based, ?robust design? capture?recapture analytic framework. We explicitly modeled and estimated ecological parameters such as time-specific abundance, density, survival, recruitment, temporary emigration, and transience, using models that incorporated effects of factors such as individual heterogeneity, trap-response, and time on probabilities of photo-capturing tigers. The model estimated a random temporary emigration parameter of =K' =Y' 0.10 ? 0.069 (values are estimated mean ? SE). When scaled to an annual basis, tiger survival rates were estimated at S = 0.77 ? 0.051, and the estimated probability that a newly caught animal was a transient was = 0.18 ? 0.11. During the period when the sampled area was of constant size, the estimated population size Nt varied from 17 ? 1.7 to 31 ? 2.1 tigers, with a geometric mean rate of annual population change estimated as = 1.03 ? 0.020, representing a 3% annual increase. The estimated recruitment of new animals, Bt, varied from 0 ? 3.0 to 14 ? 2.9 tigers. Population density estimates, D, ranged from 7.33 ? 0.8 tigers/100 km2 to 21.73 ? 1.7 tigers/100 km2 during the study. Thus, despite substantial annual losses and temporal variation in recruitment, the tiger density remained at relatively high levels in Nagarahole. Our results are consistent with the hypothesis that protected wild tiger populations can remain healthy despite heavy mortalities because of their inherently high reproductive potential. The ability to model the entire photographic capture history data set and incorporate reduced-parameter models led to estimates of mean annual population change that were sufficiently precise to be useful. This efficient, noninvasive sampling approach can be used to rigorously investigate the population dynamics of tigers and other elusive, rare, wide-ranging animal species in which individuals can be identified from photographs or other means.

Assessing tiger population dynamics using photographic capture-recapture sampling.

PubMed

Karanth, K Ullas; Nichols, James D; Kumar, N Samba; Hines, James E

2006-11-01

Although wide-ranging, elusive, large carnivore species, such as the tiger, are of scientific and conservation interest, rigorous inferences about their population dynamics are scarce because of methodological problems of sampling populations at the required spatial and temporal scales. We report the application of a rigorous, noninvasive method for assessing tiger population dynamics to test model-based predictions about population viability. We obtained photographic capture histories for 74 individual tigers during a nine-year study involving 5725 trap-nights of effort. These data were modeled under a likelihood-based, "robust design" capture-recapture analytic framework. We explicitly modeled and estimated ecological parameters such as time-specific abundance, density, survival, recruitment, temporary emigration, and transience, using models that incorporated effects of factors such as individual heterogeneity, trap-response, and time on probabilities of photo-capturing tigers. The model estimated a random temporary emigration parameter of gamma" = gamma' = 0.10 +/- 0.069 (values are estimated mean +/- SE). When scaled to an annual basis, tiger survival rates were estimated at S = 0.77 +/- 0.051, and the estimated probability that a newly caught animal was a transient was tau = 0.18 +/- 0.11. During the period when the sampled area was of constant size, the estimated population size N(t) varied from 17 +/- 1.7 to 31 +/- 2.1 tigers, with a geometric mean rate of annual population change estimated as lambda = 1.03 +/- 0.020, representing a 3% annual increase. The estimated recruitment of new animals, B(t), varied from 0 +/- 3.0 to 14 +/- 2.9 tigers. Population density estimates, D, ranged from 7.33 +/- 0.8 tigers/100 km2 to 21.73 +/- 1.7 tigers/100 km2 during the study. Thus, despite substantial annual losses and temporal variation in recruitment, the tiger density remained at relatively high levels in Nagarahole. Our results are consistent with the hypothesis that protected wild tiger populations can remain healthy despite heavy mortalities because of their inherently high reproductive potential. The ability to model the entire photographic capture history data set and incorporate reduced-parameter models led to estimates of mean annual population change that were sufficiently precise to be useful. This efficient, noninvasive sampling approach can be used to rigorously investigate the population dynamics of tigers and other elusive, rare, wide-ranging animal species in which individuals can be identified from photographs or other means.

Density and population estimate of gibbons (Hylobates albibarbis) in the Sabangau catchment, Central Kalimantan, Indonesia.

PubMed

Cheyne, Susan M; Thompson, Claire J H; Phillips, Abigail C; Hill, Robyn M C; Limin, Suwido H

2008-01-01

We demonstrate that although auditory sampling is a useful tool, this method alone will not provide a truly accurate indication of population size, density and distribution of gibbons in an area. If auditory sampling alone is employed, we show that data collection must take place over a sufficient period to account for variation in calling patterns across seasons. The population of Hylobates albibarbis in the Sabangau catchment, Central Kalimantan, Indonesia, was surveyed from July to December 2005 using methods established previously. In addition, auditory sampling was complemented by detailed behavioural data on six habituated groups within the study area. Here we compare results from this study to those of a 1-month study conducted in 2004. The total population of the Sabangau catchment is estimated to be about in the tens of thousands, though numbers, distribution and density for the different forest subtypes vary considerably. We propose that future density surveys of gibbons must include data from all forest subtypes where gibbons are found and that extrapolating from one forest subtype is likely to yield inaccurate density and population estimates. We also propose that auditory census be carried out by using at least three listening posts (LP) in order to increase the area sampled and the chances of hearing groups. Our results suggest that the Sabangau catchment contains one of the largest remaining contiguous populations of Bornean agile gibbon.

Population subdivision and molecular sequence variation: theory and analysis of Drosophila ananassae data.

PubMed

Vogl, Claus; Das, Aparup; Beaumont, Mark; Mohanty, Sujata; Stephan, Wolfgang

2003-11-01

Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter Theta to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of Theta, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

Density dependence and climate effects in Rocky Mountain elk: an application of regression with instrumental variables for population time series with sampling error.

PubMed

Creel, Scott; Creel, Michael

2009-11-01

1. Sampling error in annual estimates of population size creates two widely recognized problems for the analysis of population growth. First, if sampling error is mistakenly treated as process error, one obtains inflated estimates of the variation in true population trajectories (Staples, Taper & Dennis 2004). Second, treating sampling error as process error is thought to overestimate the importance of density dependence in population growth (Viljugrein et al. 2005; Dennis et al. 2006). 2. In ecology, state-space models are used to account for sampling error when estimating the effects of density and other variables on population growth (Staples et al. 2004; Dennis et al. 2006). In econometrics, regression with instrumental variables is a well-established method that addresses the problem of correlation between regressors and the error term, but requires fewer assumptions than state-space models (Davidson & MacKinnon 1993; Cameron & Trivedi 2005). 3. We used instrumental variables to account for sampling error and fit a generalized linear model to 472 annual observations of population size for 35 Elk Management Units in Montana, from 1928 to 2004. We compared this model with state-space models fit with the likelihood function of Dennis et al. (2006). We discuss the general advantages and disadvantages of each method. Briefly, regression with instrumental variables is valid with fewer distributional assumptions, but state-space models are more efficient when their distributional assumptions are met. 4. Both methods found that population growth was negatively related to population density and winter snow accumulation. Summer rainfall and wolf (Canis lupus) presence had much weaker effects on elk (Cervus elaphus) dynamics [though limitation by wolves is strong in some elk populations with well-established wolf populations (Creel et al. 2007; Creel & Christianson 2008)]. 5. Coupled with predictions for Montana from global and regional climate models, our results predict a substantial reduction in the limiting effect of snow accumulation on Montana elk populations in the coming decades. If other limiting factors do not operate with greater force, population growth rates would increase substantially.

