fixSpecies: Edit Scientific Name Notation
In LimaRAF/plantR: Managing Species Records from Biological Collections

fixSpecies

R Documentation

Edit Scientific Name Notation

Description

Identifies open nomenclature (aff., cf.) in scientific names, classification under species level (var. and subsp.). It creates a new column with the new suggested name and it also flags problematic names (character string with numbers, authors, wrong case, or other names besides genus and epithet etc). Names can be returned with or without infra-specific ranks (var. and subsp.) or abbreviations of unspecific names (sp. or spp.). In the case of names with authors, authorship is currently removed from scientific names.

Usage

fixSpecies(
  x = NULL,
  tax.name = "scientificName",
  rm.rank = FALSE,
  rm.indet = FALSE
)

Arguments

`x`	a vector or data.frame containing the species name
`tax.name`	character. Name of the columns containing the species name. Default to "scientificName"
`rm.rank`	logical. Should the infra-specific rank abbreviation be removed from the name? Default to FALSE
`rm.indet`	logical. Should the abbreviations for unspecific names (i.e. sp. or spp.) be removed? Default to FALSE

Details

Possible flags returned in scientificNameStatus:

possibly_ok: scientific name following the expected pattern 'Genus epithet'
not_Genus_epithet_format: scientific name not following the expected pattern Genus epithet
variety: scientific name with variety
subspecies: scientific name with subspecies
form: scientific name with form
infra_specific: scientific name with genus, specific epiteth and infra-specific, but no infra-specific rank
hybrid_species: scientific name of a hybrid species
conferre: open nomenclature cf. in the scientific name
affinis: open nomenclature aff. in the scientific name
indet: taxon identified only at genus level
subfamily_as_genus: subfamily as genus, not a valid name
family_as_genus: family as genus, not a valid name
order_as_genus: order as genus, not a valid name
incertae_sedis: scientific name of uncertain placement
species_nova: species name contains an indication of a new species, possibly not yet a valid name
name_w_authors: scientific name has authors
name_w_wrong_case: scientific name has upper/lowercase issues
name_w_non_ascii: species name has non ASCII characters, not a valid name
abbreviated_genus: genus is abbreviated
not_name_has_digits: scientific name has digits, not a valid name

Value

The original data frame (or the input vector as a data frame) with the new columns verbatimSpecies with small edits before flagging, scientificNameStatus with the flags in original data and scientificName.new with a suggestion for a more correct name. See Details for a description of flags in the column scientificNameStatus.

Author(s)

Sara Mortara & Renato A. Ferreira de Lima

References

Sigovini, M., Keppel, E. and Tagliapietra, D. (2016) Open Nomenclature in the biodiversity era. Methods in Ecology and Evolution 7(10): 1217-1225.

Examples

df <- data.frame(scientificName =
c("Lindsaea lancea", "Lindsaea lancea (L.) Bedd.",
"Lindsaea lancea var. Angulata",
"Lindsaea Aff. lancea",
"Lindsaea", "Lindsaea sp.", "Lindsaeaceae sp.",
"Lindsaea aff. lancea (L.) Bedd.",
"Lindsaea ×improvisa K.U.Kramer",
"Parablechnum C.Presl",
"Blechnum spannagelii Rosenst.",
"Blechnum occidentale leopoldense Dutra",
"Blechnum austrobrasilianum de la Sota"))

fixSpecies(df)
fixSpecies(df, rm.rank = TRUE)
fixSpecies(df, rm.rank = TRUE, rm.indet = TRUE)

LimaRAF/plantR documentation built on Jan. 1, 2023, 10:18 a.m.