pedigree: Pedigree Constructor

In pedigreemm: Pedigree-based mixed-effects models

Description

Construct an object of class "pedigree", more conveniently than by new("pedigree", ....).

Usage

pedigree(sire, dam, label)

Arguments

sire	numeric vector (with some NA entries) of integer IDs, 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 vector coercable to "character" of the same length as sire and dam giving a unique ID for the corresponding entry.

Value

an object of formal class "pedigree".

References

2010. A.I. Vazquez, D.M. Bates, G.J.M. Rosa, D. Gianola and K.A. Weigel. Technical Note: An R package for fitting generalized linear mixed models in animal breeding. Journal of Animal Science, 88:497-504.

See Also

the pedigree class.

Examples

example("pedigree-class") ## 'p1' pedigree object `the hard way'

ped <- pedigree(sire = c(NA,NA,1, 1,4,5),
                dam  = c(NA,NA,2,NA,3,2), label= 1:6)
## note that 'label' is coerced to character automatically
ped
stopifnot(identical(ped, p1))

Example output

Loading required package: lme4
Loading required package: Matrix

pdgr-c> ## Rather use, pedigree()!   The following is "raw code":
pdgr-c> ## Example from chapter 2 of Mrode (2005)
pdgr-c> p1 <- new("pedigree",
pdgr-c+           sire = as.integer(c(NA,NA,1, 1,4,5)),
pdgr-c+           dam  = as.integer(c(NA,NA,2,NA,3,2)),
pdgr-c+           label = as.character(1:6))

pdgr-c> p1
  sire  dam
1 <NA> <NA>
2 <NA> <NA>
3    1    2
4    1 <NA>
5    4    3
6    5    2

pdgr-c> (dtc <- as(p1, "sparseMatrix"))   # T-inverse in Mrode's notation
6 x 6 sparse Matrix of class "dtCMatrix" (unitriangular)
                            
1  I    .    .    .    .   .
2  .    I    .    .    .   .
3 -0.5 -0.5  I    .    .   .
4 -0.5  .    .    I    .   .
5  .    .   -0.5 -0.5  I   .
6  .   -0.5  .    .   -0.5 I

pdgr-c> solve(dtc)
6 x 6 sparse Matrix of class "dtCMatrix"
                               
[1,] 1.00 .     .    .    .   .
[2,] .    1.000 .    .    .   .
[3,] 0.50 0.500 1.00 .    .   .
[4,] 0.50 .     .    1.00 .   .
[5,] 0.50 0.250 0.50 0.50 1.0 .
[6,] 0.25 0.625 0.25 0.25 0.5 1

pdgr-c> inbreeding(p1)
[1] 0.000 0.000 0.000 0.000 0.125 0.125
  sire  dam
1 <NA> <NA>
2 <NA> <NA>
3    1    2
4    1 <NA>
5    4    3
6    5    2

pedigreemm documentation built on May 2, 2019, 5:19 p.m.