A package for inferring adaptive evolution to phylogenetic comparative data using Bayesian reversible-jump estimation of multi-optima Ornstein-Uhlenbeck models.
Methods for fitting macroevolutionary models to phylogenetic trees.
This R package matches phylogenetic trees and trait data, and
allows simultaneous manipulation of the tree and data using dplyr.
The data.table package enables high-performance extended functionality for data tables in R. treedata.table is a wrapper for data.table for phylogenetic analyses that matches a phylogeny to the data.table, and preserves matching during data.table operations.
PARAMO pipline is a set of R scripts for reconstructing organismal ancestral anatomies. It appropriately models anatomical dependencies and uses ontology-informed amalgamation of stochastic maps to reconstruct phenotypic evolution at different levels of anatomical hierarchy including entire phenotypes. This approach provides new opportunities for tracking phenotypic radiations and evolution of organismal anatomies.
treedata.table
PARAMO