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".

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Description file content

Package
POUMM
Type
Package
Title
The Phylogenetic Ornstein-Uhlenbeck Mixed Model
Version
1.3.0
Date
2017-06-15
Description
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".
License
GPL (>= 3.0)
LazyData
true
Depends
R (>= 3.1.0), stats, Rcpp, methods
LinkingTo
Rcpp, RcppArmadillo
Imports
ape, data.table, coda, foreach, ggplot2, GGally, gsl, Matrix, adaptMCMC
Suggests
testthat, TreeSim (>= 2.2), Rmpfr, mvtnorm, lmtest, knitr, rmarkdown, parallel, doParallel
RoxygenNote
5.0.1
VignetteBuilder
knitr
ByteCompile
yes
NeedsCompilation
yes
Packaged
2017-06-15 19:48:58 UTC; vmitov
Author
Venelin Mitov [aut, cre, cph]
Maintainer
Venelin Mitov
Repository
CRAN
Date/Publication
2017-06-15 23:06:56 UTC

install.packages('POUMM')

1.3.0

7 days ago

Venelin Mitov

GPL (>= 3.0)

Depends on

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

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