taxa_clean {gatoRs}

Taxonomic Cleaning - Filter and resolve taxon names

Description

The taxa_clean() function filters a data frame for relevant results, based on the scientific name given. Filtering can be done with scripts by exact or fuzzy match. Or, for a more controlled approach, this function provides interactive filtering by providing the user with prompts. The interactive method allows the user to manually determine whether they wish to keep results containing certain scientific names.

Usage

taxa_clean(
  df,
  synonyms.list,
  taxa.filter = "fuzzy",
  scientific.name = "scientificName",
  accepted.name = NA
)

Arguments

df

Data frame of occurrence records returned from gators_download().

synonyms.list

A list of synonyms for a species.

taxa.filter

The type of filter to be used–either "exact", "fuzzy", or "interactive".

scientific.name

Default = "scientificName". The name of the scientificName column in the data frame.

accepted.name

The accepted scientific name for the species. If provided, an additional column will be added to the data frame with the accepted name for further manual comparison.

Details

If users select the interactive approach, the function will first print all unique scientific names in the current data set and then ask the user to respond in the console to prompts regarding which records, if any, should be removed based on their scientific name. After filtering, based on a user-provided taxonomy, an accepted name column can be defined with an optional argument. This function relies on the user-provided taxonomy, we do not utilize any taxonomic backbone. Additionally, this function requires no additional packages.

Value

Returns data frame with filtered results and new column with the accepted name labeled as "accepted_name". Information about the columns in the returned data frame can be found in the documentation for gators_download(). An additional column named "accepted_name" will be returned if an accepted.name was provided.

Examples

cleaned_data <- taxa_clean(data, c("Galax urceolata", "Galax aphylla"), taxa.filter = "exact")
cleaned_data <- taxa_clean(data, c("Galax urceolata", "Galax aphylla"),
accepted.name = "Galax urceolata")