Random Generation of MVN Breeding Values and Phylogenetic Effects

distribution

Fits Multivariate Generalised Linear Mixed Models (and related models) using Markov chain Monte Carlo techniques (Hadfield 2010 J. Stat. Soft.).

Jarrod Hadfield

MCMCglmm

MCMC Generalised Linear Mixed Models

rbv function

<dl> <dt>pedigree</dt>
<dd>ordered pedigree with 3 columns id, dam and sire or a 
<code>phylo</code> object.</dd> <dt>G</dt>
<dd>(co)variance matrix</dd> <dt>nodes</dt>
<dd>effects for pedigree/phylogeny nodes to be returned. The default, 
<code>nodes="ALL"</code> returns effects for all individuals in a pedigree or nodes in 
a phylogeny (including ancestral nodes). For phylogenies <code>nodes="TIPS"</code> 
returns effects for the tips only, and for pedigrees a vector of ids can be 
passed to <code>nodes</code> specifying the subset of individuals for which animal 
effects are returned.</dd> <dt>scale</dt>
<dd>logical: should a phylogeny (needs to be ultrametric) be scaled to 
unit length (distance from root to tip)?</dd> <dt>ggroups</dt>
<dd>optional; vector of genetic groups</dd> <dt>gmeans</dt>
<dd>matrix of mean breeding value for genetic groups (rows) by traits (columns)</dd></dl>

Arguments

Jarrod Hadfield <a href="/link/j.hadfield%40ed.ac.uk?package=MCMCglmm&version=2.36" data-mini-rdoc="MCMCglmm::j.hadfield@ed.ac.uk">j.hadfield@ed.ac.uk</a>

Author

Random Generation of MVN Breeding Values and Phylogenetic Effects — rbv

<dl>

 <dt>pedigree</dt>
<dd>ordered pedigree with 3 columns id, dam and sire or a 
<code>phylo</code> object.</dd>

 <dt>G</dt>
<dd>(co)variance matrix</dd>

 <dt>nodes</dt>
<dd>effects for pedigree/phylogeny nodes to be returned. The default, 
<code>nodes="ALL"</code> returns effects for all individuals in a pedigree or nodes in 
a phylogeny (including ancestral nodes). For phylogenies <code>nodes="TIPS"</code> 
returns effects for the tips only, and for pedigrees a vector of ids can be 
passed to <code>nodes</code> specifying the subset of individuals for which animal 
effects are returned.</dd>

 <dt>scale</dt>
<dd>logical: should a phylogeny (needs to be ultrametric) be scaled to 
unit length (distance from root to tip)?</dd>

 <dt>ggroups</dt>
<dd>optional; vector of genetic groups</dd>

 <dt>gmeans</dt>
<dd>matrix of mean breeding value for genetic groups (rows) by traits (columns)</dd>

</dl>

Jarrod Hadfield <a href='mailto:j.hadfield@ed.ac.uk'>j.hadfield@ed.ac.uk</a>

rbv: Random Generation of MVN Breeding Values and Phylogenetic Effects

Description

Usage

Value

Arguments

Author

Examples