Open Population Capture-Recapture
Functions for non-spatial open population analysis by Cormack-Jolly-Seber (CJS) and Jolly-Seber- Schwarz-Arnason (JSSA) methods, and by spatially explicit extensions of these methods. The methods build on Schwarz and Arnason (1996), Borchers and Efford (2008) and Pledger et al. (2010) (see vignette for more comprehensive references and likelihood). The parameterisation of JSSA recruitment is flexible (options include population growth rate λ, per capita recruitment f and seniority γ). Spatially explicit analyses may assume home-range centres are static or allow dispersal between primary sessions according to various probability kernels, including bivariate normal (BVN) and bivariate t (BVT).
openCR 2.2.5 is available on CRAN.
See also --
www.otago.ac.nz/density/openCR.html
The code here is under development. It may be installed using
devtools::install_github("MurrayEfford/openCR")
Installation is rather slow, and produces voluminous messages because of the compilation of C++ code.
Borchers, D. L. and Efford, M. G. (2008) Spatially explicit maximum likelihood methods for capture--recapture studies. Biometrics 64, 377--385.
Efford, M. G. and Schofield, M. R. (2020) A spatial open-population capture--recapture model. Biometrics 76, 392--402.
Pledger, S., Pollock, K. H. and Norris, J. L. (2010) Open capture--recapture models with heterogeneity: II. Jolly-Seber model. Biometrics 66, 883--890.
Schwarz, C. J. and Arnason, A. N. (1996) A general methodology for the analysis of capture-recapture experiments in open populations. Biometrics 52, 860--873.