Check species names — check

check_names checks if the species names are correct and searches for suggestions if the name is misspelled or not found in the Flora e Funga do Brasil database

match_names finds approximate matches to the specified pattern (species) within each element of the string x (species_to_match). It is used internally by check_names.

check_names(data, species, max_distance = 0.1,
                   include_subspecies= FALSE, include_variety = FALSE,
                   kingdom = "Plantae", parallel = FALSE, ncores = 1,
                   progress_bar = FALSE)

match_names(
  species,
  species_to_match,
  max_distance = 0.1,
  parallel = FALSE,
  ncores = 1,
  progress_bar = FALSE
)

Arguments

data: (data.frame) the data.frame imported with the load_florabr function.
species: (character) names of the species to be checked.
max_distance: (numeric) Maximum distance (as a fraction) allowed for searching suggestions when the name is misspelled. It can be any value between 0 and 1. The higher the value, the more suggestions are returned. For more details, see agrep. Default = 0.1.
include_subspecies: (logical) whether to include subspecies. Default = FALSE
include_variety: (logical) whether to include varieties. Default = FALSE
kingdom: (character) the kingdom to which the species belong. It can be "Plantae" or "Fungi". Default = "Plantae".
parallel: (logical) whether to run in parallel. Setting this to TRUE is recommended for improved performance when working with 100 or more species.
ncores: (numeric) number of cores to use for parallel processing. Default is 1. This is only applicable if parallel = TRUE.
progress_bar: (logical) whether to display a progress bar during processing. Default is FALSE
species_to_match: (character) a vector of species names to match against the species parameter.

Value

a data.frame with the following columns:

input_name: the species names informed in species argument
Spelling: indicates if the species name is Correct (a perfect match with a species name in the Flora e Funga do Brasil), Probably_incorrect (partial match), or Not_found (no match with any species).
Suggested name: If Spelling is Correct, it is the same as the input_name. If Spelling is Probably_correct, one or more suggested names are listed, found according to the maximum distance. If Spelling is "Not_found", the value is NA.
Distance: The integer Levenshtein edit distance. It represents the number of single-character edits (insertions, deletions, or substitutions) required to transform the input_name into the Suggested_name.
taxonomicStatus: the taxonomic status of the species name ("Accepted" or "Synonym").
nomenclaturalStatus: the nomenclatural status of the species name. This information is not available for all species.
acceptedName: If the species name is not accepted or incorrect, the accepted name of the specie. If the species name is accepted and correct, the same as input_name and Suggested_name.
family: the family of the specie.

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

data("bf_data", package = "florabr")
spp <- c("Butia cattarinensis", "Araucaria angustifolia")
check_names(data = bf_data, species = spp)
#>               input_name           Spelling         Suggested_name Distance
#> 1 Araucaria angustifolia            Correct Araucaria angustifolia        0
#> 2    Butia cattarinensis Probably_incorrect     Butia catarinensis        1
#>   taxonomicStatus nomenclaturalStatus           acceptedName        family
#> 1        Accepted             Correct Araucaria angustifolia Araucariaceae
#> 2        Accepted                <NA>     Butia catarinensis     Arecaceae