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15 recordsLinked to original sources

Information-theoretic model selection and model averaging for closed-population capture-recapture studies

Specification of an appropriate model is critical to valid statistical inference. Given the “true model” for the data is unknown, the goal of model selection is to select a plausible approximating model that balances model bias and sampling variance. Model selection based on information criteria such as AIC or its variant AIC c , or criteria like CAIC, has proven useful in a variety of contexts including the analysis of open-population capture-recapture data. These criteria have not been intensively evaluated for closed-population capture-recapture models, which are integer parameter models used to estimate population size ( N ), and there is concern that they will not perform well. To address this concern, we evaluated AIC, AIC c , and CAIC model selection for closed-population capture-recapture models by empirically assessing the quality of inference for the population size parameter N . We found that AIC-, AIC c -, and CAIC-selected models had smaller relative mean squared errors than randomly selected models, but that confidence interval coverage on N was poor unless unconditional variance estimates (which incorporate model uncertainty) were used to compute confidence intervals. Overall, AIC and AIC c outperformed CAIC, and are preferred to CAIC for selection among the closed-population capture-recapture models we investigated. A model averaging approach to estimation, using AIC, AIC c , or CAIC to estimate weights, was also investigated and proved superior to estimation using AIC-, AIC c -, or CAIC-selected models. Our results suggested that, for model averaging, AIC or AIC c should be favored over CAIC for estimating weights.

Biometrical Journal↗

Some comments on Anderson and Pospahala's correction of bias in line transect sampling

ANDERSON and POSPAHALA (1970) investigated the estimation of wildlife population size using the belt or line transect sampling method and devised a correction for bias, thus leading to an estimator with interesting characteristics. This work was given a uniform mathematical framework in BURNHAM and ANDERSON (1976). In this paper we show that the ANDERSON-POSPAHALA estimator is optimal in the sense of being the (unique) best linear unbiased estimator within the class of estimators which are linear combinations of cell frequencies, provided certain assumptions are met.

Biometrical Journal↗

Determination of selection gradients using multiple regression versus Structural Equation Modeling (SEM)

Selection studies involving multiple intercorrelated independent variables have employed multiple regression analysis as a means to estimate and partition natural and sexual selection's direct and indirect effects. These statistical models assume that independent variables are measured without error. Most would conclude that such is not the case in the field studies for which these methods are employed. We demonstrate that the distortion of estimates resulting from error variance is not trivial. When independent variables are intercorrelated, extreme distortions may occur. We propose to use Structural Equation Models (SEM), to estimate error variance and produce highly accurate coefficients for formulation of selection gradients. This method is particularly appropriate when the selection is viewed as happening at the level of the latent variables.

Biometrical Journal↗

Two-stage sequential sampling: A neighborhood-free adaptive sampling procedure

Designing an efficient sampling scheme for a rare and clustered population is a challenging area of research. Adaptive cluster sampling, which has been shown to be viable for such a population, is based on sampling a neighborhood of units around a unit that meets a specified condition. However, the edge units produced by sampling neighborhoods have proven to limit the efficiency and applicability of adaptive cluster sampling. We propose a sampling design that is adaptive in the sense that the final sample depends on observed values, but it avoids the use of neighborhoods and the sampling of edge units. Unbiased estimators of population total and its variance are derived using Murthy's estimator. The modified two-stage sampling design is easy to implement and can be applied to a wider range of populations than adaptive cluster sampling. We evaluate the proposed sampling design by simulating sampling of two real biological populations and an artificial population for which the variable of interest took the value either 0 or 1 (e.g., indicating presence and absence of a rare event). We show that the proposed sampling design is more efficient than conventional sampling in nearly all cases. The approach used to derive estimators (Murthy's estimator) opens the door for unbiased estimators to be found for similar sequential sampling designs. ?? 2005 American Statistical Association and the International Biometric Society.

Journal of Agricultural, Biological, and Environme↗

A robust design mark-resight abundance estimator allowing heterogeneity in resighting probabilities

This article introduces the beta-binomial estimator (BBE), a closed-population abundance mark-resight model combining the favorable qualities of maximum likelihood theory and the allowance of individual heterogeneity in sighting probability (p). The model may be parameterized for a robust sampling design consisting of multiple primary sampling occasions where closure need not be met between primary occasions. We applied the model to brown bear data from three study areas in Alaska and compared its performance to the joint hypergeometric estimator (JHE) and Bowden's estimator (BOWE). BBE estimates suggest heterogeneity levels were non-negligible and discourage the use of JHE for these data. Compared to JHE and BOWE, confidence intervals were considerably shorter for the AICc model-averaged BBE. To evaluate the properties of BBE relative to JHE and BOWE when sample sizes are small, simulations were performed with data from three primary occasions generated under both individual heterogeneity and temporal variation in p. All models remained consistent regardless of levels of variation in p. In terms of precision, the AICc model-averaged BBE showed advantages over JHE and BOWE when heterogeneity was present and mean sighting probabilities were similar between primary occasions. Based on the conditions examined, BBE is a reliable alternative to JHE or BOWE and provides a framework for further advances in mark-resight abundance estimation. ?? 2006 American Statistical Association and the International Biometric Society.

