getA: Additive relationship matrix

In Rpedigree/pedigreeR: Versatile Functions for Working with Pedigrees

Additive relationship matrix

Description

Returns the additive relationship matrix for the pedigree.

Usage

getA(ped, labs = NULL)

Arguments

ped	pedigree
labs	a character vector or a factor giving individual labels to which to restrict the relationship matrix and corresponding factor. If labs is a factor then the levels of the factor are used as the labels. Default is the complete set of individuals in the pedigree.

Value

matrix (dsCMatrix - symmetric sparse)

Examples

ped <- pedigree(sire = c(NA, NA, 1,  1, 4, 5),
                dam =  c(NA, NA, 2, NA, 3, 2),
                label = 1:6)
(A <- getA(ped))

# Test for correctness
AExp <- matrix(data = c(1.0000, 0.0000, 0.5000, 0.5000, 0.5000, 0.2500,
                        0.0000, 1.0000, 0.5000, 0.0000, 0.2500, 0.6250,
                        0.5000, 0.5000, 1.0000, 0.2500, 0.6250, 0.5625,
                        0.5000, 0.0000, 0.2500, 1.0000, 0.6250, 0.3125,
                        0.5000, 0.2500, 0.6250, 0.6250, 1.1250, 0.6875,
                        0.2500, 0.6250, 0.5625, 0.3125, 0.6875, 1.1250),
               byrow = TRUE, nrow = 6)
stopifnot(!any(abs(A - AExp) > .Machine$double.eps))
stopifnot(Matrix::isSymmetric(A))

Rpedigree/pedigreeR documentation built on Oct. 13, 2023, 7:35 p.m.