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phylopath: Easy phylogenetic path analysis in R.

Wouter van der Bijl
doi: https://doi.org/10.1101/212068
Wouter van der Bijl
Stockholm University
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  • For correspondence: wouter.van.der.bijl@zoologi.su.se
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Abstract

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).

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted October 31, 2017.
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phylopath: Easy phylogenetic path analysis in R.
Wouter van der Bijl
bioRxiv 212068; doi: https://doi.org/10.1101/212068
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phylopath: Easy phylogenetic path analysis in R.
Wouter van der Bijl
bioRxiv 212068; doi: https://doi.org/10.1101/212068

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