Check species names

Source: R/check_fauna_names.R

check_fauna_names checks if the species names are correct and searches for suggestions if the name is misspelled or not found in the Fauna do Brasil database

check_fauna_names(data, species, max_distance = 0.1,
                         include_subspecies = TRUE)

Arguments

data

(data.frame) the data.frame imported with the load_faunabr 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

whether include subspecies when checking names. Default = TRUE.

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 ("valid" or "synonym").

  • nomenclaturalStatus: the nomenclatural status of the species name. This information is not available for all species.

  • validName: If the species name is not valid or incorrect, the valid name of the specie. If the species name is valid and correct, the same as input_name and Suggested_name.

  • family: the family of the specie.

References

Brazilian Zoology Group. Catálogo Taxonômico da Fauna do Brasil. Available at: https://ipt.jbrj.gov.br/jbrj/resource?r=catalogo_taxonomico_da_fauna_do_brasil

Examples

data("fauna_data")
spp <- c("Pantera onça", "Mazama bororo", "Mazama jucunda",
          "Araucaria angustifolia")
check_fauna_names(data = fauna_data, species = spp)
#>               input_name           Spelling Suggested_name Distance
#> 1          Mazama bororo            Correct  Mazama bororo        0
#> 2         Mazama jucunda            Correct Mazama jucunda        0
#> 3           Pantera onça Probably_incorrect  Panthera onca        2
#> 4 Araucaria angustifolia          Not_found           <NA>       NA
#>   taxonomicStatus nomenclaturalStatus      validName   family matches
#> 1         synonym                <NA> Mazama jucunda Cervidae  single
#> 2           valid                <NA> Mazama jucunda Cervidae  single
#> 3           valid                <NA>  Panthera onca  Felidae  single
#> 4            <NA>                <NA>           <NA>     <NA>    none