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. For examples on using the package, see the package vignettes.
| Version: | 2.1.2 |
| 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, Rmpfr, mvtnorm, lmtest, knitr, rmarkdown, parallel, doParallel |
| Published: | 2018-11-15 |
| Author: | Venelin Mitov [aut, cre, cph] |
| 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 |
| 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_2.1.2.tar.gz |
| Windows binaries: | r-devel: POUMM_2.1.2.zip, r-release: POUMM_2.1.2.zip, r-oldrel: POUMM_2.1.2.zip |
| OS X binaries: | r-release: POUMM_2.1.2.tgz, r-oldrel: POUMM_2.1.2.tgz |
| Old sources: | POUMM archive |
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