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

qcPed <- nprcgenekeepr::qcPed
ped <- qcStudbook(qcPed,
  minParentAge = 2L, reportChanges = FALSE,
  reportErrors = FALSE
)
kmat <- kinship(ped$id, ped$sire, ped$dam, ped$gen, sparse = FALSE)
currentGroups <- list(1L)
currentGroups[[1L]] <- examplePedigree$id[1L:3L]
candidates <- examplePedigree$id[examplePedigree$status == "ALIVE"]
threshold <- 0.015625
kin <- getAnimalsWithHighKinship(kmat, ped, threshold, currentGroups,
  ignore = list(c("F", "F")), minAge = 1.0
)
length(kin) # should be 259
#> [1] 259
kin[["0DAV0I"]] # should have 34 IDs
#>  [1] "95U2JO" "F50D26" "HRBVOE" "HRQJQR" "RD6KMA" "168Q0A" "6IPOZK" "96W7N8"
#>  [9] "AD0UE1" "DHCUI7" "G6P0W4" "KVPYE4" "NHE3Z8" "OTAC9O" "ZWBMTP" "4UTH8P"
#> [17] "9FR6Q8" "H00H7D" "H0UP6R" "NPK1YN" "NY9FEC" "QR5CMP" "S8IEHH" "T5KNUX"
#> [25] "ZLPSUH" "2YGWN0" "HP3E04" "MF8X1C" "RSROMX" "WMUJC5" "2IXJ2N" "CAST4W"
#> [33] "JGPN6K" "ZC5SCR"