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)