phylopath: Easy phylogenetic path analysis in R

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.

Keywords: Comparative methods; Evolution; Path analysis; Phylogenetic path analysis; R package.

Figure 1. The model set.

The model set is laid out algorithmically (A) and manually (B).

Figure 2. The relative importance of the four causal models.

Figure 3. The best supported causal model.

A visualization of the best supported causal model, and the standardized path coefficients.

Figure 4. The path coefficients.

Standardized path coefficients and their standard errors, for the best supported model (A) and the average of the top two models (B).