covVTipsGivenTreePOUMM

tree

Non-negative numeric values, parameters of the OU process.

alpha, sigma

Non-negative numeric value, environmental standard deviation at
the tips.

sigmae

Numerical matrix with the time-distance from the root of the tree
to the mrca of each tip-couple. If NULL it will be calculated.

tanc

Numerical matrix with the time (patristic) distance between each
pair of tips. If NULL, it will be calculated.

tauij

Logical indicating if a correlation matrix shall be returned.

corr

Variance covariance matrix of the values at the tips of a tree under an OU 
process

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>.

covVTipsGivenTreePOUMM: Variance covariance matrix of the values at the tips of a tree under an OU process

Description

Usage

Arguments

Value

References