inverseA {MCMCglmm}R Documentation

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 subset.
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

Author(s)

Jarrod Hadfield j.hadfield@ed.ac.uk

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)

[Package MCMCglmm version 1.06 Index]