species module¶
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species.
name_backbone
(name, rank=None, kingdom=None, phylum=None, clazz=None, order=None, family=None, genus=None, strict=False, verbose=False, start=None, limit=100, **kwargs)¶ Lookup names in the GBIF backbone taxonomy.
Parameters: - name – [str] Full scientific name potentially with authorship (required)
- rank – [str] The rank given as our rank enum. (optional)
- kingdom – [str] If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
- phylum – [str] If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
- class – [str] If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
- order – [str] If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
- family – [str] If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
- genus – [str] If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
- strict – [bool] If True it (fuzzy) matches only the given name, but never a taxon in the upper classification (optional)
- verbose – [bool] If True show alternative matches considered which had been rejected.
A list for a single taxon with many slots (with verbose=False - default), or a list of length two, first element for the suggested taxon match, and a data.frame with alternative name suggestions resulting from fuzzy matching (with verbose=True).
If you don’t get a match GBIF gives back a list of length 3 with slots synonym, confidence, and matchType=’NONE’.
reference: http://www.gbif.org/developer/species#searching
Usage:
from pygbif import species species.name_backbone(name='Helianthus annuus', kingdom='plants') species.name_backbone(name='Helianthus', rank='genus', kingdom='plants') species.name_backbone(name='Poa', rank='genus', family='Poaceae') # Verbose - gives back alternatives species.name_backbone(name='Helianthus annuus', kingdom='plants', verbose=True) # Strictness species.name_backbone(name='Poa', kingdom='plants', verbose=True, strict=False) species.name_backbone(name='Helianthus annuus', kingdom='plants', verbose=True, strict=True) # Non-existent name species.name_backbone(name='Aso') # Multiple equal matches species.name_backbone(name='Oenante')
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species.
name_suggest
(q=None, datasetKey=None, rank=None, fields=None, start=None, limit=100, **kwargs)¶ A quick and simple autocomplete service that returns up to 20 name usages by doing prefix matching against the scientific name. Results are ordered by relevance.
References: http://www.gbif.org/developer/species#searching
Parameters: - q – [str] Simple search parameter. The value for this parameter can be a simple word or a phrase. Wildcards can be added to the simple word parameters only, e.g. q=*puma* (Required)
- datasetKey – [str] Filters by the checklist dataset key (a uuid, see examples)
- rank – [str] A taxonomic rank. One of class, cultivar, cultivar_group, domain, family, form, genus, informal, infrageneric_name, infraorder, infraspecific_name, infrasubspecific_name, kingdom, order, phylum, section, series, species, strain, subclass, subfamily, subform, subgenus, subkingdom, suborder, subphylum, subsection, subseries, subspecies, subtribe, subvariety, superclass, superfamily, superorder, superphylum, suprageneric_name, tribe, unranked, or variety.
Returns: A dictionary, of results
Usage:
from pygbif import species species.name_suggest(q='Puma concolor') x = species.name_suggest(q='Puma') x['data'] x['hierarchy'] species.name_suggest(q='Puma', rank="genus") species.name_suggest(q='Puma', rank="subspecies") species.name_suggest(q='Puma', rank="species") species.name_suggest(q='Puma', rank="infraspecific_name") species.name_suggest(q='Puma', limit=2)
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species.
name_parser
(name, **kwargs)¶ Parse taxon names using the GBIF name parser
Parameters: name – [str] A character vector of scientific names. (required) reference: http://www.gbif.org/developer/species#parser
Usage:
from pygbif import species species.name_parser('x Agropogon littoralis') species.name_parser(['Arrhenatherum elatius var. elatius', 'Secale cereale subsp. cereale', 'Secale cereale ssp. cereale', 'Vanessa atalanta (Linnaeus, 1758)'])