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Lisa Madsen

Publications and source records attributed to Lisa Madsen.

8 recordsLinked to original sources

A review of N-mixture models

N-mixture models were born in 2004 of the necessity to model animal population size from point counts with imperfect detection of individuals, where capture-recapture methods are infeasible. Initially developed for applications where population size was assumed constant, N-mixture models were extended in 2011 to include population dynamics, allowing application to populations whose size fluctuates during the study. A further extension in 2014 accommodates populations with multiple “states” such as age class or sex. More recent extensions model spatial movement of animals among habitat patches or the spatial spread of infectious disease in a human population. The core idea underlying this class of models is a hierarchical structure, where the observation model is defined conditional on the model for true abundance. This hierarchy allows researchers to incorporate information about observation and abundance processes, while permitting distinct inferences about elements affecting detection and those affecting abundance. Another benefit of the hierarchical approach is the ability to accommodate many existing sampling protocols such as removal sampling and distance sampling. One drawback to N-mixture models is that since they estimate both abundance and detection from replicated but unmarked counts, model parameters may not be clearly identifiable. A second drawback is that when observed counts are large, calculating the N-mixture likelihood is computationally infeasible. This difficulty motivated an approximate likelihood based on the normal approximation to the binomial. The normal approximation provides a diagnostic of parameter estimability based on the closed-form expression of the Fisher information matrix for a multivariate normal likelihood.

WIREs Computational Statistics

Comparing methods to estimate the proportion of turbine-induced bird and bat mortality in the search area under a road and pad search protocol

Estimating bird and bat mortality at wind facilities typically involves searching for carcasses on the ground near turbines. Some fraction of carcasses inevitably lie outside the search plots, and accurate mortality estimation requires accounting for those carcasses using models to extrapolate from searched to unsearched areas. Such models should account for variation in carcass density with distance, and ideally also for variation with direction (anisotropy). We compare five methods of accounting for carcasses that land outside the searched area (ratio, weighted distribution, non-parametric, and two generalized linear models ( glm )) by simulating spatial arrival patterns and the detection process to mimic observations which result from surveying only, or primarily, roads and pads (R&P) and applying the five methods. Simulations vary R&P configurations, spatial carcass distributions (isotropic and anisotropic), and per turbine fatality rates. Our results suggest that the ratio method is less accurate with higher variation relative to the other four methods which all perform similarly under isotropy. All methods were biased under anisotropy; however, including direction covariates in the glm method substantially reduced bias. In addition to comparing methods of accounting for unsearched areas, we suggest a semiparametric bootstrap to produce confidence-based bounds for the proportion of carcasses that land in the searched area.

Environmental and Ecological Statistics

Estimating population size with imperfect detection using a parametric bootstrap

We develop a novel method of estimating population size from imperfectly detected counts of individuals and a separate estimate of detection probability. Observed counts are separated into classes within which detection probability is assumed constant. Within a detection class, counts are modeled as a single binomial observation X with success probability p where the goal is to estimate index N . We use a Horvitz–Thompson‐like estimator for N and account for uncertainty in both sample data and estimated success probability via a parametric bootstrap. Unlike capture–recapture methods, our model does not require repeated sampling of the population. Our method is able to achieve good results, even with small X . We show in a factorial simulation study that the median of the bootstrapped sample has small bias relative to N and that coverage probabilities of confidence intervals for N are near nominal under a wide array of scenarios. Our methodology begins to break down when P ( X =0)>0.1 but is still capable of obtaining reasonable confidence coverage. We illustrate the proposed technique by estimating (1) the size of a moose population in Alaska and (2) the number of bat fatalities at a wind power facility, both from samples with imperfect detection probabilities, estimated independently.

Environmetrics

GenEst statistical models—A generalized estimator of mortality

Introduction GenEst (a generalized estimator of mortality) is a suite of statistical models and software tools for generalized mortality estimation. It was specifically designed for estimating the number of bird and bat fatalities at solar and wind power facilities, but both the software (Dalthorp and others, 2018) and the underlying statistical models are general enough to be useful in various situations to estimate the size of open populations when detection probabilities and search coverages are less than 1. In this report, we outline the statistical models and data structures underlying the estimator. The models are numerous, complex, and intricately interwoven. Discussion begins with broad, high-level overviews of the general models. The lower-level technical details are then gradually added. Broader and less technical discussions on the general context and applications of the models and the use of the software are available in the software user guide (Simonis and others, 2018), vignettes bundled with the software, and the help files within the software itself.

Techniques and Methods

GenEst user guide—Software for a generalized estimator of mortality

GenEst (Generalized Estimator) is a software tool for estimating the total number of individuals arriving in an area during a specific time period when their detection probability is unknown but estimable. Its development was motivated by the need to accurately estimate the total number of bird and bat fatalities occurring at wind and solar energy facilities, but it is applicable in a variety of other contexts as well. Simple counts of carcasses are not an accurate measure of the true number of fatalities because some carcasses are inevitably missed in carcass searches. Furthermore, simple carcass counts do not allow comparison among locations or years because carcasses may be detected at different rates. This software uses data collected during carcass searches and estimates of detection rates to accurately estimate the number of fatalities and to provide a measure of precision associated with the estimate. These estimates are fundamental to understanding acute and cumulative effects of renewable energy development on wildlife populations. The software package is available with a user-friendly graphic interface as well as a flexible and powerful command-line implementation. GenEst includes tools for estimating searcher efficiency, carcass persistence, and other detection probability parameters from experimental field trials. Included in the software are example datasets for analyses, standard R package help files, this user guide, and vignettes detailing use at the command-line.

