resume_inbreed {FnR}

Calculate inbreeding coefficients from scratch or resume for new individuals in the pedigree

Description

Calculate inbreeding coefficients from scratch or resume for new individuals in the pedigree

Usage

resume_inbreed(ped, f = c(), d = c(), export_d = FALSE)

Arguments

ped

: A data frame with integer columns corresponding to ID, SIRE, and DAM. IDs should be sequential, starting from 1. Missing parents (SIRE and DAM) are denoted as 0.

f

: (Optional) If available, the vector of inbreeding coefficients from the previous calculation of inbreeding coefficients with less number of animals in the pedigree.

d

: (Optional) If available, the vector of the diagonal elements of the diagonal matrix D in \mathbf A = \mathbf{TDT}' from the previous calculation of inbreeding coefficients with less number of animals in the pedigree, where A is the numerator relationship matrix.

export_d

: FALSE (default) or TRUE. If TRUE, vector d is retuned for future use.

Value

: Vector of inbreeding coefficients if export_d == FALSE, or a list containing the vector of inbreeding coefficients and the vector of d coefficients if export_d == TRUE.

Examples

# A sample pedigree data frame:
ped <- data.frame(
    ID = 1:12,
    SIRE = c(0, 0, 0, 2, 2, 0, 4, 6, 0, 6, 10, 10),
    DAM = c(0, 0, 0, 1, 1, 0, 3, 5, 7, 8, 9, 0)
)

oldped <- ped[1:9, ]
(oldrun <- resume_inbreed(oldped, export_d = TRUE))
resume_inbreed(ped)
resume_inbreed(ped, f = oldrun$f)
resume_inbreed(ped, f = oldrun$f, d = oldrun$d)