R package for analysis of mark-recapture data solely with R
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README.md

README.md

marked - mark-recapture analysis

We developed this R package for analysis with marked animals in contrast to the R package unmarked (Fiske and Chandler 2011) that focuses on analysis with unmarked animals. The original impetus for the package was to implement the CJS model using the hierarchical likelihood construction described by Pledger et al. (2003) and to improve on execution times with RMark/MARK (White and Burnham 1999;Laake 2013) for analysis of our own large data sets with many time-varying individual (animal-specific) covariates. Subsequently, we implemented the Jolly-Seber model with the Schwarz and Arnason (1996) POPAN structure where the hierarchical likelihood construction idea extended to the entry of animals into the population. We also added a Bayesian Markov Chain Monte Carlo (MCMC) implementation of the CJS model based on the approach used by Albert and Chib (1993) for analyzing binary data with a probit regression model.

This package requires installation of ADMB if you set use.admb=TRUE. See readme.txt for installation instructions.

Download Windows package binary. From link, browse to marked and then click on the version of the package you want. You should see a listing of the package contents as files. Select File/Download. To install in R, from the R menu, use Packages\Install from Local Zip file and browse to location of downloaded zip.

Download package source files

The following are references from above:

Albert, J. and Chib, S. (1993). Bayesian-analysis of binary and polychotomous reponse data. Journal of the American Statistical Association, 88(422):669:679.

Fiske, I. J. and Chandler, R. B. (2011). unmarked : An R Package for tting hierarchical models of wildlife occurrence and abundance. 43(10):1:23.

Laake, J.L. (2013) RMark : An R Interface for Analysis of Capture-Recapture Data with MARK. AFSC Processed Rep 2013-01, 25p. Alaska Fish. Sci. Cent., NOAA, Natl. Mar. Fish. Serv., 7600 Sand Point Way NE, Seattle WA 98115.

Pledger, S., Pollock, K. H., and Norris, J. L. (2003). Open capture-recapture models with heterogeneity: I. Cormack-Jolly-Seber model. Biometrics, 59(4):786:794.

Schwarz, C. J. and Arnason, A. N. (1996). A general methodology for the analysis of capture-recapture experiments in open populations. Biometrics, 52(3):860:873. 16

White, G. C. and Burnham, K. P. (1999). Program MARK: survival estimation from populations of marked animals. Bird Study, 46:120:139.

This repository is a scientific product and is not official communication of the Alaska Fisheries Science Center, the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All AFSC Marine Mammal Laboratory (AFSC-MML) GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. AFSC-MML has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.