Grizzly bear density in Glacier National Park, Montana

USGS Publications Warehouse

Kendall, K.C.; Stetz, J.B.; Roon, David A.; Waits, L.P.; Boulanger, J.B.; Paetkau, David

2008-01-01

We present the first rigorous estimate of grizzly bear (Ursus arctos) population density and distribution in and around Glacier National Park (GNP), Montana, USA. We used genetic analysis to identify individual bears from hair samples collected via 2 concurrent sampling methods: 1) systematically distributed, baited, barbed-wire hair traps and 2) unbaited bear rub trees found along trails. We used Huggins closed mixture models in Program MARK to estimate total population size and developed a method to account for heterogeneity caused by unequal access to rub trees. We corrected our estimate for lack of geographic closure using a new method that utilizes information from radiocollared bears and the distribution of bears captured with DNA sampling. Adjusted for closure, the average number of grizzly bears in our study area was 240.7 (95% CI = 202–303) in 1998 and 240.6 (95% CI = 205–304) in 2000. Average grizzly bear density was 30 bears/1,000 km2, with 2.4 times more bears detected per hair trap inside than outside GNP. We provide baseline information important for managing one of the few remaining populations of grizzlies in the contiguous United States.

Population trends from the North American Breeding Bird Survey

USGS Publications Warehouse

Peterjohn, B.G.; Sauer, J.R.; Robbins, C.S.; Martin, Thomas E.; Finch, Deborah M.

1995-01-01

INTRODUCTION: Most Neotropical migrant birds are difficult to count accurately and are moderately common over large breeding distributions. Consequently, little historical information exists on their large-scale population changes, and most of this information is anecdotal. Surveys begun in this century such as Breeding Bird Censuses and Christmas Bird Counts have the potential to provide this information, but only the North American Breeding Bird Survey (BBS) achieves the extensive continental coverage necessary to document population changes for most Neotropical migrant birds. Conservationists and ecologists have begun to use BBS data to estimate population trends, but there is still widespread confusion over exactly what these data show regarding population changes. In this chapter, we review the current state of knowledge regarding population changes in Neotropical migrant birds and the methods used to analyze these changes. The primary emphasis is on the BBS (Robbins et al. 1986) because this survey provides the best available data for estimating trends of Neotropical migrants on a continental scale. To address questions about methods of analyzing survey data, we review and compare some alternative methods of analyzing BBS data. We also discuss the effectiveness of the BBS in sampling Neotropical migrant species, and review possibilities for use of alternative data sets to verify trends from the BBS.

Longevity of clonal plants: why it matters and how to measure it

PubMed Central

de Witte, Lucienne C.; Stöcklin, Jürg

2010-01-01

Background Species' life-history and population dynamics are strongly shaped by the longevity of individuals, but life span is one of the least accessible demographic traits, particularly in clonal plants. Continuous vegetative reproduction of genets enables persistence despite low or no sexual reproduction, affecting genet turnover rates and population stability. Therefore, the longevity of clonal plants is of considerable biological interest, but remains relatively poorly known. Scope Here, we critically review the present knowledge on the longevity of clonal plants and discuss its importance for population persistence. Direct life-span measurements such as growth-ring analysis in woody plants are relatively easy to take, although, for many clonal plants, these methods are not adequate due to the variable growth pattern of ramets and difficult genet identification. Recently, indirect methods have been introduced in which genet size and annual shoot increments are used to estimate genet age. These methods, often based on molecular techniques, allow the investigation of genet size and age structure of whole populations, a crucial issue for understanding their viability and persistence. However, indirect estimates of clonal longevity are impeded because the process of ageing in clonal plants is still poorly understood and because their size and age are not always well correlated. Alternative estimators for genet life span such as somatic mutations have recently been suggested. Conclusions Empirical knowledge on the longevity of clonal species has increased considerably in the last few years. Maximum age estimates are an indicator of population persistence, but are not sufficient to evaluate turnover rates and the ability of long-lived clonal plants to enhance community stability and ecosystem resilience. In order to understand the dynamics of populations it will be necessary to measure genet size and age structure, not only life spans of single individuals, and to use such data for modelling of genet dynamics. PMID:20880935

Application of AN Empirically Scaled Digital Echo Integrator for Assessment of Juvenile Sockeye Salmon (oncorhynchus Nerka Walbaum) Populations.

NASA Astrophysics Data System (ADS)

Nunnallee, Edmund Pierce, Jr.

1980-03-01

This dissertation consists of an investigation into the empirical scaling of a digital echo integrator for assessment of a population of juvenile sockeye salmon in Cultus Lake, British Columbia, Canada. The scaling technique was developed over the last ten years for use with totally uncalibrated but stabilized data collection and analysis equipment, and has been applied to populations of fish over a wide geographical range. This is the first investigation into the sources of bias and the accuracy of the technique, however, and constitutes a verification of the method. The initial section of the investigation describes hydroacoustic data analysis methods for estimation of effective sampling volume which is necessary for estimation of fish density. The second section consists of a computer simulation of effective sample volume estimation by this empirical method and is used to investigate the degree of bias introduced by electronic and physical parameters such as boat speed -fish depth interaction effects, electronic thresholding and saturation, transducer beam angle, fish depth stratification by size and spread of the target strength distribution of the fish. Comparisons of simulation predictions of sample volume estimation bias to actual survey results are given at the end of this section. A verification of the scaling method is then presented by comparison of a hydroacoustically derived estimation of the Cultus Lake smolt population to an independent and concurrent estimate made by counting the migrant fish as they passed through a weir in the outlet stream of the lake. Finally, the effect on conduct and accuracy of hydroacoustic assessment of juvenile sockeye salmon due to several behavioral traits are discussed. These traits include movements of presmolt fish in a lake just prior to their outmigration, daily vertical migrations and the emergence and dispersal of sockeye fry in Cultus Lake. In addition, a comparison of the summer depth preferences of the fish over their entire geographical distribution on the west coast of the U.S. and Canada are discussed in terms of hydroacoustic accessibility.

Estimating disease prevalence from two-phase surveys with non-response at the second phase

PubMed Central

Gao, Sujuan; Hui, Siu L.; Hall, Kathleen S.; Hendrie, Hugh C.

2010-01-01

SUMMARY In this paper we compare several methods for estimating population disease prevalence from data collected by two-phase sampling when there is non-response at the second phase. The traditional weighting type estimator requires the missing completely at random assumption and may yield biased estimates if the assumption does not hold. We review two approaches and propose one new approach to adjust for non-response assuming that the non-response depends on a set of covariates collected at the first phase: an adjusted weighting type estimator using estimated response probability from a response model; a modelling type estimator using predicted disease probability from a disease model; and a regression type estimator combining the adjusted weighting type estimator and the modelling type estimator. These estimators are illustrated using data from an Alzheimer’s disease study in two populations. Simulation results are presented to investigate the performances of the proposed estimators under various situations. PMID:10931514

Effective sociodemographic population assessment of elusive species in ecology and conservation management.

