Package: phylopath 1.4.0

phylopath: Perform Phylogenetic Path Analysis

A comprehensive and easy to use R implementation of confirmatory phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer (2012) <doi:10.1111/j.1558-5646.2012.01790.x>. 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").

Authors:Wouter van der Bijl [aut, cre]

phylopath_1.4.0.tar.gz
phylopath_1.4.0.zip(r-4.7-any)phylopath_1.4.0.zip(r-4.6-any)phylopath_1.4.0.zip(r-4.5-any)
phylopath_1.4.0.tgz(r-4.6-any)phylopath_1.4.0.tgz(r-4.5-any)
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phylopath_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phylopath/json (API)

# Install 'phylopath' in R:
install.packages('phylopath', repos = c('https://ax3man.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ax3man/phylopath/issues

Pkgdown/docs site:https://ax3man.github.io

Datasets:

On CRAN:

Conda:

analysiscomparative-methodspathphylogenetics

7.89 score 13 stars 1 packages 123 scripts 793 downloads 8 mentions 11 exports 64 dependencies

Last updated from:8d78f7cb2f. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK214
source / vignettesOK241
linux-releaseOK271
macos-releaseOK208
macos-oldrelOK153
windows-develOK119
windows-releaseOK140
windows-oldrelOK130
wasm-releaseOK130

Exports:averageaverage_DAGsbestchoicecoef_plotDAGdefine_model_setest_DAGphylo_pathplot_model_setshow_warnings

Dependencies:apebase64encBiocGenericsBiocManagercachemclicodetoolscpp11digestdplyrfarverfastmapfuturefuture.applygenericsggforceggmggplot2ggraphggrepelglobalsgluegraphgraphlayoutsgridExtragtableigraphisobandjsonlitelabelinglatticelifecyclelistenvmagrittrMASSMatrixmemoisenlmeparallellyphylolmpillarpkgconfigpolyclippurrrR6RColorBrewerRcppRcppArmadillorlangS7scalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewithr

Comparing causal models of binary traits using phylopath
Introduction | On phylogenetic logistic regression | On the interpretation of coefficients | Example analysis | Data and hypotheses | Defining the causal models | Comparing the models | Evaluating variable importance
Rendered frombinary_models.Rmdusingknitr::rmarkdown

Last update: 2026-08-19
Started: 2017-07-06

Introduction to phylogenetic path analysis with phylopath
Some starting notes | Starting up | Models of evolution | An example analysis | Specifying the model set | Evaluating the model set | Selecting and fitting a final model
Rendered fromintro_to_phylopath.Rmdusingknitr::rmarkdown

Last update: 2026-08-17
Started: 2016-08-09