BaSTA: an R package for Bayesian estimation of age‐specific survival from incomplete mark–recapture/recovery data with covariates

Abstract

Summary1. Understanding age‐specific survival in wild animal populations is crucial to the study of population dynamics and is therefore an essential component of several fields including evolution, management and conservation.2. We present Bayesian survival trajectory analysis (BaSTA), a free open‐source software package for estimating age‐specific survival from capture–recapture/recovery data under a Bayesian framework.3. The method copes with low recapture probabilities, unknown ages (e.g. because of left‐truncation) and unknown ages at death (e.g. because of right‐censoring). It estimates survival and detection parameters as well as the unknown birth and death times (i.e. latent states) while allowing users to test a range of survival models. In addition, the effect of continuous or categorical covariates can be evaluated.4. This tool facilitates the analysis of age patterns of survival in long‐term animal studies and will enable researchers to robustly infer the effect of covariates, even with large amounts of missing data.