allocate.mate.H: allocate.mate.H

In mghamilton/AllocateMate: An R package for mate allocation

allocate.mate.H

Description

This function generates a mating list for a set of parents. The mating list can be generated i) to minimise the average inbreeding coefficient (F) of families generated or ii) according to assortative mating principles. Inputs include a list of parents and a relationship matrix (H) including these parents.

Usage

allocate.mate.H(H, parents, max_F = 1, method = "min_F")

Arguments

H	is square additive genetic relationship matrix with individual idenifiers as rownames and colnames.
parents	data frame with the following columns (class in parentheses): 'ID' is the individual identifier (character). 'SEX' is the sex of the individual - 'M' or 'F', for male and female respectively (character). 'EBV' Estimated breeding value (EBV) of the individual - can not be NA if applying assortative mating as the method (numeric). 'N_AS_PARENT' The number of families the indivdiual is to contribute to (integer).
max_F	is the maxiumum inbreeding coefficient allowed in the offspring of parents (numeric between 0 and 1)
method	either 'min_F' (to minimise the average inbreeding in offspring) or 'assortative' (to apply assortative mating) (character)

Value

'summary' is a data frame containing a summary of all possible families generated from matings between male parents:

• 'SELECTED' N represents unselected families, Y represents selected families (i.e. mate allocations to be generated) and All represents all possible families.

• 'COUNT_FAMS' count of families.

• MEAN_EBV' mean of family EBVs.

• 'SD_EBV' standard deviation of family EBVs.

• 'MIN_EBV' minimum of family EBVs.

• 'MIN_EBV' maximum of family EBVs.

• MEAN_EBV' mean of family inbreeding coefficients (F).

• 'SD_EBV' standard deviation of family inbreeding coefficients (F).

• 'MIN_EBV' minimum of family inbreeding coefficients (F).

• 'MIN_EBV' maximum of family inbreeding coefficients (F).

'all_families' is a data frame containing details of all possible families able to be generated from matings between parents:

• 'SIRE' male parent.

• 'DAM' female parent.

• 'F' inbreeding coefficient of family members (i.e. the 'family F').

• 'EBV' mean of parent EBVs (i.e. the 'family EBV').

• 'SELECTED' N represents an unselected family (i.e. family is not to be generated), Y represents a selected family (i.e. mate allocated - family to be generated).

'optimal_families' is a data frame containing details of mate allocations (i.e.families to be generated from matings between male parents):

• 'SIRE' male parent.

• 'DAM' female parent.

• 'F' inbreeding coefficient of family members (i.e. the 'family F').

• 'EBV' mean of parent EBVs (i.e. the 'family EBV').

Examples

#Retrieve example data
H <- AllocateMate::H
parents <- AllocateMate::parents

output <- allocate.mate.H(H, parents, max_F = 0.02, method = "min_F") 
output$summary
head(output$all_families)
head(output$optimal_families)

mghamilton/AllocateMate documentation built on Jan. 30, 2025, 6:09 p.m.