The Phylogenetic Ornstein-Uhlenbeck Mixed Model

The Phylogenetic Ornstein-Uhlenbeck Mixed Model (POUMM) allows to estimate the phylogenetic heritability of continuous traits, to test hypotheses of neutral evolution versus stabilizing selection, to quantify the strength of stabilizing selection, to estimate measurement error and to make predictions about the evolution of a phenotype and phenotypic variation in a population. The package implements combined maximum likelihood and Bayesian inference of the univariate Phylogenetic Ornstein-Uhlenbeck Mixed Model, fast POUMM likelihood calculation, maximum likelihood inference of the genotypic values at the tips, functions for summarizing and plotting traces and posterior samples, functions for simulation of a univariate continuous trait evolution along a phylogenetic tree. A quick example on using the POUMM package can be found in the README. More elaborate examples and use-cases are provided in the vignette "A User Guide to The POUMM R-package".


Reference manual

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1.2.2 by Venelin Mitov, 2 days ago

Browse source code at

Authors: Venelin Mitov [aut, cre, cph]

Documentation:   PDF Manual  

GPL (>= 3.0) license

Imports ape, data.table, coda, foreach, ggplot2, GGally, gsl, Matrix

Depends on stats, Rcpp, methods

Suggests testthat, TreeSim, Rmpfr, mvtnorm, lmtest, knitr, rmarkdown, parallel, doParallel

Linking to Rcpp, RcppArmadillo

See at CRAN