Learn R Programming

phylopath (version 1.4.0)

Perform Phylogenetic Path Analysis

Description

A comprehensive and easy to use R implementation of confirmatory phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer (2012) . Note that the required package 'ggm' depends on 'graph' from Bioconductor, which is not installed automatically; the simplest route is install.packages("BiocManager"); BiocManager::install("phylopath").

Copy Link

Version

Install

install.packages('phylopath')

Monthly Downloads

716

Version

1.4.0

License

GPL-3

Maintainer

Wouter van der Bijl

Last Published

August 20th, 2026

Functions in phylopath (1.4.0)

Plot path coefficients and their confidence intervals or standard errors.

Cichlid phylogeny.

Directed acyclic graphs (DAGs)

Extract and average the best supported models from a phylogenetic path analysis.

Extract and estimate the best supported model from a phylogenetic path analysis.

coef.fitted_DAG

Extract the coefficients and confidence intervals of a fitted causal model.

Extract and estimate an arbitrary model from a phylogenetic path analysis.

as.data.frame.fitted_DAG

Extract the paths of a fitted causal model.

Perform model averaging on a list of DAGs.

Plot several causal hypothesis at once.

Compare causal models in a phylogenetic context.

define_model_set

Define a model set.

Estimate path coefficients for a DAG.

Plot a directed acyclic graph.

plot.phylopath_summary

Plot the comparison of a set of causal models.

plot.fitted_DAG

Plot a directed acyclic graph with path coefficients.

Print out warnings from a phylopath analysis.

Rhinogrades traits.

Cichlid traits and the evolution of cooperative breeding.

Data on brain size, life history and vulnerability to extinction

Rhinogrades phylogeny.

Mammalian phylogeny