PubMed

Head, Josephine S; Boesch, Christophe; Robbins, Martha M; Rabanal, Luisa I; Makaga, Loïc; Kühl, Hjalmar S

2013-09-01

Wildlife managers are urgently searching for improved sociodemographic population assessment methods to evaluate the effectiveness of implemented conservation activities. These need to be inexpensive, appropriate for a wide spectrum of species and straightforward to apply by local staff members with minimal training. Furthermore, conservation management would benefit from single approaches which cover many aspects of population assessment beyond only density estimates, to include for instance social and demographic structure, movement patterns, or species interactions. Remote camera traps have traditionally been used to measure species richness. Currently, there is a rapid move toward using remote camera trapping in density estimation, community ecology, and conservation management. Here, we demonstrate such comprehensive population assessment by linking remote video trapping, spatially explicit capture-recapture (SECR) techniques, and other methods. We apply it to three species: chimpanzees Pan troglodytes troglodytes, gorillas Gorilla gorilla gorilla, and forest elephants Loxodonta cyclotis in Loango National Park, Gabon. All three species exhibited considerable heterogeneity in capture probability at the sex or group level and density was estimated at 1.72, 1.2, and 1.37 individuals per km(2) and male to female sex ratios were 1:2.1, 1:3.2, and 1:2 for chimpanzees, gorillas, and elephants, respectively. Association patterns revealed four, eight, and 18 independent social groups of chimpanzees, gorillas, and elephants, respectively: key information for both conservation management and studies on the species' ecology. Additionally, there was evidence of resident and nonresident elephants within the study area and intersexual variation in home range size among elephants but not chimpanzees. Our study highlights the potential of combining camera trapping and SECR methods in conducting detailed population assessments that go far beyond documenting species diversity patterns or estimating single species population size. Our study design is widely applicable to other species and spatial scales, and moderately trained staff members can collect and process the required data. Furthermore, assessments using the same method can be extended to include several other ecological, behavioral, and demographic aspects: fission and fusion dynamics and intergroup transfers, birth and mortality rates, species interactions, and ranging patterns.

Effective sociodemographic population assessment of elusive species in ecology and conservation management

PubMed Central

Head, Josephine S; Boesch, Christophe; Robbins, Martha M; Rabanal, Luisa I; Makaga, Loïc; Kühl, Hjalmar S

2013-01-01

Wildlife managers are urgently searching for improved sociodemographic population assessment methods to evaluate the effectiveness of implemented conservation activities. These need to be inexpensive, appropriate for a wide spectrum of species and straightforward to apply by local staff members with minimal training. Furthermore, conservation management would benefit from single approaches which cover many aspects of population assessment beyond only density estimates, to include for instance social and demographic structure, movement patterns, or species interactions. Remote camera traps have traditionally been used to measure species richness. Currently, there is a rapid move toward using remote camera trapping in density estimation, community ecology, and conservation management. Here, we demonstrate such comprehensive population assessment by linking remote video trapping, spatially explicit capture–recapture (SECR) techniques, and other methods. We apply it to three species: chimpanzees Pan troglodytes troglodytes, gorillas Gorilla gorilla gorilla, and forest elephants Loxodonta cyclotis in Loango National Park, Gabon. All three species exhibited considerable heterogeneity in capture probability at the sex or group level and density was estimated at 1.72, 1.2, and 1.37 individuals per km2 and male to female sex ratios were 1:2.1, 1:3.2, and 1:2 for chimpanzees, gorillas, and elephants, respectively. Association patterns revealed four, eight, and 18 independent social groups of chimpanzees, gorillas, and elephants, respectively: key information for both conservation management and studies on the species' ecology. Additionally, there was evidence of resident and nonresident elephants within the study area and intersexual variation in home range size among elephants but not chimpanzees. Our study highlights the potential of combining camera trapping and SECR methods in conducting detailed population assessments that go far beyond documenting species diversity patterns or estimating single species population size. Our study design is widely applicable to other species and spatial scales, and moderately trained staff members can collect and process the required data. Furthermore, assessments using the same method can be extended to include several other ecological, behavioral, and demographic aspects: fission and fusion dynamics and intergroup transfers, birth and mortality rates, species interactions, and ranging patterns. PMID:24101982

A Methodological Approach to Small Area Estimation for the Behavioral Risk Factor Surveillance System

PubMed Central

Xu, Fang; Wallace, Robyn C.; Garvin, William; Greenlund, Kurt J.; Bartoli, William; Ford, Derek; Eke, Paul; Town, G. Machell

2016-01-01

Public health researchers have used a class of statistical methods to calculate prevalence estimates for small geographic areas with few direct observations. Many researchers have used Behavioral Risk Factor Surveillance System (BRFSS) data as a basis for their models. The aims of this study were to 1) describe a new BRFSS small area estimation (SAE) method and 2) investigate the internal and external validity of the BRFSS SAEs it produced. The BRFSS SAE method uses 4 data sets (the BRFSS, the American Community Survey Public Use Microdata Sample, Nielsen Claritas population totals, and the Missouri Census Geographic Equivalency File) to build a single weighted data set. Our findings indicate that internal and external validity tests were successful across many estimates. The BRFSS SAE method is one of several methods that can be used to produce reliable prevalence estimates in small geographic areas. PMID:27418213

Comparison of wildfire smoke estimation methods and associations with cardiopulmonary-related hospital admissions.

PubMed

Gan, Ryan W; Ford, Bonne; Lassman, William; Pfister, Gabriele; Vaidyanathan, Ambarish; Fischer, Emily; Volckens, John; Pierce, Jeffrey R; Magzamen, Sheryl

2017-03-01

Climate forecasts predict an increase in frequency and intensity of wildfires. Associations between health outcomes and population exposure to smoke from Washington 2012 wildfires were compared using surface monitors, chemical-weather models, and a novel method blending three exposure information sources. The association between smoke particulate matter ≤2.5 μm in diameter (PM 2.5 ) and cardiopulmonary hospital admissions occurring in Washington from 1 July to 31 October 2012 was evaluated using a time-stratified case-crossover design. Hospital admissions aggregated by ZIP code were linked with population-weighted daily average concentrations of smoke PM 2.5 estimated using three distinct methods: a simulation with the Weather Research and Forecasting with Chemistry (WRF-Chem) model, a kriged interpolation of PM 2.5 measurements from surface monitors, and a geographically weighted ridge regression (GWR) that blended inputs from WRF-Chem, satellite observations of aerosol optical depth, and kriged PM 2.5 . A 10 μg/m 3 increase in GWR smoke PM 2.5 was associated with an 8% increased risk in asthma-related hospital admissions (odds ratio (OR): 1.076, 95% confidence interval (CI): 1.019-1.136); other smoke estimation methods yielded similar results. However, point estimates for chronic obstructive pulmonary disease (COPD) differed by smoke PM 2.5 exposure method: a 10 μg/m 3 increase using GWR was significantly associated with increased risk of COPD (OR: 1.084, 95%CI: 1.026-1.145) and not significant using WRF-Chem (OR: 0.986, 95%CI: 0.931-1.045). The magnitude (OR) and uncertainty (95%CI) of associations between smoke PM 2.5 and hospital admissions were dependent on estimation method used and outcome evaluated. Choice of smoke exposure estimation method used can impact the overall conclusion of the study.