Journal of Agricultural, Biological, and Environme↗

Estimation and confidence intervals for empirical mixing distributions

Questions regarding collections of parameter estimates can frequently be expressed in terms of an empirical mixing distribution (EMD). This report discusses empirical Bayes estimation of an EMD, with emphasis on the construction of interval estimates. Estimation of the EMD is accomplished by substitution of estimates of prior parameters in the posterior mean of the EMD. This procedure is examined in a parametric model (the normal-normal mixture) and in a semi-parametric model. In both cases, the empirical Bayes bootstrap of Laird and Louis (1987, Journal of the American Statistical Association 82, 739-757) is used to assess the variability of the estimated EMD arising from the estimation of prior parameters. The proposed methods are applied to a meta-analysis of population trend estimates for groups of birds.

Biometrics↗

A goodness-of-fit test for capture-recapture model Mt under closure

A new, fully efficient goodness-of-fit test for the time-specific closed-population capture-recapture model M t is presented. This test is based on the residual distribution of the capture history data given the maximum likelihood parameter estimates under model M t , is partitioned into informative components, and is based on chi-square statistics. Comparison of this test with Leslie's test (Leslie, 1958, Journal of Animal Ecology , 27 , 84–86) for model M t , using Monte Carlo simulations, shows the new test generally outperforms Leslie's test. The new test is frequently computable when Leslie's test is not, has Type I error rates that are closer to nominal error rates than Leslie's test, and is sensitive to behavioral variation and heterogeneity in capture Probabilities. Leslie's test is not sensitive to behavioral variation in capture probabilities but, when computable, has greater power to detect heterogeneity than the new test.

Biometrics↗

N-mixture models for estimating population size from spatially replicated counts

Spatial replication is a common theme in count surveys of animals. Such surveys often generate sparse count data from which it is difficult to estimate population size while formally accounting for detection probability. In this article, I describe a class of models (n-mixture models) which allow for estimation of population size from such data. The key idea is to view site-specific population sizes, n, as independent random variables distributed according to some mixing distribution (e.g., Poisson). Prior parameters are estimated from the marginal likelihood of the data, having integrated over the prior distribution for n. Carroll and Lombard (1985, Journal of American Statistical Association 80, 423-426) proposed a class of estimators based on mixing over a prior distribution for detection probability. Their estimator can be applied in limited settings, but is sensitive to prior parameter values that are fixed a priori. Spatial replication provides additional information regarding the parameters of the prior distribution on n that is exploited by the n-mixture models and which leads to reasonable estimates of abundance from sparse data. A simulation study demonstrates superior operating characteristics (bias, confidence interval coverage) of the n-mixture estimator compared to the Caroll and Lombard estimator. Both estimators are applied to point count data on six species of birds illustrating the sensitivity to choice of prior on p and substantially different estimates of abundance as a consequence.

Biometrics↗

Combining band recovery data and Pollock's robust design to model temporary and permanent emigration

Capture-recapture models are widely used to estimate demographic parameters of marked populations. Recently, this statistical theory has been extended to modeling dispersal of open populations. Multistate models can be used to estimate movement probabilities among subdivided populations if multiple sites are sampled. Frequently, however, sampling is limited to a single site, Models described by Burnham (1993, in Marked Individuals in the Study of Bird Populations , 199–213), which combined open population capture-recapture and band-recovery models, can be used to estimate permanent emigration when sampling is limited to a single population. Similarly, Kendall, Nichols, and Hines (1997, Ecology 51 , 563–578) developed models to estimate temporary emigration under Pollock's (1982, Journal of Wildlife Management 46 , 757–760) robust design. We describe a likelihood-based approach to simultaneously estimate temporary and permanent emigration when sampling is limited to a single population. We use a sampling design that combines the robust design and recoveries of individuals obtained immediately following each sampling period. We present a general form for our model where temporary emigration is a first-order Markov process, and we discuss more restrictive models. We illustrate these models with analysis of data on marked Canvasback ducks. Our analysis indicates that probability of permanent emigration for adult female Canvasbacks was 0.193 ( ) and that birds that were present at the study area in year i — 1 had a higher probability of presence in year i than birds that were not present in year i — 1.

Biometrics↗

Juvenile sea lamprey (Petromyzon marinus) have a wide window of elevated salinity tolerance that is eventually limited during springtime warming

The present study examined changes in biometric characteristics, osmoregulatory capacity, and seawater (SW) tolerance of juvenile sea lamprey ( Petromyzon marinus ) throughout the varying thermal changes from late autumn to late spring. Body length, mass, and condition factor were maintained until April, when significant declines in mass and condition factor were observed to correspond with increases in temperature. Nearly 100% survival in SW was maintained through April. In May, after river and estuarine temperatures had increased, significant mortality in SW (up to 50%) was observed. After SW acclimation, plasma chloride was maintained at an elevated set point, and gill Na + /K + -ATPase activity was elevated. Neither parameter appeared to be affected during springtime warming. Together, these results provide a first characterization of the sustained osmoregulatory performance of juvenile sea lamprey after metamorphosis and show that the window of increased hypo-osmoregulatory performance for SW entry lasts for at least 5 months but may ultimately be limited by increases in river water temperatures in late spring.

