getAnimalsWithHighKinship: Forms a list of animal Ids and animals related to them

In rmsharp/nprcmanager: Genetic Tools for Colony Management

Description

Forms a list of animal Ids and animals related to them

Usage

getAnimalsWithHighKinship(kmat, ped, threshold, currentGroups, ignore, minAge)

Arguments

kmat	numeric matrix of pairwise kinship values. Rows and columns are named with animal IDs.
ped	dataframe that is the 'Pedigree'. It contains pedigree information including the IDs listed in candidates.
threshold	numeric value indicating the minimum kinship level to be considered in group formation. Pairwise kinship below this level will be ignored.
currentGroups	list of character vectors of IDs of animals currently assigned to the group. Defaults to character(0) assuming no groups are existent.
ignore	list of character vectors representing the sex combinations to be ignored. If provided, the vectors in the list specify if pairwise kinship should be ignored between certain sexes. Default is to ignore all pairwise kinship between females.
minAge	integer value indicating the minimum age to consider in group formation. Pairwise kinships involving an animal of this age or younger will be ignored. Default is 1 year.

Value

A list of named character vectors where each name is an animal Id and the character vectors are made up of animals sharing a kinship value greater than our equal to the threshold value.

Examples

examplePedigree <- nprcgenekeepr::examplePedigree
ped <- qcStudbook(examplePedigree, minParentAge = 2, reportChanges = FALSE,
                  reportErrors = FALSE)
kmat <- kinship(ped$id, ped$sire, ped$dam, ped$gen, sparse = FALSE)
currentGroups <- list(1)
currentGroups[[1]] <- examplePedigree$id[1:3]
candidates <- examplePedigree$id[examplePedigree$status == "ALIVE"]
threshold <- 0.015625
kin <- getAnimalsWithHighKinship(kmat, ped, threshold, currentGroups,
                                 ignore = list(c("F", "F")), minAge = 1)
length(kin) # should be 2412
kin[["1SPLS8"]] # should have 14 IDs

rmsharp/nprcmanager documentation built on April 24, 2021, 3:13 p.m.