How many Laysan Teal Anas laysanensis are on Midway Atoll? Methods for monitoring abundance after reintroduction

USGS Publications Warehouse

Reynolds, Michelle H.; Courtot, Karen; Hatfield, Jeffrey

2017-01-01

Wildlife managers often request a simple approach to monitor the status of species of concern. In response to that need, we used eight years of monitoring data to estimate population size and test the validity of an index for monitoring accurately the abundance of reintroduced, endangered Laysan Teal Anas laysanensis. The population was established at Midway Atoll in the Hawaiian archipelago after 42 wild birds were translocated from Laysan Island during 2004–2005. We fitted 587 birds with unique markers during 2004–2015, recorded 21,309 sightings until March 2016, and conducted standardised survey counts during 2007–2015. A modified Lincoln-Petersen mark-resight estimator and ANCOVA models were used to test the relationship between survey counts, seasonal detectability, and population abundance. Differences were found between the breeding and non-breeding seasons in detection and how maximum counts recorded related to population estimates. The results showed strong, positive correlations between the seasonal maximum counts and population estimates. The ANCOVA models supported the use of standardised bi-monthly counts of unmarked birds as a valid index to monitor trends among years within a season at Midway Atoll. The translocated population increased to 661 adult and juvenile birds (95% CI = 608–714) by 2010, then declined by 38% between 2010 and 2012 after the Toˉhoku Japan earthquake-generated tsunami inundated 41% of the atoll and triggered an Avian Botulism type C Clostridium botulinum outbreak. Following another severe botulism outbreak during 2015, the population experienced a 37% decline. Data indicated that the Midway Atoll population, like the founding Laysan Island population, is susceptible to catastrophic population declines. Consistent standardised monitoring using simple counts, in place of mark-recapture and resightings surveys, can be used to evaluate population status over the long-term. We estimate there were 314–435 Laysan Teal (95% CI for population estimate; point estimate = 375 individuals) at Midway Atoll in 2015; c. 50% of the global population. In comparison, the most recent estimate for numbers on Laysan Island was of 339 individuals in 2012 (95% CI = 265–413). We suggest that this approach can be used to validate a survey index for any marked, reintroduced resident wildlife population.

Portrait of a small population of boreal toads (Anaxyrus boreas)

USGS Publications Warehouse

Muths, Erin; Scherer, Rick D.

2011-01-01

Much attention has been given to the conservation of small populations, those that are small because of decline, and those that are naturally small. Small populations are of particular interest because ecological theory suggests that they are vulnerable to the deleterious effects of environmental, demographic, and genetic stochasticity as well as natural and human-induced catastrophes. However, testing theory and developing applicable conservation measures for small populations is hampered by sparse data. This lack of information is frequently driven by computational issues with small data sets that can be confounded by the impacts of stressors. We present estimates of demographic parameters from a small population of Boreal Toads (Anaxyrus boreas) that has been surveyed since 2001 by using capture-recapture methods. Estimates of annual adult survival probability are high relative to other Boreal Toad populations, whereas estimates of recruitment rate are low. Despite using simple models, clear patterns emerged from the analyses, suggesting that population size is constrained by low recruitment of adults and is declining slowly. These patterns provide insights that are useful in developing management directions for this small population, and this study serves as an example of the potential for small populations to yield robust and useful information despite sample size constraints.

Comparing estimates of genetic variance across different relationship models.

PubMed

Legarra, Andres

2016-02-01

Use of relationships between individuals to estimate genetic variances and heritabilities via mixed models is standard practice in human, plant and livestock genetics. Different models or information for relationships may give different estimates of genetic variances. However, comparing these estimates across different relationship models is not straightforward as the implied base populations differ between relationship models. In this work, I present a method to compare estimates of variance components across different relationship models. I suggest referring genetic variances obtained using different relationship models to the same reference population, usually a set of individuals in the population. Expected genetic variance of this population is the estimated variance component from the mixed model times a statistic, Dk, which is the average self-relationship minus the average (self- and across-) relationship. For most typical models of relationships, Dk is close to 1. However, this is not true for very deep pedigrees, for identity-by-state relationships, or for non-parametric kernels, which tend to overestimate the genetic variance and the heritability. Using mice data, I show that heritabilities from identity-by-state and kernel-based relationships are overestimated. Weighting these estimates by Dk scales them to a base comparable to genomic or pedigree relationships, avoiding wrong comparisons, for instance, "missing heritabilities". Copyright © 2015 Elsevier Inc. All rights reserved.

An Admittance Survey of Large Volcanoes on Venus: Implications for Volcano Growth

NASA Technical Reports Server (NTRS)

Brian, A. W.; Smrekar, S. E.; Stofan, E. R.

2004-01-01

Estimates of the thickness of the venusian crust and elastic lithosphere are important in determining the rheological and thermal properties of Venus. These estimates offer insights into what conditions are needed for certain features, such as large volcanoes and coronae, to form. Lithospheric properties for much of the large volcano population on Venus are not well known. Previous studies of elastic thickness (Te) have concentrated on individual or small groups of edifices, or have used volcano models and fixed values of Te to match with observations of volcano morphologies. In addition, previous studies use different methods to estimate lithospheric parameters meaning it is difficult to compare their results. Following recent global studies of the admittance signatures exhibited by the venusian corona population, we performed a similar survey into large volcanoes in an effort to determine the range of lithospheric parameters shown by these features. This survey of the entire large volcano population used the same method throughout so that all estimates could be directly compared. By analysing a large number of edifices and comparing our results to observations of their morphology and models of volcano formation, we can help determine the controlling parameters that govern volcano growth on Venus.

Tower counts

USGS Publications Warehouse

Woody, Carol Ann; Johnson, D.H.; Shrier, Brianna M.; O'Neal, Jennifer S.; Knutzen, John A.; Augerot, Xanthippe; O'Neal, Thomas A.; Pearsons, Todd N.

2007-01-01

Counting towers provide an accurate, low-cost, low-maintenance, low-technology, and easily mobilized escapement estimation program compared to other methods (e.g., weirs, hydroacoustics, mark-recapture, and aerial surveys) (Thompson 1962; Siebel 1967; Cousens et al. 1982; Symons and Waldichuk 1984; Anderson 2000; Alaska Department of Fish and Game 2003). Counting tower data has been found to be consistent with that of digital video counts (Edwards 2005). Counting towers do not interfere with natural fish migration patterns, nor are fish handled or stressed; however, their use is generally limited to clear rivers that meet specific site selection criteria. The data provided by counting tower sampling allow fishery managers to determine reproductive population size, estimate total return (escapement + catch) and its uncertainty, evaluate population productivity and trends, set harvest rates, determine spawning escapement goals, and forecast future returns (Alaska Department of Fish and Game 1974-2000 and 1975-2004). The number of spawning fish is determined by subtracting subsistence, sport-caught fish, and prespawn mortality from the total estimated escapement. The methods outlined in this protocol for tower counts can be used to provide reasonable estimates ( plus or minus 6%-10%) of reproductive salmon population size and run timing in clear rivers. 

