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set_taxonomy#

Note

Higher order taxonomy information is not required by the ALA, but it is nice to have.

One of the functions you can use to check your data is set_taxonomy(). This function aims to check if you have the following:

  • kingdom: the kingdom of identified taxon

  • phylum: the phylum of identified taxon

  • taxon_class: the class of identified taxon. It is specified as taxon_class here because class is denoting a class object in Python.

  • order: the order of identified taxon

  • family: the family of identified taxon

  • genus: the genus of identified taxon

  • specificEpithet: The name of the first species or species epithet of the scientificName

  • vernacularName: The common or vernacular name of the identified taxon

specifying higher taxonomy#

Note

Adding this taxonomic information automatically is potentially planned for future releases of galaxias.

To determine the what all the higher taxonomic information is for the ALA, visit ala.org.au and search for your taxon. Each argument for set_taxonomy will either take a str (denoting a column name or a higher taxon) or a list. An example of this is below:

>>> import pandas as pd
>>> occ = pd.DataFrame({'scientificName': ['Eolophus roseicapilla','Eolophus roseicapilla']})
>>> my_dwca = galaxias.dwca(ooccurrences=occ)
>>> my_dwca.set_taxonomy(dataframe=occ,kingdom='Animalia',phylum='Chordata',taxon_class='Aves',
...                      order='Psittaciformes',family='Cacatuidae',genus='Eolophus',
...                      specificEpithet='roseicapilla',vernacularName='Galah')
>> my_dwca.occurrences.head()

          scientificName   kingdom    phylum class           order      family     genus specificEpithet vernacularName
0  Eolophus roseicapilla  Animalia  Chordata  Aves  Psittaciformes  Cacatuidae  Eolophus    roseicapilla          Galah
1  Eolophus roseicapilla  Animalia  Chordata  Aves  Psittaciformes  Cacatuidae  Eolophus    roseicapilla          Galah

Other functions#

To learn more about how to use other functions, go to

Optional functions:

Creating Unique IDs:

Passing Dataset:

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