pedigree-class {lme4}R Documentation

Class "pedigree"

Description

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 from the Class

Objects can be created by calls of the form new("pedigree", ...), or more conveniently, pedigree(sire= ., dam = ., label = .).

Slots

sire:
integer vector (with some NA entries), denoting a previous entry in the pedigree corresponding to the current entry's “father”.
dam:
similarly as sire for the “mother” of each entry.
label:
a "character" vector of the same length as sire and dam giving a unique ID for the corresponding entry.

Methods

chol
signature(x = "pedigree"
: returns the lower-triangular, sparse matrix (a dtCMatrix object) that is the left Cholesky factor of the relationship matrix of the pedigree.
coerce
signature(from = "pedigree", to = "dtCMatrix"): ...
coerce
signature(from = "pedigree", to = "data.frame"): ...
head
signature(x = "pedigree"): ...
show
signature(object = "pedigree"): ...
tail
signature(x = "pedigree"): ...

References

R. A. Mrode, Linear Models for the Prediction of Animal Breeding Values, 2nd ed, CABI Publishing, 2005.

See Also

pedigree

Examples

## 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

[Package lme4 version 0.9975-9 Index]