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Taxon Rectification

Source: R/taxonRectification.R
taxonRectification.Rd

An function that takes an input taxonomic name, checks against taxonomic database, returns vector for use in database queries, as well as warnings if the name is invalid.

Usage

taxonRectification(taxName = NULL, datasources = NULL, skipTaxize = FALSE)

Arguments

taxName

A string that, ideally, is a taxonomic name

datasources

A vector of taxonomic data sources implemented in taxize::gnr_resolve(). See the Global Names List for more information.

skipTaxize

If skipTaxize = TRUE, occCite will skip taxonomic rectification using taxize, which has been orphaned on CRAN. Setting this option to `TRUE` will result in a check for the taxize package before taxonomic rectification is attempted. *The code using `taxize` has been disabled to comply with CRAN.*

Value

A string with the closest match according to taxize::gnr_resolve(), and a list of taxonomic data sources that contain the matching name.

Examples

# Inputting taxonomic name and specifying what taxonomic sources to search
taxonRectification(
  taxName = "Buteo buteo hartedi",
  datasources = "National Center for Biotechnology Information",
  skipTaxize = TRUE
)
#>            Input Name          Best Match
#> 1 Buteo buteo hartedi Buteo buteo hartedi
#>   Searched Taxonomic Databases w/ Matches
#> 1                          Not rectified.