Use of the Petersen Capture-Recapture estimates in fisheries management.
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CRAN Download the Petersen package
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Github To install the latest development version from Github, install the newest version of the devtools package; then run
devtools::install_github("cschwarz-stat-sfu-ca/Petersen", dependencies = TRUE,
build_vignettes = TRUE)
Extensive user manual available at:
https://github.com/cschwarz-stat-sfu-ca/Petersen/tree/master/PetersenMonograph
The Petersen-method is the simplest of more general capture-recapture methods which are extensively reviewed in Williams et al. (2002). Despite the Petersen method's simplicity, many of the properties of the estimator, and the effects of violations of assumptions are similar to these more complex capture-recapture studies. Consequently, a firm understanding of the basic principles learned from studying this method are extremely useful to develop an intuitive understanding of the larger class of studies.
The purpose of this R package is to bring together a wide body of older and newer literature on the design and analysis of the "simple" two-sample capture-recapture study. This monograph builds upon the comprehensive summaries found in Ricker (1975), Seber (1982), and William et AL (2002), and incorporates newer works that have not yet summarized. While the primary emphasis is on the application to fisheries management, the methods are directly applicable to many other studies.
The core of the package is the use of conditional likelihood estimation that allows for covariates which are not observed on animals not handled.
The packages includes functions for the analysis of
- simple studies with no covariates or strata
- simple stratified-Petersen studies or fixed continuous covariates
- incompletely stratified studies where only a sub-sample is stratified to save costs
- geographically stratified studies (wrapper to SPAS)
- temporally-stratified studies (wrapper to BTSPAS)
- double tagging studies including reward tagging studies
- multiple-Petersen studies (call RMark/MARK and use mark-resight methods therein)
- forward and reverse-Petersen studies and their combination
Petersen, C. G. J. (1896). The Yearly Immigration of Young Plaice into the Limfjord from the German Sea, Etc. Report Danish Biological Station 6, 1--48.
Seber, G. A. F. (1982). The Estimation of Animal Abundance and Related Parameters. 2nd ed. London: Griffin.
Williams, B. K., J. D. Nichols, and M. J. Conroy. (2002). Analysis and Management of Animal Populations. New York: Academic Press.