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 parallel 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".

Documentation

Manual: POUMM.pdf
Vignette: A User Guide to The POUMM R-package

Maintainer: Venelin Mitov <vmitov at gmail.com>

Author(s): Venelin Mitov*

Install package and any missing dependencies by running this line in your R console:

install.packages("POUMM")

Depends R (>= 3.1.0), stats, Rcpp, methods
Imports ape, data.table, coda, foreach, ggplot2, GGally, gsl, Matrix, adaptMCMC
Suggests testthat, TreeSim(>=2.2), Rmpfr, mvtnorm, lmtest, knitr, rmarkdown, parallel, doParallel
Enhances
Linking to Rcpp, RcppArmadillo
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Package POUMM
Materials
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Version 1.3.0
Published 2017-06-15
License GPL (>= 3.0)
BugReports
SystemRequirements
NeedsCompilation yes
Citation
CRAN checks POUMM check results
Package source POUMM_1.3.0.tar.gz