maxLikPOUMMGivenTreeVTips

function(par, memo, parFixedNoAlpha)

loglik

a list-object returned by the pruneTree(tree, z) function.

pruneInfo

Two named numeric vectors indicating the boundaries of 
the search region. Default values are parLower = c(alpha = 0, theta = 0, 
sigma = 0, sigmae = 0) and parUpper = c(alpha = 100, theta = 10, sigma = 20, 
sigmae = 10).

parLower, parUpper

A named vector (like parLower and parUpper) or a list of such
vectors - starting points for optim.

parInitML

List of parameters passed on to optim, default 
list(factr = 1e8, fnscale = -1), see ?optim.

control

A logical indicating whether to print informative messages on 
the standard output.

verbose

A logical indicating whether to print debug messages 
(currently not implemented).

debug

Find a maximum likelihood fit of the POUMM 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>.

maxLikPOUMMGivenTreeVTips: Find a maximum likelihood fit of the POUMM model

Description

Usage

Arguments

Value