Estimating closed population size from capture-recapture data
This page provides R functions to fit some models of capture heterogeneity to estimate N, the size of a closed population, from capture-recapture data. This is joint work with Byron Morgan.
In the most general model that we consider, captures are modelled as a mixture of binomial and beta-binomial counts. This generalises the beta-binomial model considered, for example, by Dorazio and Royle [Ref 1] and the (two-component form of) finite mixture model considered, for example, by Pledger [Ref 2]. Our new model is described in Refs  and  below, which also provide other references to the existing literature.
There are important issues of identifiability in models of capture heterogeneity, see for example [Ref 5]. Our model does not resolve these problems, but it does offer a broad and flexible class of models within which to investigate and compare estimates of N.
A user guide explains how to use the software and gives details about computational methods. You need to download the file estimateN.R into a suitable directory on your computer. This contains all the functions needed to fit the models. You should not need to look at this code unless you want to see the details of what's going on. The code should work in R 2.6.1 onwards.
These files illustrate the use of the software:
All the data sets used in Refs  and  are in this file.
 Dorazio, R.M. and Royle, J.A. (2003). Mixture models for estimating the size of a closed population when capture rates vary among individuals. Biometrics, 59, 351-364.
 Pledger, S. (2000). Unified maximum likelihood estimates for closed capture-recapture models using mixtures. Biometrics, 56, 434-442.
 Morgan, B.J.T. and Ridout, M.S. (2008) A new mixture model for capture heterogeneity. Applied Statistics, 57, 433-446. [ journal link]
 Morgan, B.J.T. and Ridout, M.S. (2008) Estimating N: a robust approach to capture heterogeneity. In: Thomson, D.L. and Cooch, E.G. and Conroy, M.J., eds. Modelling Demographic Processes in Marked Populations. Environmental and Ecological Statistics. Springer, New York, pp. 1069-1080. ISBN 978-0-387-78150-1. [journal link]
 Link, W.A. (2003). Nonindentifiability of population size from capture-recapture data with heterogeneous detection probabilities. Biometrics, 59, 1123-1130.