Henderson (1976) and Meuwissen and Luo (1992) algorithm for inverting relatedness matrices, and Hadfield and Nakagawa (2010) algorithm for inverting phylogenetic covariance matrices.
inverseA(pedigree=NULL, nodes="ALL", scale=TRUE, reduced=FALSE,
tol = .Machine$double.eps^0.5)
inverse as sparseMatrix
inbreeding coefficients/branch lengths
pedigree/pedigree representation of phylogeny
ordered pedigree with 3 columns: id, dam and sire, or a
phylo
object.
"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.
logical: should a phylogeny (needs to be ultrametric) be scaled to unit length (distance from root to tip)?
logical: should childless nodes be dropped from the inverse and the pedigree/phylogeny representation be reduced?
numeric: differences in branch length smaller than this are ignored when assessing whether a tree is ultrametric.
Jarrod Hadfield j.hadfield@ed.ac.uk
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
data(bird.families)
Ainv<-inverseA(bird.families)
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