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Last data update: 2014.03.03

R: Random Generation of MVN Breeding Values and Phylogenetic...

rbv	R Documentation

Random Generation of MVN Breeding Values and Phylogenetic Effects

Description

Random Generation of MVN Breeding Values and Phylogenetic Effects

Usage

rbv(pedigree, G, nodes="ALL", scale=TRUE, ggroups=NULL, gmeans=NULL)

Arguments

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

Value

matrix of breeding values/phylogenetic effects

Author(s)

Jarrod Hadfield j.hadfield@ed.ac.uk

Examples

data(bird.families)
bv<-rbv(bird.families, diag(2))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MCMCglmm)
Loading required package: Matrix
Loading required package: coda
Loading required package: ape
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MCMCglmm/rbv.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rbv
> ### Title: Random Generation of MVN Breeding Values and Phylogenetic
> ###   Effects
> ### Aliases: rbv
> ### Keywords: distribution
> 
> ### ** Examples
> 
> data(bird.families)
> bv<-rbv(bird.families, diag(2))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>