United Nations population estimates and projections with special reference to the Arab world.

PubMed

1980-06-01

The United Nations Population Division has been preparing world population estimates and projections by region since 1951, by country since 1958, and by sex and age for each country since 1968. The latest revision of the projections was prepared in 1978. The 2 basic methods of preparing population projections are mathematical and component, and the component methods are most widely used at present, by both national governments and the United Nations. Before projections are prepared, the base data must be evaluated and adjusted. In the UN projections, the assumptions imply that orderly progress will be made and that there will be no catastrophes such as famines and epidemics during the projection period. The projectins are prepared in 4 variants--"medium", "high," "low," and "constant." A major source of uncertainty in populations arises from the problem of estimating future fertility. Changes in fertility affect the age distribution and the total population size more than changes in mortality. At the UN, mortality assumptions are initially made in terms of life expectancy at birth and then in terms of age-sex patterns of probabilities of survival corresponding to different life expectancy levels at birth. Some of the results of the 1978 revision of the medium variant of the estimates and projections are shown in table form. The world total population of 4,033,000,000 in 1975 is projected to reach 6,199,000,000 by the year 2000. Among the major areas and regions of the world, the most rapid population growth for the future is projected for the Arab countries, Africa and Latin America. Of the 2 Arab regions, North Africa and Southwest Asia, Southwest Asia is expected to have the higher rate of growth because of assumed continued immigration. Within the Arab regions, there has been an increasing diversity in the rate of population growth. This divergence is expected to narrow with assumed decreased migration rates during the 1980s.

Estimating population parameters for northern and southern breeding populations of Canada geese

USGS Publications Warehouse

Hestbeck, J.B.; Rusch, Donald H.; Samuel, Michael D.; Humburg, Dale D.; Sullivan, Brian D.

1998-01-01

Canada geese (Branta canadensis) have been managed largely as a migratory resource. In the 1960's, Canada goose flocks were restored to historic breeding ranges in the United States and southern Canada to enhance recreational opportunity for observation and harvest. These populations of southern breeding geese have rapidly expanded, increasing conflicts with social and economic interests and causing the Midwinter Waterfowl Survey to be less effective as a management tool to monitor migrant populations. Wildlife agencies need methods to control local, southern breeding geese that reduce conflicts while providing adequate protection to populations of northern breeding geese. New techniques have been developed using mark-resight data from neck-banded geese to estimate distribution and population size during the late summer, fall, and mid-winter. Survival and movement rates can be estimated over special early or late hunting seasons, traditional fall-winter hunting season, and nonharvest periods. Direct recovery rates can be estimated for special and traditional harvest periods and these recovery rates can be related to survival and movement rates. Changes in harvest regulations can be related to changes in recovery, survival, and movement rates for specific cohorts of Canada geese. These techniques can be used to monitor population status and determine more appropriate harvest strategies.

Population delineation of polar bears using satellite collar data

USGS Publications Warehouse

Bethke, R.; Taylor, Mitchell K.; Amstrup, Steven C.; Messier, François

1996-01-01

To produce reliable estimates of the size or vital rates of a given population, it is important that the boundaries of the population under study are clearly defined. This is particularly critical for large, migratory animals where levels of sustainable harvest are based on these estimates, and where small errors may have serious long-term consequences for the population. Once populations are delineated, rates of exchange between adjacent populations can be determined and accounted/corrected for when calculating abundance (e.g., based on mark-recapture data). Using satellite radio-collar locations for polar bears in the western Canadian Arctic, we illustrate one approach to delineating wildlife populations that integrates cluster analysis methods for determining group membership with home range plotting procedures to define spatial utilization. This approach is flexible with respect to the specific procedures used and provides an objective and quantitative basis for defining population boundaries.

Correspondence regarding Zhong et al., BMC Bioinformatics 2013 Mar 7;14:89.

PubMed

Kuhn, Alexandre

2014-11-28

Computational expression deconvolution aims to estimate the contribution of individual cell populations to expression profiles measured in samples of heterogeneous composition. Zhong et al. recently proposed Digital Sorting Algorithm (BMC Bioinformatics 2013 Mar 7;14:89) and showed that they could accurately estimate population-specific expression levels and expression differences between two populations. They compared DSA with Population-Specific Expression Analysis (PSEA), a previous deconvolution method that we developed to detect expression changes occurring within the same population between two conditions (e.g. disease versus non-disease). However, Zhong et al. compared PSEA-derived specific expression levels across different cell populations. Specific expression levels obtained with PSEA cannot be directly compared across different populations as they are on a relative scale. They are accurate as we demonstrate by deconvolving the same dataset used by Zhong et al. and, importantly, allow for comparison of population-specific expression across conditions.

Overcoming statistical bias to estimate genetic mating systems in open populations: a comparison of Bateman's principles between the sexes in a sex-role-reversed pipefish.

PubMed

Mobley, Kenyon B; Jones, Adam G

2013-03-01

The genetic mating system is a key component of the sexual selection process, yet methods for the quantification of mating systems remain controversial. One approach involves metrics derived from Bateman's principles, which are based on variances in mating and reproductive success and the relationship between them. However, these measures are extremely difficult to measure for both sexes in open populations, because missing data can result in biased estimates. Here, we develop a novel approach for the estimation of mating system metrics based on Bateman's principles and apply it to a microsatellite-based parentage analysis of a natural population of the dusky pipefish, Syngnathus floridae. Our results show that both male and female dusky pipefish have significantly positive Bateman gradients. However, females exhibit larger values of the opportunity for sexual selection and the opportunity for selection compared to males. These differences translate into a maximum intensity of sexual selection (S'max) for females three times larger than that for males. Overall, this study identifies a critical source of bias that affects studies of mating systems in open populations, presents a novel method for overcoming this bias, and applies this method for the first time in a sex-role-reversed pipefish. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Population models for passerine birds: structure, parameterization, and analysis

USGS Publications Warehouse

Noon, B.R.; Sauer, J.R.; McCullough, D.R.; Barrett, R.H.

