| pedigree-class {lme4} | R Documentation |
Objects of class "pedigree" represent a set of
individuals that can have two parents including their parent-child
relations. The terminology has been taken from cattle breeding.
Objects can be created by calls of the form new("pedigree",
...), or more conveniently, pedigree(sire= ., dam = ., label = .).
sire:NA entries),
denoting a previous entry in the pedigree corresponding to
the current entry's “father”.dam:sire for the “mother”
of each entry.label:"character" vector of the same length
as sire and dam giving a unique ID for the
corresponding entry.signature(x = "pedigree"dtCMatrix object) that is
the left Cholesky factor of the relationship matrix of the pedigree.signature(from = "pedigree", to = "dtCMatrix"): ... signature(from = "pedigree", to = "data.frame"): ... signature(x = "pedigree"): ... signature(object = "pedigree"): ... signature(x = "pedigree"): ... R. A. Mrode, Linear Models for the Prediction of Animal Breeding Values, 2nd ed, CABI Publishing, 2005.
## Rather use, pedigree()! The following is "raw code":
## Example from chapter 2 of Mrode (2005)
p1 <- new("pedigree",
sire = as.integer(c(NA,NA,1, 1,4,5)),
dam = as.integer(c(NA,NA,2,NA,3,2)),
label = as.character(1:6))
p1
(dtc <- as(p1, "dtCMatrix")) # T-inverse in Mrode's notation
solve(dtc)
chol(p1) # (left) Cholesky factor of A, the relationship matrix