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9 results for “capture-recapture studies”
Acoustic spatial capture-recapture study on vocalising bowhead whales
<h1>Acoustic spatial capture-recapture study on vocalising bowhead whales</h1> <p>Contains the code and data used for the analysis of the case study data and run the simulation study. <br>The results of this study have been peer-reviewed and published (DOI: https://doi.org/10.1007/s13253-023-00563-0) and also appear in Chapter 2 and 3 of the PhD thesis "Advancements in methods for estimating the abundance of marine megafauna using novel sampling techniques" by Felix T Petersma. <br>We provide some information in support of the files presented here; however, for extensive background we kindly refer you to the publication.</p> <p>Most of the functionality of the model fitting is contained in the 'ascrRcpp'-package. <br>This package has been included pre-built and can be installed using the file 'ascrRcpp_1.0.tar.gz'.<br>Once this package is installed, all scripts included in this location should run fine, given that all other packages that are used will be installed as well.</p> <p> </p>
Modeling the demography of species providing extended parental care: A capture-recapture approach with a case study on Polar Bears (Ursus maritimus)
<p><span><span><span><span><span><span><span><span><span><span><span>1. In species providing extended parental care, one or both parents care for altricial young over a period including more than one breeding season. We expect large parental investment and long-term dependency within family units to cause high variability in life trajectories among individuals with complex consequences at the population level. So far, models for estimating demographic parameters in free-ranging animal populations mostly ignore extended parental care, thereby limiting our understanding of its consequences on parents and offspring life histories.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>2. We designed a capture-recapture multi-event model for studying the demography of species providing extended parental care. It handles statistical multiple-year dependency among individual demographic parameters grouped within family units, variable litter size, and uncertainty on the timing at offspring independence. It allows for the evaluation of trade-offs among demographic parameters, the influence of past reproductive history on the caring parent's survival status, breeding probability and litter size probability, while accounting for imperfect detection of family units. We assess the model performance using simulated data, and illustrate its use with a long-term dataset collected on the Svalbard polar bears (<i>Ursus maritimus</i>).</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>3. Our model performed well in terms of bias and mean square error and in estimating demographic parameters in all simulated scenarios, both when offspring departure probability from the family unit occurred at a constant rate or varied during the field season depending on the date of capture. For the polar bear case study, we provide estimates of adult and dependent offspring survival rates, breeding probability and litter size probability. Results showed that the outcome of the previous reproduction influenced breeding probability.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>4. Overall, our results show the importance of accounting for i) the multiple-year statistical dependency within family units, ii) uncertainty on the timing at offspring independence, and iii) past reproductive history of the caring parent. If ignored, estimates obtained for breeding probability, litter size, and survival can be biased. This is of interest in terms of conservation because species providing extended parental care are often long-living mammals vulnerable or threatened with extinction.</span></span></span></span></span></span></span></span></span></span></span></p>
R code and simulation output for Efford, M. G. & Boulanger, J. 2019. Fast evaluation of study designs for spatially explicit capture-recapture. Methods in Ecology and Evolution
<p>R code and simulation output for Efford, M. G. & Boulanger,<br> J. 2019. Fast evaluation of study designs for spatially explicit<br> capture-recapture. Methods in Ecology and Evolution In press.</p> <p>R code draws on previously published R packages 'secr' and 'secrdesign' available from CRAN:</p> <p><a href="https://CRAN.R-project.org/package=secr">https://CRAN.R-project.org/package=secr</a></p> <p><a href="https://CRAN.R-project.org/package=secrdesign">https://CRAN.R-project.org/package=secrdesign</a></p>
Modeling the demography of species providing extended parental care: A capture-recapture approach with a case study on Polar Bears (Ursus maritimus)
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Complete tag loss in capture-recapture studies affects abundance estimates: an elephant seal case study
<p>1. In capture-recapture studies, recycled individuals occur when individuals lose all of their tags and are recaptured as though they were new individuals. Typically, the effect of these recycled individuals is assumed negligible.</p> <p>2. Through a simulation-based study of double tagging experiments, we examined the effect of recycled individuals on parameter estimates in the Jolly-Seber model with tag loss (Cowen & Schwarz, 2006). We validated the simulation framework using long-term census data of elephant seals.</p> <p>3. Including recycled individuals did not affect estimates of capture, survival, and tag-retention probabilities. However, with low tag-retention rates, high capture rates, and high survival rates, recycled individuals produced over estimates of population size. For the elephant seal case study, we found population size estimates to be between 8 and 53% larger when recycled individuals were ignored.</p> <p>4. Ignoring the effects of recycled individuals can cause large biases in population size estimates. These results are particularly noticeable in longer studies.</p>
Complete tag loss in capture-recapture studies affects abundance estimates: an elephant seal case study
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Data from: Simulation-based validation of spatial capture-recapture models: a case study using mountain lions
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Data from: Comparison of photo-matching algorithms commonly used for photographic capture-recapture studies
Photographic capture–recapture is a valuable tool for obtaining demographic information on wildlife populations due to its noninvasive nature and cost-effectiveness. Recently, several computer-aided photo-matching algorithms have been developed to more efficiently match images of unique individuals in databases with thousands of images. However, the identification accuracy of these algorithms can severely bias estimates of vital rates and population size. Therefore, it is important to understand the performance and limitations of state-of-the-art photo-matching algorithms prior to implementation in capture–recapture studies involving possibly thousands of images. Here, we compared the performance of four photo-matching algorithms; Wild-ID, I3S Pattern+, APHIS, and AmphIdent using multiple amphibian databases of varying image quality. We measured the performance of each algorithm and evaluated the performance in relation to database size and the number of matching images in the database. We found that algorithm performance differed greatly by algorithm and image database, with recognition rates ranging from 100% to 22.6% when limiting the review to the 10 highest ranking images. We found that recognition rate degraded marginally with increased database size and could be improved considerably with a higher number of matching images in the database. In our study, the pixel-based algorithm of AmphIdent exhibited superior recognition rates compared to the other approaches. We recommend carefully evaluating algorithm performance prior to using it to match a complete database. By choosing a suitable matching algorithm, databases of sizes that are unfeasible to match "by eye" can be easily translated to accurate individual capture histories necessary for robust demographic estimates.
Data from: Comparison of photo-matching algorithms commonly used for photographic capture-recapture studies
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