MCMCglmm: inverseA – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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 (2010) algorithm for inverting phylogenetic covariance matrices.

Usage

inverseA(pedigree=NULL, nodes="ALL", scale=TRUE, reduced=FALSE,
     tol = .Machine$double.eps^0.5)

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)?
`reduced`	logical: should childless nodes be dropped from the inverse and the pedigree/phylogeny representation be reduced?
`tol`	numeric: differences in branch length smaller than this are ignored when assessing whether a tree is ultrametric.

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, C.R. (1976) Biometrics 32 (1) 69:83

Quaas, R. L. and Pollak, E. J. (1980) Journal of Animal Science 51:1277-1287.

Meuwissen, T.H.E and Luo, Z. (1992) Genetic Selection Evolution 24 (4) 305:313

Hadfield, J.D. and Nakagawa, S. (2010) Journal of Evolutionary Biology 23 494-508

Examples

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

MCMCglmm

MCMC Generalised Linear Mixed Models

v2.32

GPL (>= 2)

Authors

Jarrod Hadfield

Initial release

2021-03-12