taxonRectification: Taxon Rectification

In occCite: Querying and Managing Large Biodiversity Occurrence Datasets

Taxon Rectification

Description

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
)

occCite documentation built on Nov. 2, 2024, 1:11 a.m.