updateSAwithTaxonFromSL: Function which changes the value of SAspeCode in SA.

In ices-tools-dev/icesRDBES: Functions for the ICES Regional Database and Estimation System (RDBES)

Function which changes the value of SAspeCode in SA.

Description

Function checks the rank of aphia id in both of tables SA and SL, and tries to replace a more accurate rank in SA with a broader rank from SL. There are 3 possible situations:

1. If the aphiaid id in the SA table is more accurate than in the SL table and the aphiaids are from the same kingdom, phylum, class, order, family, or genus then the aphiaid in the SA table is changed to the aphia id from the SL table.

2. If the aphia Ids are from different kingdom, phylum, class, order, family, or genus then the function retains the original SA species code.

3. If the SL table has a more accurate rank than in the SA table, the function also retains the original SA species code.

Usage

updateSAwithTaxonFromSL(
  RDBESDataObject,
  validate = TRUE,
  verbose = FALSE,
  strict = TRUE
)

Arguments

RDBESDataObject	An RDBESDataObject.
validate	Set to TRUE if you want validation to be carried out. The default if TRUE.
verbose	(Optional) Set to TRUE if you want informative text on validation printed out, or FALSE if you don't. The default is FALSE.
strict	(Optional) This function can validate its input data - should the validation be strict? The default is TRUE.

Value

RDBES data object where species in SA were renaming for species occuring in SL for level of species rank. If in SA is Sprat(126425), in SL Clupeidae (125464) function renameSpeciesSA rename Sprat from SA to Clupeidae. Clupeidae(family rank) is higher rank than Sprat(species rank).

Examples

## Not run: 
myObject <- createRDBESDataObject(input = "WGRDBES-EST/personal/Kasia/vignettes/vignetteData")
renameSpeciesSA(RDBESDataObject=myObject,validate,verbose,strict)
## End(Not run)

ices-tools-dev/icesRDBES documentation built on April 17, 2025, 1:58 p.m.