Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses

This add-in package for Mathematica performs basic phylogenetic functions, including reading and drawing Newick format trees, calculating phylogenetically independent contrasts, reconstructing ancestral values for continuous traits, performing random walks, and simulating continuous traits on phylogenetic trees.

Workshop on Phylogenetic Comparative Methods using R instructed during the 2018 QCBS R Symposium

Data and code for Ghilardi et al. (2021) Phylogeny, body morphology, and trophic level shape intestinal traits in coral reef fishes. Ecology and Evolution

Library and command-line program calculating the generalized RF metrics; Used to compare phylogenetic trees.

This repository contains data and scripts to study phenotypic macroevolution and ecogeographical rules in Rana genus

bifrost is an R package for detecting shifts in multivariate evolutionary dynamics on phylogenies

A (not so) basic course of comparative biology.

Function to estimate evolutionary parameter in PGLS models using log-likelihood

Supplementary code and data for "The paradox of predictability"

Code and data for "Tempo and mode of diapause evolution in butterflies" Halali et al., 2024

Data and R scripts for the manuscript "Environment predicts repeated body size shifts in a recent radiation of Australian mammals"

TMB-based GLLVM engine for unit × trait data. First-class phylogenetic + spatial random effects; rr / diag / propto / spde dispatch; gaussian / binomial / poisson / lognormal / Gamma families; correlation / communality extractors; parametric bootstrap. Builds on sdmTMB / glmmTMB / galamm / MCMCglmm. Experimental (0.x).