Skip to contents

Botanical Correction

Source: R/BotanicalCorrection.R
BotanicalCorrection.Rd

Botanical Correction

Usage

BotanicalCorrection(Data, Sources = c("wfo"))

Arguments

Data

Dataset (data.frame or data.table); it must contain Site and IdTree

Sources

Character vector. Taxonomic source to use. Only option is "wfo"

Value

A list with a complete log of the botanical corrections and Data with new columns:

  • Accepted_family_DataHarmonizationCor (character): corrected family name

  • Accepted_genus_DataHarmonizationCor (character): corrected genus name

  • Accepted_species_DataHarmonizationCor (character): corrected species name

  • Accepted_name_DataHarmonizationCor (character): corrected name (at any taxonomic level)

  • Accepted_name_rank_DataHarmonizationCor (character): Taxonomic rank of name matched by the TNRS

Details

  • The function uses TNRS package provided by BIEN, https://bien.nceas.ucsb.edu/bien/tools/tnrs/

  • It resolves plant taxonomic names using World Flora Online

  • No special characters (typography)

  • The suffix "aceae" is restricted to families, and words ending with "aceae" are deleted anywhere else

  • Correct spelling of botanical names

  • Update the families according to APG

  • The log contains a flag if there is more than one name for one Site x IdTree combination

  • The log contains all details returned by TNRS (authors, etc.). Data just keeps the basic corrected names.

Examples

if (FALSE) {
library(data.table)
data(TestData)
Rslt <- BotanicalCorrection(TestData)
}