Rcapture: Loglinear models for capture-recapture in R

This article introduces Rcapture, an R package for capture-recapture experiments. The data for analysis consists of the frequencies of the observable capture histories over the t capture occasions of the experiment. A capture history is a vector of zeros and ones where one stands for a capture and zero for a miss. Rcapture can fit three types of models. With a closed population model, the goal of the analysis is to estimate the size N of the population which is assumed to be constant throughout the experiment. The estimator depends on the way in which the capture probabilities of the animals vary. Rcapture features several models for these capture probabilities that lead to different estimators for N. In an open population model, immigration and death occur between sampling periods. The estimation of survival rates is of primary interest. Rcapture can fit the basic Cormack-Jolly-Seber and Jolly-Seber model to such data. The third type of models fitted by Rcapture are robust design models. It features two levels of sampling; closed population models apply within primary periods and an open population model applies between periods. Most models in Rcapture have a loglinear form; they are fitted by carrying out a Poisson regression with the R function glm. Estimates of the demographic parameters of interest are derived from the loglinear parameter estimates; their variances are obtained by linearization. The novel feature of this package is the provision of several new options for modeling capture probabilities heterogeneity between animals in both closed population models and the primary periods of a robust design. It also implements many of the techniques developed by R. M. Cormack for open population models.