The module v.in.pygbif is a wrapper around the
pygbif package.
Thus, pygbif is a dependency of v.in.pygbif. pygbif can be installed like this:
pip install pygbif
Through pygbif, the module allows to download data from the Global Biodiversity Information Facility (GBIF) using different search ⁄ filter criteria.
Since some of the Darwin Core attribute columns represent SQL key-words, the prefix "g_" was added to all attribute columns. The names of taxa provided at input to the search are written to the column "g_search".
The point data is downloaded and projected into the current location. By default
import is limited to the current computational region in order to avoid
possible projection errors, e.g. when projecting global data into UTM locations.
However, in lat⁄lon location this limitation can be skiped using the -r
flag.
Providing a mask automatically overrides the limitation of the search to the current
computational region.
Terminology in v.in.pygbif is oriented on the Darwin Core standard: http://rs.tdwg.org/dwc/.
Please note that the GBIF Search API has a hard limit of 200,000 occurrences
per request. If you want to fetch more records, either subivide your area of
interest or split up your search by using different search criteria.
When a list of taxa is given as input, v.in.pygbif issues a search for each taxon individually. Thus, in order to split up a search it is recommended to either use different filters on time or space.
# Check matching taxon names and alternatives in GBIF: v.in.pygbif taxa="Poa,Plantago" rank=genus -p # Check matching taxon names and alternatives in GBIF and print output in table: v.in.pygbif taxa="Poa pratensis,Plantago media,Acer negundo" rank=species -t # Get number of occurrences for two geni: v.in.pygbif taxa="Poa,Plantago" rank=genus -o # Get number of occurrences for two species: v.in.pygbif taxa="Poa pratensis,Plantago media" rank=species -o # Fetch occurrences for two species into a map for each species: v.in.pygbif taxa="Poa pratensis,Plantago media" rank=species output=gbif -i