mvMORPH: An R package for fitting multivariate evolutionary models to morphometric data

Abstract

Summary: We present mvMORPH, a package of multivariate phylogenetic comparative methods for the r statistical environment. mvMORPH is freely available on the cran package repository (http://cran.r-project.org/web/packages/mvMORPH/). mvMORPH allows fitting a range of multivariate evolutionary models under a maximum-likelihood criterion. Initially developed in the context of phylogenetic analysis of multiple morphometric traits, its use can be extended to any biological data set with one or multiple covarying continuous traits. All the fitting models include the possibility to use simmap-like mapping, which may be useful for fitting changes along lineages at a given point in time. All models provide diagnostic metrics for convergence and reliability of estimates, as well as the possibility to include trait measurement errors in model estimates. New features provided by the mvMORPH package include the possibility of fitting models with changes in the mode of evolution along the phylogeny, which will be particularly meaningful in comparative analyses that include extinct taxa, for example when testing changes in evolutionary mode associated with global biotic/abiotic events. We briefly describe the models already included in mvMORPH and provide some demonstration of the use of the package with two simulated worked examples.