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 model along a phylogenetic tree. So far, the package has been used for estimating the heritability of quantitative traits in macroevolutionary and epidemiological studies, see e.g. Bertels et al. (2017) <doi:10.1093/molbev/msx246> and Mitov and Stadler (2018) <doi:10.1093/molbev/msx328>. The algorithm for parallel POUMM likelihood calculation has been published in Mitov and Stadler (2019) <doi:10.1111/2041-210X.13136>.

Version: 2.1.5
Depends: R (≥ 3.1.0), stats, Rcpp, methods
Imports: ape, data.table (≥ 1.10.4), coda, foreach, ggplot2, lamW, adaptMCMC, utils
LinkingTo: Rcpp
Suggests: testthat, usethis, Rmpfr, mvtnorm, lmtest, knitr, rmarkdown, parallel, doParallel
Published: 2019-03-27
Author: Venelin Mitov [aut, cre, cph], Matt Dowle [ctb]
Maintainer: Venelin Mitov <vmitov at gmail.com>
BugReports: https://github.com/venelin/POUMM/issues
License: GPL (≥ 3.0)
URL: https://venelin.github.io/POUMM/index.html, https://github.com/venelin/POUMM
NeedsCompilation: yes
Citation: POUMM citation info
Materials: README NEWS
CRAN checks: POUMM results


Reference manual: POUMM.pdf
Vignettes: Interpreting the POUMM model parameters
A User Guide to The POUMM R-package
Package source: POUMM_2.1.5.tar.gz
Windows binaries: r-devel: POUMM_2.1.5.zip, r-release: POUMM_2.1.5.zip, r-oldrel: POUMM_2.1.5.zip
OS X binaries: r-release: POUMM_2.1.5.tgz, r-oldrel: POUMM_2.1.5.tgz
Old sources: POUMM archive


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