pedfclass: Summarize Inbreeding Levels

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

Summarize Inbreeding Levels

Description

Classifies individuals into inbreeding levels based on their inbreeding coefficients (F) according to standard or user-defined thresholds.

Usage

pedfclass(ped, breaks = c(0.0625, 0.125, 0.25), labels = NULL)

Arguments

ped	A tidyped object.
breaks	Numeric vector of strictly increasing positive upper bounds for inbreeding classes. Default is c(0.0625, 0.125, 0.25), corresponding approximately to half-sib, avuncular/grandparent, and full-sib/parent-offspring mating thresholds. The class "F = 0" is always kept as a fixed first level. A final open-ended class "F > max(breaks)" is always appended automatically.
labels	Optional character vector of interval labels. If NULL, labels are generated automatically from breaks. When supplied, its length must equal length(breaks), with each element naming the bounded interval (breaks[i-1], breaks[i]]. The open-ended tail class is always auto-generated and cannot be overridden.

Details

The default thresholds follow common pedigree interpretation rules:

• F = 0.0625: approximately the offspring of half-sib mating.

• F = 0.125: approximately the offspring of avuncular or grandparent-grandchild mating.

• F = 0.25: approximately the offspring of full-sib or parent-offspring mating.

Therefore, assigning F = 0.25 to the class "0.125 < F <= 0.25" is appropriate. If finer reporting is needed, supply custom breaks, for example to separate 0.25, 0.375, or 0.5.

Value

A data.table with 3 columns:

FClass

An ordered factor. By default it contains 5 levels: "F = 0", "0 < F <= 0.0625", "0.0625 < F <= 0.125", "0.125 < F <= 0.25", and "F > 0.25". The number of levels equals length(breaks) + 2 (the fixed zero class plus one class per bounded interval plus the open-ended tail).

Count

Integer. Number of individuals in each class.

Percentage

Numeric. Percentage of individuals in each class.

Examples

tp <- tidyped(simple_ped, addnum = TRUE)
pedfclass(tp)

# Finer custom classes (4 breaks, labels auto-generated)
pedfclass(tp, breaks = c(0.03125, 0.0625, 0.125, 0.25))

# Custom labels aligned to breaks (3 labels for 3 breaks; tail is auto)
pedfclass(tp, labels = c("Low", "Moderate", "High"))


tp_inbred <- tidyped(inbred_ped, addnum = TRUE)
pedfclass(tp_inbred)

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