modSummaryStatsServer: Summary Statistics Module - Server Function

In nprcgenekeepr: Genetic Tools for Colony Management

Summary Statistics Module - Server Function

Description

Server logic for summary statistics module displaying genetic analysis results including kinship statistics, histograms, box plots, and relationship designation analysis.

Usage

modSummaryStatsServer(
  id,
  geneticValues,
  pedigree,
  kinshipMatrix = NULL,
  founderStats = NULL,
  kinshipOverrides = NULL
)

Arguments

id	character vector of length 1. Module namespace identifier.
geneticValues	reactive returning genetic value analysis results. Must be a data frame with columns id, indivMeanKin, and gu. Optional zScore column enables z-score plots.
pedigree	reactive returning pedigree data frame with columns id, sire, dam, and sex. Optionally gen.
kinshipMatrix	optional reactive returning kinship matrix. If NULL, the module will calculate kinship from the pedigree.
founderStats	optional reactive returning a list of founder statistics (fe, fg, total, nMaleFounders, nFemaleFounders). When supplied, a founder summary table is rendered on the Summary Statistics tab (monolith parity). If NULL, it is omitted.
kinshipOverrides	optional reactive returning a validated outside-information kinship-override data frame (id1, id2, kinship); see applyKinshipOverrides. When the module recomputes kinship from the pedigree (the usual path), the overrides are applied to that matrix, so the relationship table and the kinship CSV export reflect the supplied values regardless of tab order. The override moves the kinship value only; the relation label stays pedigree-derived (it is computed from pedigree structure, not from the kinship value). Overridden pairs are flagged with a logical overridden column in the relationship table. NULL (the default) is a no-op.

Details

This module provides:

• Summary statistics (counts, mean kinship, genome uniqueness)

• Histograms and box plots for genetic value distributions

• Relationship classification using convertRelationships()

• Relationship class frequency tables using makeRelationClassesTable()

• First-order relative counts using countFirstOrder()

• Export functionality for kinship matrix, founders, and relationships

Value

A list with reactive components:

• summaryData - Summary statistics (nAnimals, meanMK, meanGU)

• relationships - Pairwise relationship designations from convertRelationships(). When kinshipOverrides are supplied, a logical overridden column flags the pairs whose kinship value came from an override.

• relationClasses - Relationship class frequency table from makeRelationClassesTable()

• firstOrderCounts - First-order relative counts per animal from countFirstOrder()

• mkSummary - Six-number summary of mean kinship

• guSummary - Six-number summary of genome uniqueness

See Also

modSummaryStatsUI for the user interface

convertRelationships for relationship classification

makeRelationClassesTable for relationship class summary

countFirstOrder for first-order relative counting

kinship for kinship matrix calculation

Other Shiny modules: modBreedingGroupsServer(), modBreedingGroupsUI(), modGeneticDiversityServer(), modGeneticDiversityUI(), modGeneticValueServer(), modGeneticValueUI(), modGvAndBgDescServer(), modGvAndBgDescUI(), modInputServer(), modInputUI(), modORIPReportingServer(), modORIPReportingUI(), modPedigreeServer(), modPedigreeUI(), modPotentialParentsServer(), modPotentialParentsUI(), modPyramidServer(), modPyramidUI(), modSummaryStatsUI()

nprcgenekeepr documentation built on July 26, 2026, 5:06 p.m.