1992-01-01

Population models have great potential as management tools, as they use infonnation about the life history of a species to summarize estimates of fecundity and survival into a description of population change. Models provide a framework for projecting future populations, determining the effects of management decisions on future population dynamics, evaluating extinction probabilities, and addressing a variety of questions of ecological and evolutionary interest. Even when insufficient information exists to allow complete identification of the model, the modelling procedure is useful because it forces the investigator to consider the life history of the species when determining what parameters should be estimated from field studies and provides a context for evaluating the relative importance of demographic parameters. Models have been little used in the study of the population dynamics of passerine birds because of: (1) widespread misunderstandings of the model structures and parameterizations, (2) a lack of knowledge of life histories of many species, (3) difficulties in obtaining statistically reliable estimates of demographic parameters for most passerine species, and (4) confusion about functional relationships among demographic parameters. As a result, studies of passerine demography are often designed inappropriately and fail to provide essential data. We review appropriate models for passerine bird populations and illustrate their possible uses in evaluating the effects of management or other environmental influences on population dynamics. We identify environmental influences on population dynamics. We identify parameters that must be estimated from field data, briefly review existing statistical methods for obtaining valid estimates, and evaluate the present status of knowledge of these parameters.

Implementing a novel movement-based approach to inferring parturition and neonate caribou calf survival.

PubMed

Bonar, Maegwin; Ellington, E Hance; Lewis, Keith P; Vander Wal, Eric

2018-01-01

In ungulates, parturition is correlated with a reduction in movement rate. With advances in movement-based technologies comes an opportunity to develop new techniques to assess reproduction in wild ungulates that are less invasive and reduce biases. DeMars et al. (2013, Ecology and Evolution 3:4149-4160) proposed two promising new methods (individual- and population-based; the DeMars model) that use GPS inter-fix step length of adult female caribou (Rangifer tarandus caribou) to infer parturition and neonate survival. Our objective was to apply the DeMars model to caribou populations that may violate model assumptions for retrospective analysis of parturition and calf survival. We extended the use of the DeMars model after assigning parturition and calf mortality status by examining herd-wide distributions of parturition date, calf mortality date, and survival. We used the DeMars model to estimate parturition and calf mortality events and compared them with the known parturition and calf mortality events from collared adult females (n = 19). We also used the DeMars model to estimate parturition and calf mortality events for collared female caribou with unknown parturition and calf mortality events (n = 43) and instead derived herd-wide estimates of calf survival as well as distributions of parturition and calf mortality dates and compared them to herd-wide estimates generated from calves fitted with VHF collars (n = 134). For our data, the individual-based method was effective at predicting calf mortality, but was not effective at predicting parturition. The population-based method was more effective at predicting parturition but was not effective at predicting calf mortality. At the herd-level, the predicted distributions of parturition date from both methods differed from each other and from the distribution derived from the parturition dates of VHF-collared calves (log-ranked test: χ2 = 40.5, df = 2, p < 0.01). The predicted distributions of calf mortality dates from both methods were similar to the observed distribution derived from VHF-collared calves. Both methods underestimated herd-wide calf survival based on VHF-collared calves, however, a combination of the individual- and population-based methods produced herd-wide survival estimates similar to estimates generated from collared calves. The limitations we experienced when applying the DeMars model could result from the shortcomings in our data violating model assumptions. However despite the differences in our caribou systems, with proper validation techniques the framework in the DeMars model is sufficient to make inferences on parturition and calf mortality.

Implementing a novel movement-based approach to inferring parturition and neonate caribou calf survival

PubMed Central

Ellington, E. Hance; Lewis, Keith P.; Vander Wal, Eric

2018-01-01

In ungulates, parturition is correlated with a reduction in movement rate. With advances in movement-based technologies comes an opportunity to develop new techniques to assess reproduction in wild ungulates that are less invasive and reduce biases. DeMars et al. (2013, Ecology and Evolution 3:4149–4160) proposed two promising new methods (individual- and population-based; the DeMars model) that use GPS inter-fix step length of adult female caribou (Rangifer tarandus caribou) to infer parturition and neonate survival. Our objective was to apply the DeMars model to caribou populations that may violate model assumptions for retrospective analysis of parturition and calf survival. We extended the use of the DeMars model after assigning parturition and calf mortality status by examining herd-wide distributions of parturition date, calf mortality date, and survival. We used the DeMars model to estimate parturition and calf mortality events and compared them with the known parturition and calf mortality events from collared adult females (n = 19). We also used the DeMars model to estimate parturition and calf mortality events for collared female caribou with unknown parturition and calf mortality events (n = 43) and instead derived herd-wide estimates of calf survival as well as distributions of parturition and calf mortality dates and compared them to herd-wide estimates generated from calves fitted with VHF collars (n = 134). For our data, the individual-based method was effective at predicting calf mortality, but was not effective at predicting parturition. The population-based method was more effective at predicting parturition but was not effective at predicting calf mortality. At the herd-level, the predicted distributions of parturition date from both methods differed from each other and from the distribution derived from the parturition dates of VHF-collared calves (log-ranked test: χ2 = 40.5, df = 2, p < 0.01). The predicted distributions of calf mortality dates from both methods were similar to the observed distribution derived from VHF-collared calves. Both methods underestimated herd-wide calf survival based on VHF-collared calves, however, a combination of the individual- and population-based methods produced herd-wide survival estimates similar to estimates generated from collared calves. The limitations we experienced when applying the DeMars model could result from the shortcomings in our data violating model assumptions. However despite the differences in our caribou systems, with proper validation techniques the framework in the DeMars model is sufficient to make inferences on parturition and calf mortality. PMID:29466451

Population size and trend of Yellow-billed Loons in northern Alaska

USGS Publications Warehouse

Earnst, Susan L.; Stehn, R.A.; Platte, Robert; Larned, W.W.; Mallek, E.J.

2005-01-01

The Yellow-billed Loon (Gavia adamsii) is of conservation concern due to its restricted range, small population size, specific habitat requirements, and perceived threats to its breeding and wintering habitat. Within the U.S., this species breeds almost entirely within the National Petroleum Reserve-Alaska, nearly all of which is open, or proposed to be opened, for oil development. Rigorous estimates of Yellow-billed Loon population size and trend are lacking but essential for informed conservation. We used two annual aerial waterfowl surveys, conducted 1986a??2003 and 1992a??2003, to estimate population size and trend on northern Alaskan breeding grounds. In estimating population trend, we used mixed-effects regression models to reduce bias and sampling error associated with improvement in observer skill and annual effects of spring phenology. The estimated population trend on Alaskan breeding grounds since 1986 was near 0 with an estimated annual change of a??0.9% (95% CI of a??3.6% to +1.8%). The estimated population size, averaged over the past 12 years and adjusted by a correction factor based on an intensive, lake-circling, aerial survey method, was 2221 individuals (95% CI of 1206a??3235) in early June and 3369 individuals (95% CI of 1910a??4828) in late June. Based on estimates from other studies of the proportion of loons nesting in a given year, it is likely that <1000 nesting pairs inhabit northern Alaska in most years. The highest concentration of Yellow-billed Loons occurred between the Meade and Ikpikpuk Rivers; and across all of northern Alaska, 53% of recorded sightings occurred within 12% of the area.

A revised load estimation procedure for the Susquehanna, Potomac, Patuxent, and Choptank rivers

USGS Publications Warehouse

Yochum, Steven E.

