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.
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.
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.
Examples
cleaned_data <- taxa_clean(data, c("Galax urceolata", "Galax aphylla"), taxa.filter = "exact")
#> Current scientific names:
#> [1] "Galax urceolata (Poir.) Brummitt" "Galax aphylla L."
#> [3] "Galax urceolata" "Galax aphylla"
#> User selected a(n) exact match.
cleaned_data <- taxa_clean(data, c("Galax urceolata", "Galax aphylla"),
accepted.name = "Galax urceolata")
#> Current scientific names:
#> [1] "Galax urceolata (Poir.) Brummitt" "Galax aphylla L."
#> [3] "Galax urceolata" "Galax aphylla"
#> User selected a(n) fuzzy match.