Canadian Journal of Fisheries and Aquatic Sciences↗

Fidelity and breeding probability related to population density and individual quality in black brent geese Branta bernicla nigricans

1. Patterns of temporary emigration (associated with non-breeding) are important components of variation in individual quality. Permanent emigration from the natal area has important implications for both individual fitness and local population dynamics. 2. We estimated both permanent and temporary emigration of black brent geese (Branta bernicla nigricans Lawrence) from the Tutakoke River colony, using observations of marked brent geese on breeding and wintering areas, and recoveries of ringed individuals by hunters. We used the likelihood developed by Lindberg, Kendall, Hines & Anderson 2001 (Combining band recovery data and Pollock's robust design to model temporary and permanent emigration. Biometrics, 57, 273-281) to assess hypotheses and estimate parameters. 3. Temporary emigration (the converse of breeding) varied among age classes up to age 5, and differed between individuals that bred in the previous years vs. those that did not. Consistent with the hypothesis of variation in individual quality, individuals with a higher probability of breeding in one year also had a higher probability of breeding the next year. 4. Natal fidelity of females ranged from 0.70 ?? 0.07-0.96 ?? 0.18 and averaged 0.83. In contrast to Lindberg et al. (1998), we did not detect a relationship between fidelity and local population density. Natal fidelity was negatively correlated with first-year survival, suggesting that competition among individuals of the same age for breeding territories influenced dispersal. Once females nested at the Tutakoke River, colony breeding fidelity was 1.0. 5. Our analyses show substantial variation in individual quality associated with fitness, which other analyses suggest is strongly influenced by early environment. Our analyses also suggest substantial interchange among breeding colonies of brent geese, as first shown by Lindberg et al. (1998).

Journal of Animal Ecology↗

Heteropolaria colisarum Foissner and Schubert, 1977 (Protozoa: Epistylididae) or North American freshwater fishes

The peritrichous ciliate ‘Epistylis sp.’ involved in the‘red-sore’ disease of various North American freshwater fishes is identified as Heteropolaria colisarum Foissner & Schubert, 1977. Its morphology is redescribed from observations of living and silver-stained organisms and biometrically analysed individuals. Extended zooids can be easily identified by their highly characteristic (elongated) body. Silver impregnations show a very high number of silverlines and a band-like, irregularly formed macronucleus. The genus Heteropolaria belongs to the family Epistylididae and is characterized by the eccentric location of the scopula of the swarmer and a peculiar myoneme in the peristomal disc that branches off the myoneme of the peristomal collar. Autochthonous occurrences of this species are known only from North America. In Europe only the related species H. lwoffi has been found. Histological sections give some evidence that the terminal platelet of the stalk is embedded in the dermal epithelium. This suggests that H. colisarum could be a parasite rather than an epizoon and that the often associated bacterium Aeromonas hydrophila is a secondary invader. However, further studies are necessary. Experiments showed a high infectivity of the ciliate and no host specificity. These characteristics are supported by the observations of other researchers. Preliminary laboratory tests showed that a single treatment with salt solution (NaCl) at a rate of 1.5% for 3h controlled H. colisarum.

Journal of Fish Diseases↗

Predicting rare plant occurrence in Great Smoky Mountains National Park, USA

We investigated the applicability of biometric habitat modeling to rare plant inventory and conservation by developing and field testing a geographically explicit model for Cardamine clematitis Shuttleworth ex A. Gray (mountain bittercress), an endemic plant of the southern Blue Ridge Mountains, USA. For each of 187 confirmed coordinates for C. clematitis in Great Smoky Mountains National Park, 13 habitat variables were measured with a geographic information system. These data were used to calculate Mahalanobis distances for each 30-m x 30-m pixel within the study area; small values of Mahalanobis distance represented site conditions similar to those of known locations of C. clematitis , whereas larger distance values represented dissimilar conditions. Following model development, we tested model performance by sampling 120 randomly distributed plots for C. clematitis presence. Logistic regression showed that Mahalanobis distance values were strongly related to C. clematitis occurrence (P = 0.039). Overall, 75% of all known occurrences of C. clematitis had associated Mahalanobis distance values below 17.7, and 95% of all occurrences were below 33.8; the median Mahalanobis distance value for the study area as a whole was 40.0. A habitat suitability cutoff value was defined which identified roughly 23,640 ha (19.5% of the study area) as suitable habitat. Although the model successfully predicted species absence in test plots with high Mahalanobis distance values, many sites with low values did not contain C. clematitis . Only 16.2% of test plots below the habitat suitability cutoff contained C. clematitis . The absence of C. clematitis from sites with low Mahalanobis distance values (low specificity) is not necessarily indicative of a poor model; metapopulation processes (e.g., recolonizations, local extinctions) have been shown to play a major role in presence or absence of many plant species. That may be partially the case with our model as evidenced by a relationship between C. clematitis presence and habitat patch size.

North Carolina, Tennesse↗