Make a relation classes table from kinship pairs

Counts the pairs of animals in each relationship class of a long-form kinship table.

Usage

makeRelationClassesTable(kin)

Arguments

kin

a dataframe with columns id1, id2, kinship, and relation. It is a long-form table of pairwise kinships, with relationship categories included for each pair.

Value

A data.frame with columns Relationship Class and Frequency: the number of pairs in each of the following relationship classes: Parent-Offspring, Full-Siblings, Half-Siblings, Grandparent-Grandchild, Full-Cousins, Cousin - Other, Full-Avuncular, Avuncular - Other, Other, and No Relation. Self pairs are not counted, and classes with no pairs are left out.

Examples

library(nprcgenekeepr)
suppressMessages(library(dplyr))

qcPed <- nprcgenekeepr::qcPed
qcPed <- qcPed[1:50, ] # Comment out for full example
bkmat <- kinship(qcPed$id, qcPed$sire, qcPed$dam, qcPed$gen,
  sparse = FALSE
)
kin <- convertRelationships(bkmat, qcPed)
relClasses <- makeRelationClassesTable(kin)
relClasses$`Relationship Class` <-
  as.character(relClasses$`Relationship Class`)
relClassTbl <- kin[!kin$relation == "Self", ] |>
  group_by(relation) |>
  summarise(count = n())
relClassTbl
#> # A tibble: 1 × 2
#>   relation    count
#>   <chr>       <int>
#> 1 No Relation  1225