Skip to contents

Easy phylogenetic path analysis in R

Use the phylopath package for an easy to use framework to perform phylogenetic path analysis (PPA).

PPA can be used to compare support for competing causal models of trait evolution, while taking shared ancestry into account. All you need is: 1. A clear set of models to test. 2. A data set of species with trait values. 3. A phylogeny of your species.

For a complete worked example, click “Get Started” above, or see the PeerJ paper.

Installation 

install.packages("BiocManager")
BiocManager::install("phylopath")

phylopath relies on ggm, which in turn needs graph from Bioconductor. BiocManager::install() installs from CRAN as well as Bioconductor, so this single command obtains all three. A plain install.packages("phylopath") works only if you already have graph.

This method was developed by Von Hardenberg and Gonzalez-Voyer. See citation() for info on correct citations.

A grid of nine small causal diagrams, one per candidate model, each showing directed arrows between the five rhinograde traits body mass, litter size, nose length, dry days and range size.

The fitted best supported causal model, with arrows labelled by their standardized path coefficients and drawn with a width proportional to the strength of the effect.

phylopath has been used by >200 publications so far!