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Check species names in biodiversity data from separate sources

This process XYZ HERE PLEASE, from the sources GBIF, iNaturalist and VertNet, with data provided by the user or other sources. For more details, please ask BOKU.

pan-european use case AquaINFRA R

Inputs
Id Title Data Type Description
species_names_list Species names (List of species) string List of species names to check from the standard database (FishBase).
species_names_url Species names to check string URL to a table containing the occurrences from any source. This can be the outcome of the match-data process.
colname_species Column name including species names string Column name that indicate the Species in the provided dataset. Only required you provide tabular occurrence data. Example: "species"
percent_correctness Species name correctness in percent number An number indicating the percentage of species name correctness that should be allowed to be replaced. High values ensure a perfect match from the standard database.
bool_merge Merge checked species names on the dataset boolean If a dataframe with species names is provided and this is YES, then all columns are returned. For only one species, the merge will be set automatically to false.
bool_synonym Synonym checks boolean Return synonym checks from FishBase.
bool_ecosystem_type Output ecosytem types boolean Return ecoystem checks for species from FishBase including marine, freshwater, and brackish.
bool_rm_duplicates Remove duplicates boolean Remove duplicates from the dataset.
Outputs
Id Title Description
cleannames_df Dataframe with checked or quality controlled species data. A table containing a column speciescheck with names checked with databases for consistency. For fish species, FishBase is used as a standard database.

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