RT Journal Article
SR Electronic
T1 phylopath: Easy phylogenetic path analysis in R
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 212068
DO 10.1101/212068
A1 Wouter van der Bijl
YR 2017
UL http://biorxiv.org/content/early/2017/10/31/212068.abstract
AB Confirmatory path analysis allows researchers to evaluate and compare causal models using observational data. This tool has great value for comparative biologists since they are often unable to gather experimental data on macro-evolutionary hypotheses, but is cumbersome and error-prone to perform.I introduce phylopath, an R package that implements phylogenetic path analysis (PPA) as described by Von Hardenberg & Gonzalez-Voyer (2013). In addition to the published method, I provide support for the inclusion of binary variables.I illustrate PPA and phylopath by recreating part of a study on the relationship between brain size and vulnerability to extinction.The package aims to make the analysis straight-forward, providing convenience functions and several plotting methods, which I hope will encourage the spread of the method.phylopath is released under the GPL-3 license, and is freely available on CRAN (https://cran.r-project.org/web/packages/phylopath/index.html) and GitHub (https://github.com/Ax3man/phylopath).