strandCet: R package for estimating natural and non-natural mortality-at-age of cetaceans from age-structured strandings

PeerJ. 2018 Oct 9:6:e5768. doi: 10.7717/peerj.5768. eCollection 2018.

Abstract

Mortality is one of the most important parameters for the study of population dynamics. One of the main sources of information to calculate the mortality of cetaceans arises from the observed age-structure of stranded animals. A method based on an adaptation of a Heligman-Pollard model is proposed. A freely accessible package of functions (strandCet) has been created to apply this method in the statistical software R. Total, natural, and anthropogenic mortality-at-age is estimated using only data of stranded cetaceans whose age is known. Bayesian melding estimation with Incremental Mixture Importance Sampling is used for fitting this model. This characteristic, which accounts for uncertainty, further eases the estimation of credible intervals. The package also includes functions to perform life tables, Siler mortality models to calculate total mortality-at-age and Leslie matrices to derive population projections. Estimated mortalities can be tested under different scenarios. Population parameters as population growth, net production or generation time can be derived from population projections. The strandCet R package provides a new analytical framework to assess mortality in cetacean populations and to explore the consequences of management decisions using only stranding-derived data.

Keywords: Anthropogenic mortality; Bycatch; Cetaceans; Mortality-at-age; Natural mortality; Strandings.

Grants and funding

The research leading to these results has received funding from the European Union’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no 613571—MareFrame. The author received a pre-doctoral grant from the Spanish Institute of Oceanography (BOE-A-2011-2541). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.