Check and clean species names to match standard names in the database.

Usage

clean_names(
  sp,
  grouplists,
  prechecks = FALSE,
  standard_dataset = NULL,
  percenterror = 80,
  errorness = 30,
  full = FALSE,
  warn,
  taxalevel
)

Arguments

sp: string or vector. Species scientific names to be checked. Although the spellings are checked, the users should check for the species name provided to avoid not being being detected in the database.
grouplists: list. List of data downloaded in the fw_searchdata function. If species considered in sp parameter are fishes, then the fishes lists should be provided otherwise the species names will be rejected.
prechecks, standard_dataset: logical. If TRUE the standard prechecks will be done on both the invertebrates and bentho species names before search for ecological parameters from the database. The standard names is provided with the dataset to reduce on the time in identifying the standard tyxonomic names for the macroinvertebrates in the database. @param taxalevel string Allowed taxonomic levels at which data can retrieved. Default is 'species' but data can also be downloaded at family level, genus, and taxa group level.
percenterror: numeric. The number used as a cutoff to infer similarity of the user provided name and what is found in the database. The higher the percentage, the higher the similarity the species name provided by the user and the one in the database. percenterror ranges from 0 to 100 but the default is 80 to ensure that wrong names are not selected at low similarity percentage cutoff.
errorness: numeric Similar to percenterror, errorness parameter uses the distance differences between the user-provided names and all the taxa group species standard names. The lower the percentage error, the higher the similarity in the species names provided. Default is 20 and beyond 30, a warning is showed to avoid wrong species replace the user provided name, which leads to extracting wrong traits.
full: logical TRUE if a dataframe with both cleaned and uncleaned species are required. If FALSE then the a species list will be produced after cleaning. Default FALSE.
warn: To alert user on the species names cleaning errors and warnings.
taxalevel: string Allowed taxonomic levels at which data can retrieved. Default is 'species' but data can also be downloaded at family level, genus, and taxa group level.

Value

vector or string clean species name that is also found in the database.