This function generates a taxonomy table for a specified SAFE dataset record. Each row represent a taxon used in the data worksheets in the dataset and the table fields show the taxonomic hierarchy, taken from GBIF, for those taxa.
get_taxa(obj)A single record id, or an existing safedata dataframe.
A taxonomy table of classes "safe_taxa" and "data.frame".
All SAFE datasets containing taxa must include a Taxa worksheet, which
must contain all of the taxa referred to in taxon fields in data
worksheets. All entries in this worksheet are validated against the
GBIF database before publication and are used to populate the taxonomic
index for the SAFE datasets. The validated taxonomic hierarchy for the
data is also available in the metadata for a record and this function
converts the metadata into a taxonomy table. If the Taxa worksheet for
a SAFE project dataset is empty, because the data does not contain
observations on taxa, get_taxa will return NULL.
The taxonomy table includes the eight "backbone" taxonomic ranks used
in the GBIF database: Kingdom, Phylum, Class, Order, Family, Genus,
Species and Subspecies. It also includes three further fields:
taxon_name, taxon_rank and gbif_status. These
record the original taxa provided in the Taxa worksheet and show
where the taxonomic name used in a dataset differs from the canonical
name used in GBIF. The row names of the taxon table are the labels
used in data worksheets and are used to match a taxonomy table to a
loaded data worksheet (see add_taxa).
For more details on the structure of the Taxa worksheet see: https://safedata-validator.readthedocs.io/en/latest/data_format/taxa.html
set_example_safe_dir()
#> Loading and caching index
#> Validating directory
taxa <- get_taxa(1400562)
unset_example_safe_dir()
#> Loading and caching index
#> Validating directory