Package: phylowise 0.0.1

Jordan Douglas

phylowise: Phylogenetic Pairwise Contrasts

A phylogenetic comparative method for finding associations between biological traits and molecular evolutionary rates. The method samples pairs from a phylogeny such that each pair has non-overlapping edge paths, and can therefore be treated as statistically independent observations. Linear regression is performed on the pair contrasts. This approach is similar to phylogenetically independent contrasts (PIC) but without reconstructing the traits at internal nodes, and is better suited for finding trait-rate associations than phylogenetic generalised least squares (PGLS). Refer to Douglas and Bromham (2026) <doi:10.64898/2026.08.13.744736> for further details.

Authors:Jordan Douglas [aut, cre], Lindell Bromham [aut]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
phylowise/json (API)

# Install 'phylowise' in R:

install.packages('phylowise', repos = c('https://jordandouglas.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jordandouglas/phylowise/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.48 score 1 stars 204 downloads 7 exports 16 dependencies

Last updated from:06b9af4a4b. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	118
linux-devel-x86_64	OK	156
source / vignettes	OK	210
linux-release-arm64	OK	112
linux-release-x86_64	OK	142
macos-release-arm64	OK	251
macos-release-x86_64	OK	313
macos-oldrel-arm64	OK	187
macos-oldrel-x86_64	OK	322
windows-devel-arm64	OK	338
windows-devel-x86_64	OK	148
windows-release-arm64	OK	428
windows-release-x86_64	OK	110
windows-oldrel-x86_64	OK	109
wasm-release	OK	97

Exports:getDistanceMatrix plotPairs PPC.test readBeastTrees sampleTaxonPairs simulateSubstitutions simulateTrait

Dependencies:ape BMA DEoptimR digest inline lattice leaps Matrix mvtnorm nlme pcaPP phylotate Rcpp robustbase rrcov survival

Help page	Topics
Build a distance matrix from a tree (time tree or substitution tree)	getDistanceMatrix
Plot a set of sampled pairs onto a tree	plotPairs
Phylogenetic pairwise contrast test on a series of taxon pairs, using ordinary least squares and Bayesian model averaging (BMA). This method does not do multivariate regression, but it returns the data frame that can be used for it.	PPC.test
Read a single summary tree or a posterior distribution of annotated nexus trees generated by the BEAST software suites, and apply burn-in. Built on top of the phylotate::read_annotated function.	readBeastTrees
Sample a set of taxon pairs from the tree. These taxa will have non-overlapping edges between their paths and can this be treated as statistically independent. The algorithm iteratively searches for two random taxa that satisfy sampling requirements until there are no more valid pairs. Each pair must descend from an MRCA with dist.min <= tMRCA <= dist.max. c++ is used to speed up the runtime of this code.	sampleTaxonPairs
Simulate a substitution count down each branch of a tree. First, the branch rates are sampled from a correlated, uncorrelated or OU process that can be dependent on traits. Then the number of substitutions along each branch is sampled from a Poisson distribution.	simulateSubstitutions
Simulate a trait down a tree using Brownian motion (BM)	simulateTrait

Package: phylowise 0.0.1

phylowise: Phylogenetic Pairwise Contrasts

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