List each animal's high-kinship relatives

Usage

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

Arguments

kmat: a numeric matrix of pairwise kinship coefficients. Animal IDs are the row and column names.
ped: The pedigree information in data.frame format
threshold: numeric value representing 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. Required (no default); use character(0L) when no groups exist.
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. Required (no default); filterPairs() itself ignores female-female pairs when called directly.
minAge: integer value indicating the minimum age to consider in group formation. Required (no default). Pairwise kinships involving an animal younger than this age are ignored; animals of exactly this age or with a missing age are retained.

Value

A one-dimensional array of mode list (from tapply()), not a plain list. Its names are animal IDs, and each element is a character vector of animals sharing a kinship value greater than or equal to the threshold value. names() and [[ work as for a list.

Examples

qcPed <- nprcgenekeepr::qcPed
ped <- qcStudbook(qcPed,
  minSireAge = 2L, minDamAge = 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"