pedpartial: Calculate Partial Inbreeding

In visPedigree: Tidying, Analysis, and Fast Visualization of Animal and Plant Pedigrees

Calculate Partial Inbreeding

Description

Decomposes individuals' inbreeding coefficients into marginal contributions from specific ancestors. This allows identifying which ancestors or lineages are responsible for the observed inbreeding.

Usage

pedpartial(ped, ancestors = NULL, top = 20)

Arguments

ped	A tidyped object.
ancestors	Character vector. IDs of ancestors to calculate partial inbreeding for. If NULL, the top ancestors by marginal contribution are used.
top	Integer. Number of top ancestors to include if ancestors is NULL.

Details

The sum of all partial inbreeding coefficients for an individual (including contributions from founders) equals $1 + f_i$, where $f_i$ is the total inbreeding coefficient. This function specifically isolates the terms in the Meuwissen & Luo (1992) decomposition that correspond to the selected ancestors.

Value

A data.table with the first column as Ind and subsequent columns representing the partial inbreeding ($pF$) from each ancestor.

References

Lacey, R. C. (1996). A formula for determining the partial inbreeding coefficient, F_{ij}. Journal of Heredity, 87(4), 337-339.

Meuwissen, T. H., & Luo, Z. (1992). Computing inbreeding coefficients in large populations. Genetics Selection Evolution, 24(4), 305-313.

Examples

library(data.table)
tp <- tidyped(inbred_ped)
# Calculate partial inbreeding originating from specific ancestors
target_ancestors <- inbred_ped[is.na(Sire) & is.na(Dam), Ind]
pF <- pedpartial(tp, ancestors = target_ancestors)
print(tail(pF))

visPedigree documentation built on March 30, 2026, 9:07 a.m.