nprcgenekeepr: Genetic Management Functions
In rmsharp/nprcmanager: Genetic Tools for Colony Management

Primary Data Structure — Pedigree

Contains studbook information for a number of individuals. ASSUME: All IDs listed in the sire or dam columns must have a row entry in the id column

getIncludeColumns to get set of columns that can be used in a pedigree file

A Pedigree is a data frame within the R environment with the following possible columns:

id – character vector with unique identifier for an individual
sire – character vector with unique identifier for an individual's father (NA if unknown).
dam – character vector with unique identifier for an individual's mother (NA if unknown).
sex – factor levels: "M", "F", "U" Sex specifier for an individual
gen – integer vector with the generation number of the individual
birth – Date or NA (optional) with the individual's birth date
exit – Date or NA (optional) with the individual's exit date (death, or departure if applicable)
ancestry – character vector or NA (optional) that indicates the geographic population to which the individual belongs.
age – numeric or NA (optional) indicating the individual's current age or age at exit.
population – logical (optional) Is the id part of the extant population?
origin – character vector or NA (optional) that indicates the name of the facility that the individual was imported from if other than local.NA indicates the individual was not imported.

Pedigree File Testing Functions

qcStudbook — Main pedigree curation function that performs basic quality control on pedigree information
fixColumnNames — Changes original column names and into standardized names.
checkRequiredCols — Examines column names, cols, to see if all required column names are present.
correctParentSex — Sets sex for animals listed as either a sire or dam.
getDateErrorsAndConvertDatesInPed — Converts columns of dates in text form to Date object columns
checkParentAge — Check parent ages to be at least minParentAge
removeDuplicates — Remove duplicate records from pedigree

Gene Dropping Function

geneDrop — Performs a gene drop simulation based on the provided pedigree information

Genetic Value Analysis Functions

Contains functions to calculate the kinship coefficient and genome uniqueness for animals listed in a Pedigree table.

meanKinship — Calculates the mean kinship for each animal in a kinship matrix
calcA — Calculates a, the number of an individual's alleles that are rare in each simulation.
alleleFreq — Calculates the count of each allele in the provided vector.
calcFE — Calculates founder equivalents.
calcFG — Calculates founder genome equivalents.
calcFEFG— Returns founder equivalents FE and FG as elements in a list.
calcGU — Calculates genome uniqueness for each ID that is part of the population.
geneDrop — Performs a gene drop simulation based on the pedigree information.
chooseAlleles — Combines two vectors of alleles by randomly selecting one allele or the other at each position.
calcRetention — Calculates allelic retention.
filterKinMatrix — Filters a kinship matrix to include only the egos listed in 'ids'
kinship — Generates a kinship matrix
reportGV — Generates a genetic value report for a provided pedigree.