Assemble breeding-group genetic diversity heat-map statistics

Assemble breeding-group genetic diversity heat-map statistics

Usage

getGeneticDiversityStats(
  groups,
  ped,
  geneticValues,
  kmat,
  housing = "shelter_pens",
  currentDate = Sys.Date()
)

Arguments

groups

List of character vectors of animal IDs, one per breeding group (for example the groups returned by modBreedingGroupsServer). If the list is named, the names become the group row labels; otherwise labels are "Group 1", "Group 2", and so on.

ped

Dataframe that is the Pedigree. The id, dam, sex, birth, and exit columns are required; an optional ancestry column enables the Origin metric.

geneticValues

Dataframe of the genetic value report (for example reportGV(ped)$report). The id and value columns are required; value holds the labels produced by rankSubjects ("Low Value", "High Value", "Undetermined").

kmat

Square kinship matrix whose row and column names are animal IDs and that covers every member of every group (for example the matrix returned by kinship).

housing

Character housing type passed to getProductionStatus, either "shelter_pens" or "corral". Length 1 (applied to every group) or one value per group. Defaults to "shelter_pens".

currentDate

Date used to derive age and the production birth window. Defaults to Sys.Date().

Value

A data frame with one row per group: the first column group holds the group label and each remaining column (Value, Origin when available, Production, Inbreeding) holds an integer color index in c(1, 2, 3). Production is NA for a group with no breeding-age females.

Details

For each breeding group this builds the heat-map color indices by calling the per-group providers: Value from getProportionLow, Origin from getIndianOriginStatus, Production from getProductionStatus, and Inbreeding from getKinshipWithMaleStatus. The result is the group-by-metric data frame consumed by makeGeneticDiversityHeatmap: the first column holds the group label and each remaining column holds a color index (1 red, 2 yellow, 3 green).

Age is derived from each member's birth date using currentDate rather than read from a possibly-absent age column, so the age filters and the production birth window share one reference date. Genetic-value labels of "Undetermined" are dropped before the Value proportion is taken. A group with no assessed value, and a group whose Inbreeding metric is undefined (no breeding-age females), are both scored red so that missing data is surfaced rather than shown as healthy green. When the pedigree has no ancestry column the Origin metric cannot be computed and its column is omitted.

Production is the number of births in the two calendar years ending the year before currentDate that lived at least 30 days, divided by the number of breeding-age females in the group: females at least 3 years old. A female with no birth date has no age. She counts as a breeding-age female only when the pedigree (ped) lists at least one animal as her offspring, looked up in the whole pedigree and not only in her group, so a mother whose offspring are in another group still counts. A female with no birth date and no offspring is left out, and so is an animal with a blank sex. A group with no breeding-age females has no Production value: its entry is NA, and the heat map draws that cell gray.

The Inbreeding column counts breeding-age females by the same rule: a female with no birth date counts when the pedigree lists an offspring for her, and is left out otherwise. A male with no birth date is never counted as a potential mate.