vignetteCachedResults

A list containing a simulated tree, trait-values and POUMM objects (model 
fits). To use these objects in examples you can load them into the global 
workspace with the command: 
`data(vignetteCachedResults); list2env(vignetteCachedResults, globalenv());`.

datasets

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>.

Venelin Mitov

POUMM

The Phylogenetic Ornstein-Uhlenbeck Mixed Model

Matt Dowle

vignetteCachedResults function

This is a list containing the following named elements:<dl class="dl-horizontal">
 <dt>g, z, e </dt><dd>numeric vectors of simulated genotypic values, phenotypic values and measurement errors.</dd>
 <dt>tree </dt><dd>a simulated phylogenetic tree.</dd>
 <dt>fitPOUMM, fitPOUMM2, fitH2tMean </dt><dd>POUMM fit objects to tree and z.</dd>
</dl>

Format

Cached objects for the POUMM vignettes and examples — vignetteCachedResults

This is a list containing the following named elements:<dl class='dl-horizontal'>
 <dt>g, z, e </dt><dd>numeric vectors of simulated genotypic values, phenotypic values and measurement errors.</dd>
 <dt>tree </dt><dd>a simulated phylogenetic tree.</dd>
 <dt>fitPOUMM, fitPOUMM2, fitH2tMean </dt><dd>POUMM fit objects to tree and z.</dd>
</dl>

vignetteCachedResults: Cached objects for the POUMM vignettes and examples

Description

Usage

Arguments

Format