Comments (5)
I would say: querying from GBIF.
from occ-cube-alien.
@peterdesmet: For step 1, filtering on alien species
should we filter by downloading the unified checklist from GBIF or by using the GitHub version from https://github.com/trias-project/unified-checklist? Using GBIF checklist would make workflow more repeatable worldwide.
from occ-cube-alien.
Here below how I get three data cubes, one for each of the three filters mentioned above.
- For alien taxa where
rank
=SPECIES
and taxonomicStatus one ofACCEPTED
orDOUBTFUL
:
year | eea_cell_code | speciesKey | n |
---|---|---|---|
1792 | 1kmE3865N3144 | 2769766 | 1 |
Occurrences referring to species synonyms, subspecies/varieties and their synonyms are automatically included.
- For alien taxa where
rank
belowSPECIES
andtaxonomicStatus
one ofACCEPTED
orDOUBTFUL
:
year | eea_cell_code | acceptedTaxonKey | n |
---|---|---|---|
2018 | 1kmE4012N3120 | 6411098 | 3 |
Occurrences referring to synonyms have been included in the query, that means searching occurrences where acceptedTaxonKey
is one of nubKey
from unified checklist. Contrarely to name data, in occurrence data the field acceptedTaxonKey
is always present and it is equal to taxonKey
in case of not synonyms (see issue in gbif checklistbank repo).
- For alien taxa where
taxonomicStatus
is NOT one ofACCEPTED
orDOUBTFUL
, i.e. synonyms:
year | eea_cell_code | taxonKey | n |
---|---|---|---|
1940 | 1kmE3927N3130 | 3022668 | 1 |
Occurrences where taxonKey
is one of nubKey
from unified checklist.
Question
How to call the column name containing speciesKey
/acceptedTaxonKey
/taxonKey
?
Possible solution
My suggestion is to use column name taxonKey
:
year | eea_cell_code | taxonKey | n |
---|---|---|---|
1792 | 1kmE3865N3144 | 2769766 | 1 |
2018 | 1kmE4012N3120 | 6411098 | 3 |
1940 | 1kmE3927N3130 | 3022668 | 1 |
@peterdesmet: what do you think?
from occ-cube-alien.
Discussed with @peterdesmet : we use taxonKey
.
from occ-cube-alien.
Done. Documentation about structure and workflow added in README.md of the repo. Issue can be closed or left for informative reasons.
from occ-cube-alien.
Related Issues (20)
- Baseline datacube at classis level HOT 3
- eea grid code HOT 8
- Aggregate data at species level for broader use HOT 1
- Add GBIF key to name of output datacube HOT 1
- Remove speciesKey from cube_europe
- Save output files as csv instead of tsv HOT 4
- Additional checks for vague date ranges required? HOT 12
- Discard occurrences with unverified identificationVerificationStatus HOT 5
- Add PRA species to modelling taxa for European occurrence cube HOT 10
- Update the modelling species list HOT 5
- set seed HOT 3
- Add kingdom to taxonomic compendium
- Simplify workflow using Arrow C++ library in R HOT 1
- error rendering create_db for Belgium HOT 1
- Celastrus : GBIF code changed or inaccurate ? HOT 1
- baseline incomplete for trachemis ? HOT 1
- Automate updating of occ-cubes using github actions
- Where can I find the be_classes_cube.csv? HOT 2
- Occurrences from new zenodo cube all over the place HOT 8
- Add reference file for taxa included in cube
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