extBatchMarking: An R package for hidden Markov models for extended batch data

Abstract

We describe a new R package for extended batch‐mark methods. Extended batch marking is a valuable and efficient technique for estimating population sizes and survival probabilities of wild animals. It assigns the same identifier to a group of animals simultaneously, allowing researchers to track their survival over time. By analysing the proportions of batch‐marked individuals in subsequent samples, population size and survival probabilities, whether constant or time‐varying, can be estimated accurately. Despite its advantages, extended batch marking is not widely supported in R statistical software. To address this gap, we present extBatchMarking , an R package for fitting extended batch‐mark models using Hidden Markov Models and integrated population frameworks. We demonstrate the package's functionality through applications using datasets and simulation studies that show how the choice of package arguments can affect the parameter estimates.