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Load user-configurable species reproductive-parameter overrides

Source: R/loadSpeciesOverrides.R
loadSpeciesOverrides.Rd

Reads the optional species-override settings from the user's site configuration file (~/.nprcgenekeepr_config, or ~/_nprcgenekeepr_config on Windows) and assembles the override tables and fallbacks consumed by the Genetic Value Analysis. The configuration may carry up to three optional keys, each looked up softly (the getConfigApiKey pattern – absent keys are not an error and never touch the fixed-schema getSiteInfo parser):

  • speciesOverridesPath – path to a CSV with the four speciesGestation columns (species, gestation, minMaleBreedingAge, minFemaleBreedingAge; header required, matched by name). A colony lists only the rows (species) it wants to change; the CSV is merged onto the bundled table, so every unlisted species keeps its bundled value (not replaced).

  • minBreedingAgeDefault – numeric fallback (years) for a species absent from the table (bundled built-in 2.0).

  • gestationDefault – integer fallback (days) for a species absent from the table (bundled built-in 210).

Usage

loadSpeciesOverrides()

Value

A named list with elements breedingTable, gestationTable (each the merged speciesGestation-shaped data.frame, or NULL when no CSV is configured), breedingAgeDefault (numeric or NULL), and gestationDefault (integer or NULL). A NULL element means "use the bundled value / built-in default".

Details

Like loadSiteConfig, this never crashes the application on boot: a missing configuration file, a missing override key, or a missing/malformed CSV all fall back to the bundled values (a warning is raised for an unreadable CSV).

See also

loadSiteConfig, getSpeciesMinBreedingAge, getSpeciesGestation, reportGV

Examples

library(nprcgenekeepr)
## Reads optional species overrides from the user's site config
## file; with no config file every element is NULL, meaning "use
## the bundled speciesGestation values / built-in defaults".
overrides <- loadSpeciesOverrides()
str(overrides)
#> List of 4
#>  $ breedingTable     : NULL
#>  $ gestationTable    : NULL
#>  $ breedingAgeDefault: NULL
#>  $ gestationDefault  : NULL