2000-01-01

The U.S. Geological Survey?s Chesapeake Bay River Input Program has updated the nutrient and suspended-sediment load data base for the Susquehanna, Potomac, Patuxent, and Choptank Rivers using a multiple-window, center-estimate regression methodology. The revised method optimizes the seven-parameter regression approach that has been used historically by the program. The revised method estimates load using the fifth or center year of a sliding 9-year window. Each year a new model is run for each site and constituent, the most recent year is added, and the previous 4 years of estimates are updated. The fifth year in the 9-year window is considered the best estimate and is kept in the data base. The last year of estimation shows the most change from the previous year?s estimate and this change approaches a minimum at the fifth year. Differences between loads computed using this revised methodology and the loads populating the historical data base have been noted but the load estimates do not typically change drastically. The data base resulting from the application of this revised methodology is populated by annual and monthly load estimates that are known with greater certainty than in the previous load data base.

Estimation of infection prevalence and sensitivity in a stratified two-stage sampling design employing highly specific diagnostic tests when there is no gold standard.

PubMed

Miller, Ezer; Huppert, Amit; Novikov, Ilya; Warburg, Alon; Hailu, Asrat; Abbasi, Ibrahim; Freedman, Laurence S

2015-11-10

In this work, we describe a two-stage sampling design to estimate the infection prevalence in a population. In the first stage, an imperfect diagnostic test was performed on a random sample of the population. In the second stage, a different imperfect test was performed in a stratified random sample of the first sample. To estimate infection prevalence, we assumed conditional independence between the diagnostic tests and develop method of moments estimators based on expectations of the proportions of people with positive and negative results on both tests that are functions of the tests' sensitivity, specificity, and the infection prevalence. A closed-form solution of the estimating equations was obtained assuming a specificity of 100% for both tests. We applied our method to estimate the infection prevalence of visceral leishmaniasis according to two quantitative polymerase chain reaction tests performed on blood samples taken from 4756 patients in northern Ethiopia. The sensitivities of the tests were also estimated, as well as the standard errors of all estimates, using a parametric bootstrap. We also examined the impact of departures from our assumptions of 100% specificity and conditional independence on the estimated prevalence. Copyright © 2015 John Wiley & Sons, Ltd.

Accounting for shared and unshared dosimetric uncertainties in the dose response for ultrasound-detected thyroid nodules after exposure to radioactive fallout.

PubMed

Land, Charles E; Kwon, Deukwoo; Hoffman, F Owen; Moroz, Brian; Drozdovitch, Vladimir; Bouville, André; Beck, Harold; Luckyanov, Nicholas; Weinstock, Robert M; Simon, Steven L

2015-02-01

Dosimetic uncertainties, particularly those that are shared among subgroups of a study population, can bias, distort or reduce the slope or significance of a dose response. Exposure estimates in studies of health risks from environmental radiation exposures are generally highly uncertain and thus, susceptible to these methodological limitations. An analysis was published in 2008 concerning radiation-related thyroid nodule prevalence in a study population of 2,994 villagers under the age of 21 years old between August 1949 and September 1962 and who lived downwind from the Semipalatinsk Nuclear Test Site in Kazakhstan. This dose-response analysis identified a statistically significant association between thyroid nodule prevalence and reconstructed doses of fallout-related internal and external radiation to the thyroid gland; however, the effects of dosimetric uncertainty were not evaluated since the doses were simple point "best estimates". In this work, we revised the 2008 study by a comprehensive treatment of dosimetric uncertainties. Our present analysis improves upon the previous study, specifically by accounting for shared and unshared uncertainties in dose estimation and risk analysis, and differs from the 2008 analysis in the following ways: 1. The study population size was reduced from 2,994 to 2,376 subjects, removing 618 persons with uncertain residence histories; 2. Simulation of multiple population dose sets (vectors) was performed using a two-dimensional Monte Carlo dose estimation method; and 3. A Bayesian model averaging approach was employed for evaluating the dose response, explicitly accounting for large and complex uncertainty in dose estimation. The results were compared against conventional regression techniques. The Bayesian approach utilizes 5,000 independent realizations of population dose vectors, each of which corresponds to a set of conditional individual median internal and external doses for the 2,376 subjects. These 5,000 population dose vectors reflect uncertainties in dosimetric parameters, partly shared and partly independent, among individual members of the study population. Risk estimates for thyroid nodules from internal irradiation were higher than those published in 2008, which results, to the best of our knowledge, from explicitly accounting for dose uncertainty. In contrast to earlier findings, the use of Bayesian methods led to the conclusion that the biological effectiveness for internal and external dose was similar. Estimates of excess relative risk per unit dose (ERR/Gy) for males (177 thyroid nodule cases) were almost 30 times those for females (571 cases) and were similar to those reported for thyroid cancers related to childhood exposures to external and internal sources in other studies. For confirmed cases of papillary thyroid cancers (3 in males, 18 in females), the ERR/Gy was also comparable to risk estimates from other studies, but not significantly different from zero. These findings represent the first reported dose response for a radiation epidemiologic study considering all known sources of shared and unshared errors in dose estimation and using a Bayesian model averaging (BMA) method for analysis of the dose response.

Estimating abundance of mountain lions from unstructured spatial sampling

USGS Publications Warehouse

Russell, Robin E.; Royle, J. Andrew; Desimone, Richard; Schwartz, Michael K.; Edwards, Victoria L.; Pilgrim, Kristy P.; Mckelvey, Kevin S.

2012-01-01

Mountain lions (Puma concolor) are often difficult to monitor because of their low capture probabilities, extensive movements, and large territories. Methods for estimating the abundance of this species are needed to assess population status, determine harvest levels, evaluate the impacts of management actions on populations, and derive conservation and management strategies. Traditional mark–recapture methods do not explicitly account for differences in individual capture probabilities due to the spatial distribution of individuals in relation to survey effort (or trap locations). However, recent advances in the analysis of capture–recapture data have produced methods estimating abundance and density of animals from spatially explicit capture–recapture data that account for heterogeneity in capture probabilities due to the spatial organization of individuals and traps. We adapt recently developed spatial capture–recapture models to estimate density and abundance of mountain lions in western Montana. Volunteers and state agency personnel collected mountain lion DNA samples in portions of the Blackfoot drainage (7,908 km2) in west-central Montana using 2 methods: snow back-tracking mountain lion tracks to collect hair samples and biopsy darting treed mountain lions to obtain tissue samples. Overall, we recorded 72 individual capture events, including captures both with and without tissue sample collection and hair samples resulting in the identification of 50 individual mountain lions (30 females, 19 males, and 1 unknown sex individual). We estimated lion densities from 8 models containing effects of distance, sex, and survey effort on detection probability. Our population density estimates ranged from a minimum of 3.7 mountain lions/100 km2 (95% Cl 2.3–5.7) under the distance only model (including only an effect of distance on detection probability) to 6.7 (95% Cl 3.1–11.0) under the full model (including effects of distance, sex, survey effort, and distance x sex on detection probability). These numbers translate to a total estimate of 293 mountain lions (95% Cl 182–451) to 529 (95% Cl 245–870) within the Blackfoot drainage. Results from the distance model are similar to previous estimates of 3.6 mountain lions/100 km2 for the study area; however, results from all other models indicated greater numbers of mountain lions. Our results indicate that unstructured spatial sampling combined with spatial capture–recapture analysis can be an effective method for estimating large carnivore densities.

