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. When no pair of different animals is left to count, the table has its two columns and no rows.

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