Calculate the sex ratio of a set of animals

The Males are counted when the ped$sex value is "M". Females are counted when the ped$sex value is not "M". This means animals with ambiguous sex are counted with the females.

Usage

calculateSexRatio(ids, ped, additionalMales = 0L, additionalFemales = 0L)

Arguments

ids

character vector of animal IDs

ped

dataframe that is the Pedigree. It contains pedigree information including the IDs listed in ids.

additionalMales

Integer value of males to add to those within the group when calculating the ratio. The additions always count, except when ids has no animals or no males: with no males, the ratio is Inf unless additionalMales is greater than 0 (then additionalFemales still counts); with no animals, see Value. Default is 0.

additionalFemales

Integer value of females to add to those within the group when calculating the ratio. The additions always count, except as described for additionalMales. Default is 0.

Value

Numeric value of the sex ratio of the animals provided, expressed as the number of non-males per male. It is Inf when there are no males (and no males are added) but at least one non-male; 0 when ids is empty, no females are added and males are added; and NA when ids is empty and nothing is added.

Examples

library(nprcgenekeepr)
data("qcBreeders")
data("pedWithGenotype")
available <- c(
  "JGPN6K", "8KM1MP", "I9TQ0T", "Q0RGP7", "VFS0XB", "CQC133",
  "2KULR3", "HOYW0S", "FHV13N", "OUM6QF", "6Z7MD9", "CFPEEU",
  "HLI95R", "RI0O7F", "7M51X5", "DR5GXB", "170ZTZ", "C1ICXL"
)
nonMales <- c(
  "JGPN6K", "8KM1MP", "I9TQ0T", "Q0RGP7", "CQC133",
  "2KULR3", "HOYW0S", "FHV13N", "OUM6QF", "6Z7MD9", "CFPEEU",
  "HLI95R", "RI0O7F", "7M51X5", "DR5GXB", "170ZTZ", "C1ICXL"
)
male <- "VFS0XB"
calculateSexRatio(ids = male, ped = pedWithGenotype)
#> [1] 0
calculateSexRatio(ids = nonMales, ped = pedWithGenotype)
#> [1] Inf
calculateSexRatio(ids = available, ped = pedWithGenotype)
#> [1] 17
calculateSexRatio(
  ids = available, ped = pedWithGenotype,
  additionalMales = 1L
)
#> [1] 8.5
calculateSexRatio(
  ids = available, ped = pedWithGenotype,
  additionalFemales = 1L
)
#> [1] 18
calculateSexRatio(
  ids = available, ped = pedWithGenotype,
  additionalMales = 1, additionalFemales = 1L
)
#> [1] 9
calculateSexRatio(
  ids = nonMales, ped = pedWithGenotype,
  additionalMales = 1, additionalFemales = 0L
)
#> [1] 17
calculateSexRatio(
  ids = character(0), ped = pedWithGenotype,
  additionalMales = 1, additionalFemales = 0L
)
#> [1] 0