Predicting Intra-Urban Population Densities in Africa using SAR and Optical Remote Sensing Data

NASA Astrophysics Data System (ADS)

Linard, C.; Steele, J.; Forget, Y.; Lopez, J.; Shimoni, M.

2017-12-01

The population of Africa is predicted to double over the next 40 years, driving profound social, environmental and epidemiological changes within rapidly growing cities. Estimations of within-city variations in population density must be improved in order to take urban heterogeneities into account and better help urban research and decision making, especially for vulnerability and health assessments. Satellite remote sensing offers an effective solution for mapping settlements and monitoring urbanization at different spatial and temporal scales. In Africa, the urban landscape is covered by slums and small houses, where the heterogeneity is high and where the man-made materials are natural. Innovative methods that combine optical and SAR data are therefore necessary for improving settlement mapping and population density predictions. An automatic method was developed to estimate built-up densities using recent and archived optical and SAR data and a multi-temporal database of built-up densities was produced for 48 African cities. Geo-statistical methods were then used to study the relationships between census-derived population densities and satellite-derived built-up attributes. Best predictors were combined in a Random Forest framework in order to predict intra-urban variations in population density in any large African city. Models show significant improvement of our spatial understanding of urbanization and urban population distribution in Africa in comparison to the state of the art.

Productivity and population density estimates of the dengue vector mosquito Aedes aegypti (Stegomyia aegypti) in Australia.

PubMed

Williams, C R; Johnson, P H; Ball, T S; Ritchie, S A

2013-09-01

New mosquito control strategies centred on the modifying of populations require knowledge of existing population densities at release sites and an understanding of breeding site ecology. Using a quantitative pupal survey method, we investigated production of the dengue vector Aedes aegypti (L.) (Stegomyia aegypti) (Diptera: Culicidae) in Cairns, Queensland, Australia, and found that garden accoutrements represented the most common container type. Deliberately placed 'sentinel' containers were set at seven houses and sampled for pupae over 10 weeks during the wet season. Pupal production was approximately constant; tyres and buckets represented the most productive container types. Sentinel tyres produced the largest female mosquitoes, but were relatively rare in the field survey. We then used field-collected data to make estimates of per premises population density using three different approaches. Estimates of female Ae. aegypti abundance per premises made using the container-inhabiting mosquito simulation (CIMSiM) model [95% confidence interval (CI) 18.5-29.1 females] concorded reasonably well with estimates obtained using a standing crop calculation based on pupal collections (95% CI 8.8-22.5) and using BG-Sentinel traps and a sampling rate correction factor (95% CI 6.2-35.2). By first describing local Ae. aegypti productivity, we were able to compare three separate population density estimates which provided similar results. We anticipate that this will provide researchers and health officials with several tools with which to make estimates of population densities. © 2012 The Royal Entomological Society.

A geographic information system-based method for estimating cancer rates in non-census defined geographical areas.

PubMed

Freeman, Vincent L; Boylan, Emma E; Pugach, Oksana; Mclafferty, Sara L; Tossas-Milligan, Katherine Y; Watson, Karriem S; Winn, Robert A

2017-10-01

To address locally relevant cancer-related health issues, health departments frequently need data beyond that contained in standard census area-based statistics. We describe a geographic information system-based method for calculating age-standardized cancer incidence rates in non-census defined geographical areas using publically available data. Aggregated records of cancer cases diagnosed from 2009 through 2013 in each of Chicago's 77 census-defined community areas were obtained from the Illinois State Cancer Registry. Areal interpolation through dasymetric mapping of census blocks was used to redistribute populations and case counts from community areas to Chicago's 50 politically defined aldermanic wards, and ward-level age-standardized 5-year cumulative incidence rates were calculated. Potential errors in redistributing populations between geographies were limited to <1.5% of the total population, and agreement between our ward population estimates and those from a frequently cited reference set of estimates was high (Pearson correlation r = 0.99, mean difference = -4 persons). A map overlay of safety-net primary care clinic locations and ward-level incidence rates for advanced-staged cancers revealed potential pathways for prevention. Areal interpolation through dasymetric mapping can estimate cancer rates in non-census defined geographies. This can address gaps in local cancer-related health data, inform health resource advocacy, and guide community-centered cancer prevention and control.

Economic Impact of Dyspepsia in Rural and Urban Malaysia: A Population-Based Study

PubMed Central

Yadav, Hematram; Everett, Simon M; Goh, Khean-Lee

2012-01-01

Background/Aims The economic impact of dyspepsia in regions with a diverse healthcare system remains uncertain. This study aimed to estimate the costs of dyspepsia in a rural and urban population in Malaysia. Methods Economic evaluation was performed based on the cost-of-illness method. Resource utilization and quality of life data over a specific time frame, were collected to determine direct, indirect and intangible costs related to dyspepsia. Results The prevalences of dyspepsia in the rural (n = 2,000) and urban (n = 2,039) populations were 14.6% and 24.3% respectively. Differences in socioeconomic status and healthcare utilisation between both populations were considerable. The cost of dyspepsia per 1,000 population per year was estimated at USD14,816.10 and USD59,282.20 in the rural and urban populations respectively. The cost per quality adjusted life year for dyspepsia in rural and urban adults was USD16.30 and USD69.75, respectively. Conclusions The economic impact of dyspepsia is greater in an urban compared to a rural setting. Differences in socioeconomic status and healthcare utilisation between populations are thought to contribute to this difference. PMID:22323987

Using Survival Analysis to Improve Estimates of Life Year Gains in Policy Evaluations.

PubMed

Meacock, Rachel; Sutton, Matt; Kristensen, Søren Rud; Harrison, Mark

2017-05-01

Policy evaluations taking a lifetime horizon have converted estimated changes in short-term mortality to expected life year gains using general population life expectancy. However, the life expectancy of the affected patients may differ from the general population. In trials, survival models are commonly used to extrapolate life year gains. The objective was to demonstrate the feasibility and materiality of using parametric survival models to extrapolate future survival in health care policy evaluations. We used our previous cost-effectiveness analysis of a pay-for-performance program as a motivating example. We first used the cohort of patients admitted prior to the program to compare 3 methods for estimating remaining life expectancy. We then used a difference-in-differences framework to estimate the life year gains associated with the program using general population life expectancy and survival models. Patient-level data from Hospital Episode Statistics was utilized for patients admitted to hospitals in England for pneumonia between 1 April 2007 and 31 March 2008 and between 1 April 2009 and 31 March 2010, and linked to death records for the period from 1 April 2007 to 31 March 2011. In our cohort of patients, using parametric survival models rather than general population life expectancy figures reduced the estimated mean life years remaining by 30% (9.19 v. 13.15 years, respectively). However, the estimated mean life year gains associated with the program are larger using survival models (0.380 years) compared to using general population life expectancy (0.154 years). Using general population life expectancy to estimate the impact of health care policies can overestimate life expectancy but underestimate the impact of policies on life year gains. Using a longer follow-up period improved the accuracy of estimated survival and program impact considerably.