POUMM: 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 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".

Version: 1.3.2
Depends: R (≥ 3.1.0), stats, Rcpp, methods
Imports: ape, data.table (≥ 1.10.4), coda, foreach, ggplot2, GGally, gsl, adaptMCMC, utils
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, TreeSim (≥ 2.2), Rmpfr, mvtnorm, lmtest, knitr, rmarkdown, parallel, doParallel, microbenchmark
Published: 2017-07-02
Author: Venelin Mitov [aut, cre, cph]
Maintainer: Venelin Mitov <vmitov at gmail.com>
License: GPL (≥ 3.0)
NeedsCompilation: yes
Citation: POUMM citation info
Materials: README
CRAN checks: POUMM results


Reference manual: POUMM.pdf
Vignettes: A User Guide to The POUMM R-package
Package source: POUMM_1.3.2.tar.gz
Windows binaries: r-devel: POUMM_1.3.2.zip, r-release: POUMM_1.3.2.zip, r-oldrel: POUMM_1.3.2.zip
OS X El Capitan binaries: r-release: POUMM_1.3.2.tgz
OS X Mavericks binaries: r-oldrel: POUMM_1.3.2.tgz
Old sources: POUMM archive


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