Techniques and Methods

Estimating wind-turbine-caused bird and bat fatality when zero carcasses are observed

Many wind-power facilities in the United States have established effective monitoring programs to determine turbine-caused fatality rates of birds and bats, but estimating the number of fatalities of rare species poses special difficulties. The loss of even small numbers of individuals may adversely affect fragile populations, but typically, few (if any) carcasses are observed during monitoring. If monitoring design results in only a small proportion of carcasses detected, then finding zero carcasses may give little assurance that the number of actual fatalities is small. Fatality monitoring at wind-power facilities commonly involves conducting experiments to estimate the probability ( g ) an individual will be observed, accounting for the possibilities that it falls in an unsearched area, is scavenged prior to detection, or remains undetected even when present. When g < 1, the total carcass count ( X ) underestimates the total number of fatalities ( M ). Total counts can be 0 when M is small or when M is large and g ≪1. Distinguishing these two cases is critical when estimating fatality of a rare species. Observing no individuals during searches may erroneously be interpreted as evidence of absence. We present an approach that uses Bayes' theorem to construct a posterior distribution for M , i.e., P ( M | X , ĝ ), reflecting the observed carcass count and previously estimated g . From this distribution, we calculate two values important to conservation: the probability that M is below a predetermined limit and the upper bound ( M * ) of the 100(1 &minus; &alpha;)% credible interval for M . We investigate the dependence of M * on &alpha;, g , and the prior distribution of M , asking what value of g is required to attain a desired M * for a given &alpha;. We found that when g < ~0.15, M * was clearly influenced by the mean and variance of ĝ and the choice of prior distribution for M , but the influence of these factors is minimal when g > ~0.45. Further, we develop extensions for temporal replication that can inform prior distributions of M and methods for combining information across several areas or time periods. We apply the method to data collected at a wind-power facility where scheduled searches yielded X = 0 raptor carcasses

Ecological Applications

Impacts of multispecies parasitism on juvenile coho salmon (Oncorhynchus kisutch) in Oregon

We are studying the impacts of parasites on threatened stocks of Oregon coastal coho salmon (Oncorhynchus kisutch). In our previous studies, we have found high infections of digeneans and myxozoans in coho salmon parr from the lower main stem of West Fork Smith River (WFSR), Oregon. In contrast parr from tributaries of this river, and outmigrating smolts, harbor considerably less parasites. Thus, we have hypothesized that heavy parasite burdens in parr from this river are associated with poor overwintering survival. The objective of the current study was to ascertain the possible effects these parasites have on smolt fitness. We captured parr from the lower main stem and tributaries of WFSR and held them in the laboratory to evaluate performance endpoints of smolts with varying degrees of infection by three digeneans (Nanophyetus salmincola, Apophallus sp., and neascus) and one myxozoan (Myxobolus insidiosus). The parameters we assessed were weight, fork length, growth, swimming stamina, and gill Na + ,K + -ATPase activity. We repeated our study on the subsequent year class and with hatchery reared coho salmon experimentally infected with N. salmincola. The most significant associations between parasites and these performance or fitness endpoints were observed in the heavily infected groups from both years. We found that all parasite species, except neascus, were negatively associated with fish fitness. This was corroborated for N. salmincola causing reduced growth with our experimental infection study. Parasites were most negatively associated with growth and size, and these parameters likely influenced the secondary findings with swimming stamina and ATPase activity levels.

Oregon

Estimating riparian understory vegetation cover with beta regression and copula models

Understory vegetation communities are critical components of forest ecosystems. As a result, the importance of modeling understory vegetation characteristics in forested landscapes has become more apparent. Abundance measures such as shrub cover are bounded between 0 and 1, exhibit heteroscedastic error variance, and are often subject to spatial dependence. These distributional features tend to be ignored when shrub cover data are analyzed. The beta distribution has been used successfully to describe the frequency distribution of vegetation cover. Beta regression models ignoring spatial dependence (BR) and accounting for spatial dependence (BRdep) were used to estimate percent shrub cover as a function of topographic conditions and overstory vegetation structure in riparian zones in western Oregon. The BR models showed poor explanatory power (pseudo-R 2 &le; 0.34) but outperformed ordinary least-squares (OLS) and generalized least-squares (GLS) regression models with logit-transformed response in terms of mean square prediction error and absolute bias. We introduce a copula (COP) model that is based on the beta distribution and accounts for spatial dependence. A simulation study was designed to illustrate the effects of incorrectly assuming normality, equal variance, and spatial independence. It showed that BR, BRdep, and COP models provide unbiased parameter estimates, whereas OLS and GLS models result in slightly biased estimates for two of the three parameters. On the basis of the simulation study, 93&ndash;97% of the GLS, BRdep, and COP confidence intervals covered the true parameters, whereas OLS and BR only resulted in 84&ndash;88% coverage, which demonstrated the superiority of GLS, BRdep, and COP over OLS and BR models in providing standard errors for the parameter estimates in the presence of spatial dependence.

Forest Science