getPossibleCols: Get possible column names for a studbook.

In rmsharp/nprcmanager: Genetic Tools for Colony Management

Get possible column names for a studbook.

Description

Pedigree curation function

Usage

getPossibleCols()

Value

A character vector of the possible columns that can be in a studbook. The possible columns are as follows:

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 N (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	– an optional logical argument indicating whether or not the id is part of the extant population.
origin	– character vector or NA (optional) that indicates the name of the facility that the individual was imported from. NA indicates the individual was not imported.
status	– an optional factor indicating the status of an individual with levels ALIVE, DEAD, and SHIPPED.
condition	– character vector or NA (optional) that indicates the restricted status of an animal. "Nonrestricted" animals are generally assumed to be naive.
spf	– character vector or NA (optional) indicating the specific pathogen-free status of an individual.
vasxOvx	– character vector indicating the vasectomy/ovariectomy status of an animal where NA indicates an intact animal and all other values indicate surgical alteration.
pedNum	– integer vector indicating generation numbers for each id, starting at 0 for individuals lacking IDs for both parents.

Examples

library(nprcgenekeepr)
getPossibleCols()

rmsharp/nprcmanager documentation built on Feb. 2, 2025, 12:45 a.m.