GRIIS checklist class

class b3alien.griis.CheckList(filePath: str)[source]

Bases: object

Load a GRIIS checklist from GBIF.

Parameters:: filepath (str) – Path to the distribution.txt file of the checklist.
Returns:: A checklist object containing the list of species.
Return type:: griis.Checklist

_add_species(new_species)[source]

Add new species to the checklist.

Parameters:: new_species (list) – A list of speciesKey(s) to add to the checklist.
Return type:: None

_load_GRIIS(filePath)[source]

Load the checklist and extract speciesKey(s).

Parameters:: filePath (str) – Path to the distribution.txt file of the checklist.
Returns:: A list of speciesKey(s) in the checklist.
Return type:: list

_remove_species(rem_species)[source]

Remove species from the checklist.

Parameters:: rem_species (list) – A list of speciesKey(s) to remove from the checklist.
Return type:: None

GRIIS checklist functions

b3alien.griis.do_taxon_matching(dirPath)[source]

Match keys between taxon.txt and distribution.txt

Parameters:: dirPath (str) – Path to the directory of the checklist
Return type:: Saves a new checklist file ‘merged_distr.txt’ in the checklist directory

b3alien.griis.get_speciesKey(sciname)[source]

Resolve a scientific name to its GBIF taxonKey. If the name is a genus, retrieve all species under that genus. :param sciname: The scientific name to resolve. :type sciname: str

Returns:: A list of resolved speciesKey(s) or [“Uncertain”] if unresolved.
Return type:: list

b3alien.griis.get_species_under_genus(taxon_key)[source]

Get all the keys of the species listed under a specific genus.

Parameters:: taxon_key (int) – The GBIF taxonKey of the genus.
Returns:: A list of speciesKey(s) under the specified genus.
Return type:: list

b3alien.griis.read_checklist(filePath, cl_type='detailed', locality='Belgium')[source]

Read a GRIIS checklist and extract speciesKey(s) and time series of species numbers over time. :param filePath: Path to the directory of the checklist (must contain distribution.txt and taxon.txt if cl

type is not ‘detailed’).

Parameters:

cl_type (str) – Type of checklist: ‘detailed’ (with eventDate) or ‘simple’ ( without eventDate, requires taxon.txt and distribution.txt).
locality (str) – The locality to filter on (default is ‘Belgium’).

Returns:

A tuple containing: - list of speciesKey(s) in the checklist - pd.DataFrame with columns ‘introDate’ and ‘cumulative_total’ representing the

cumulative number of species over time.

Return type:

tuple

b3alien.griis.split_event_date(eventDate)[source]

Interprete the event date as introduction date and date of last seen, when this information is available in the checklist.

Parameters:: eventDate (str) – Text string of eventDate
Returns:: A series containing introduction date (‘intro’) and date last seen (‘outro’)
Return type:: pd.Series