Get possible column names for a studbook.

Source: R/getPossibleCols.R

Pedigree curation function

getPossibleCols()

Details

@return 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 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 -- 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

# \donttest{
library(nprcgenekeepr)
getPossibleCols()

#>  [1] "id"           "sire"         "dam"          "sex"          "gen"         
#>  [6] "birth"        "exit"         "death"        "age"          "ancestry"    
#> [11] "population"   "origin"       "status"       "condition"    "departure"   
#> [16] "spf"          "vasxOvx"      "pedNum"       "first"        "second"      
#> [21] "first_name"   "second_name"  "recordStatus"
# }