nprcgenekeepr (version 1.0.5)

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

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

# NOT RUN {
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
# }