loglik_abc_g0_g0Prior

a vector of 3 numerical values denoting the corresponding 
coefficients in the POUMM likelihood presented as exp(a g0^2 + b g0 + c).

alpha, theta, sigma

initial value at the root of the tree (can be NA). See argument
parMapping in ?specifyPOUMM.

list object. See parameter g0Prior in ?specifyPOUMM.

g0Prior

Processing of the root value and calculation of the maximum log-likelihood 
for the given coefficients abc, and parameters theta, g0 and g0Prior. This is
an internal function.

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

loglik_abc_g0_g0Prior function

Processing of the root value and calculation of the maximum log-likelihood 
for the given coefficients abc, and parameters theta, g0 and g0Prior. This is
an internal function. — loglik_abc_g0_g0Prior

Processing of the root value and calculation of the maximum log-likelihood 
for the given coefficients abc, and parameters theta, g0 and g0Prior. This is
an internal function.

loglik_abc_g0_g0Prior: Processing of the root value and calculation of the maximum log-likelihood for the given coefficients abc, and parameters theta, g0 and g0Prior. This is an internal function.

Description

Usage

Arguments