regi0.taxonomic.gnr

regi0.taxonomic.gnr.get_classification(names: Union[list, pandas.Series, str], add_supplied_names: bool = False, add_source: bool = False, expand: bool = True, **kwargs) → pandas.DataFrame

Gets the complete classification of multiple scientific names using the Global Names Resolver.

Parameters

  • names (list, Series or str) – Scientific name(s) to get results for.

  • add_supplied_names (bool) – Add supplied scientific names to the resulting DataFrame.

  • add_source (bool) – Add source column to the resulting DataFrame.

  • expand (bool) –

    Whether to expand result rows to match names size. If False, the number of rows will correspond to the number of unique names in names. Only has effect if best_match_only=True or if only one

    data source id is passed.

  • **kwargs – Keyword arguments of the resolve function.

Returns

DataFrame with the ranks for each match.

Return type

DataFrame

regi0.taxonomic.gnr.resolve(names: Union[list, pandas.Series, str], data_source_ids: Optional[list] = None, resolve_once: bool = False, best_match_only: bool = False, with_context: bool = False, with_vernaculars: bool = False, with_canonical_ranks: bool = False, expand: bool = True) → pandas.DataFrame

Receives a list of names and resolves each against the entire resolver database or against specific data sources using the Global Names Resolver (GNR) API. Underlying resolving and scoring algorithms are described at: http://resolver.globalnames.org/about

Parameters

  • names (list, Series or str) – List of species names to resolve.

  • data_source_ids (list) – List of specific data sources IDs to resolve against. A list of all the available data sources and their IDs can be found at: http://resolver.globalnames.org/data_sources.

  • resolve_once (bool) – Find the first available match instead of matches across all data sources with all possible renderings of a name.

  • best_match_only (bool) – Returns just one result with the highest score.

  • with_context (bool) – Reduce the likelihood of matches to taxonomic homonyms. When True, a common taxonomic context is calculated for all supplied names from matches in data sources that have classification tree paths. Names out of determined context are penalized during score calculation.

  • with_vernaculars (bool) – Return ‘vernacular’ field to present common names provided by a data source for a particular match.

  • with_canonical_ranks (bool) – Returns ‘canonical_form’ with infraspecific ranks, if they are present.

  • expand (bool) –

    Whether to expand result rows to match names size. If False, the number of rows will correspond to the number of unique names in names. Only has effect if best_match_only=True or if only one

    data source id is passed.

Returns

DataFrame where rows are the result for each match.

Return type

DataFrame