MCMCglmm (version 1.06)

inverseA: Inverse Relatedness Matrix and Phylogenetic Covariance Matrix

Description

Henderson (1976) and Meuwissen and Luo (1992) algorithm for inverting relatedness matrices, and Hadfield and Nakagawa (2009) algorithm for inverting phylogenetic covariance matrices.

Usage

inverseA(pedigree=NULL, nodes="ALL", scale=TRUE)

Arguments

pedigree

ordered pedigree with 3 columns: id, dam and sire, or a phylo object.

nodes

"ALL" calculates the inverse for all individuals/nodes. For phylogenies "TIPS" calculates the inverse for the species tips only, and for pedigrees a vector of id's can be passed which inverts the relatedness matrix for that

scale

logical: should a phylogeny (needs to be ultrametric) be scaled to unit length (distance from root to tip)?

Value

• Ainv
  inverse as sparseMatrix
• inbreeding
  inbreeding coefficients/branch lengths
• pedigree
  pedigree/pedigree representation of phylogeny

References

Henderson (1976) Biometrics 32 (1) 69:83 Meuwissen and Luo (1992) 24 (4) 305:313 Hadfield and Nakagawa (2009) submitted

Examples

data(bird.families)
Ainv<-inverseA(bird.families)