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Sanitising functions

sanitise_name.Rd

Functions to clean and standardise taxonomic names and authors.

Usage

sanitise_name(taxon_name)

sanitise_authors(taxon_authors)

sanitise_names_authors(
  taxon_names,
  taxon_authors = NA,
  taxon_names_full = NA,
  console_message = FALSE
)

sanitise_names_authors_report(
  collection,
  taxon_name_column = "TaxonName",
  taxon_name_full_column = NA,
  taxon_author_column = NA,
  console_message = FALSE
)

Arguments

taxon_name

The taxonomic name of a plant.

taxon_authors

Vector of taxonomic authors.

taxon_names

Vector of taxonomic names.

taxon_names_full

Vector of joined taxonomic name and author.

console_message

Flag (TRUE/FALSE) for showing progress bar in the console.

collection

A data frame of a collection.

taxon_name_column

The name of the column in the collection corresponding to taxonomic names.

taxon_name_full_column

The name of the column in the collection corresponding to joined taxonomic names and authors.

taxon_author_column

The name of the column in the collection corresponding to the authors of the taxonomic names.

Details

sanitise_name() returns the sanitised name of a single taxonomic name.

sanitise_authors() returns the sanitised name of a taxonomic authors. Where by characters are coerced to Latin-ASCII, thereby removing diacritics (e.g umlauts).

clean_names_authors() sanitises multiple taxonomic names with or without the corresponding authors, by applying sanitise_name() and sanitise_authors(). As input a vector of taxonomic names is required (taxon_names), in addition a vector of the authors (taxon_authors) or joined taxonomic name and authors (taxon_names_full) can be provided. If neither taxon_authors or taxon_names_full are provided the author names are set to ''. A list is returned where:

  • $taxon_name a vector of the sanitised taxonomic names,

  • $authora vector of the sanitised authors,

  • $sanitised is a logical vector of whether the taxon_name was sanitised.

clean_names_authors_report() applies clean_names_authors() to a collection where the inputs are:

  • a data frame of the collection (collection),

  • column name for the taxonomic names (taxon_name_column, required),

  • column name of the authors of the taxonomic names (taxon_author_column, optional),

  • column name of the combined taxonomic name and author (taxon_name_full_column, optional).

Examples

sanitise_name('TRIGONELLA afghanica')
#> [1] "Trigonella afghanica"
sanitise_name('Halimium X pauanum')
#> [1] "Halimium × pauanum"
sanitise_name('Aruncus dioicus var acuminatus')
#> [1] "Aruncus dioicus var. acuminatus"
sanitise_authors('Stehlé')
#> [1] "Stehle"

taxon_names = c('TRIGONELLA afghanica', 'Halimium X pauanum',
 'Aruncus dioicus var acuminatus', 'Eupatorium magdalenae')
taxon_authors = c('Vassilcz', 'Font Quer', '(Douglas ex Hook.) H.Hara', 'Stehlé')

sanitise_names_authors(taxon_names, taxon_authors)
#> $taxon_name
#> [1] "Trigonella afghanica"            "Halimium × pauanum"             
#> [3] "Aruncus dioicus var. acuminatus" "Eupatorium magdalenae"          
#> 
#> $author
#> [1] "Vassilcz"                  "Font Quer"                
#> [3] "(Douglas ex Hook.) H.Hara" "Stehle"                   
#> 
#> $sanitised
#> [1]  TRUE  TRUE  TRUE FALSE
#> 

collection = data.frame(names = taxon_names, full = paste0(taxon_names, ' ', taxon_authors))
sanitise_names_authors_report(collection, taxon_name_column = 'names',
 taxon_name_full_column = 'full')
#> $taxon_name
#> [1] "Trigonella afghanica"            "Halimium × pauanum"             
#> [3] "Aruncus dioicus var. acuminatus" "Eupatorium magdalenae"          
#> 
#> $author
#> [1] "Vassilcz"                  "Font Quer"                
#> [3] "(Douglas ex Hook.) H.Hara" "Stehle"                   
#> 
#> $sanitised
#> [1]  TRUE  TRUE  TRUE FALSE
#>