Dear list,
My group has been developing some tools that depend on the occurrence
density data that GBIF provides through its API:
https://www.gbif.org/en/developer/maps
We have been using the R function rgbif::map_fetch to query the api. The
data is returned faithfully but we are experiencing some issues with
projections of the raster data.
I have posted a reproducible example in R here:
https://github.com/ropensci/rgbif/issues/366 . But briefly the issue is
that EPSG:3857 that is downloaded from the API has an extent from -180 to
180 in the x-axis and -86 to 86 in the y-axis but when converting longitude
latitude coordinates into the EPSG:3857 coordinate reference system the
spatial domain is much larger (I think because it is defined in meters
rather than degrees). What am I missing here? I am still a neophyte when it
comes to projections so I apologize if this an obvious question.
One other quick point is that the GBIF maps API does not seem to serve up
the same spatial domain for each projection that is possible. Specifically
compare the following two queries to the api:
https://api.gbif.org/v2/map/occurrence/density/0/0/0@1x.png?srs=EPSG:3857https://api.gbif.org/v2/map/occurrence/density/0/0/0@1x.png?srs=EPSG:4326
Note that EGSG:4326 is on a smaller spatial domain that does not include
the whole Earth. Maybe this is by design but this webpage led me to believe
differently: https://tile.gbif.org/ui/ '
Thanks in advance for your help!
Dan
--
Daniel J. McGlinn, PhD
Assistant Professor
mailing address:
Department of Biology
College of Charleston
66 George Street
Charleston, SC 29424
https://www.mcglinnlab.org
physical address:
Rita Hollings Science Center (office: 239, lab: 292)
58 Coming Street, Suite 245-255
Charleston, SC 29401
office: 843-953-0190
Thanks Kathryn
This happens when you provide a classification where the terminal taxa is not known to the backbone taxonomy.
What it returns is the higher node in the tree that matches, and stating it with the “HIGHER_RANK” flag.
Periodically we rebuild the backbone using the best available checklists. If you find cases where this happens the best approach today would be to help register good checklists through which we can build the backbone. The next backbone build is likely to happen within the next 2-3 months.
I hope this helps.
Best wishes,
Tim
From: API-users <api-users-bounces(a)lists.gbif.org> on behalf of Kathryn Reynolds <K.Reynolds(a)cabi.org>
Date: Tuesday, 9 July 2019 at 10.59
To: "api-users(a)lists.gbif.org" <api-users(a)lists.gbif.org>
Subject: [API-users] rgbif - species match with higher rank
Hi All,
I am using the rgbif package to match up names in a database with the accepted name on gbif (name_lookup). In the output for some instances, the data returned is for the species, and the species exists on GBIF. However, the match type is “higher rank” (see attached file for a sample). I was wondering if anyone could explain to me why this is the case? It seems to be happening most often with bacterial or parasitic species…
Thanks in advance,
Kathryn Reynolds
Junior Data Analyst
CABI Head Office
Nosworthy Way
Wallingford
Oxfordshire
OX10 8DE
United Kingdom
Telephone: +44 (0)1491 8293<tel:+44%201491%20829305>58
Email: K.Reynolds<mailto:K.Reynolds@cabi.org>@cabi.org
Visit us at www.cabi.org<http://www.cabi.org/>
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information and applying scientific expertise to solve
problems in agriculture and the environment
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Hi All,
I am using the rgbif package to match up names in a database with the accepted name on gbif (name_lookup). In the output for some instances, the data returned is for the species, and the species exists on GBIF. However, the match type is "higher rank" (see attached file for a sample). I was wondering if anyone could explain to me why this is the case? It seems to be happening most often with bacterial or parasitic species...
Thanks in advance,
Kathryn Reynolds
Junior Data Analyst
CABI Head Office
Nosworthy Way
Wallingford
Oxfordshire
OX10 8DE
United Kingdom
Telephone: +44 (0)1491 8293<tel:+44%201491%20829305>58
Email: K.Reynolds<mailto:K.Reynolds@cabi.org>@cabi.org
Visit us at www.cabi.org<http://www.cabi.org/>
CABI improves people's lives worldwide by providing
information and applying scientific expertise to solve
problems in agriculture and the environment
P Think Green - don't print this email unless you really need to
************************************************************************
The information contained in this e-mail and any files transmitted with it is confidential and is for the exclusive use of the intended recipient. If you are not the intended recipient please note that any distribution, copying or use of this communication or the information in it is prohibited.
Whilst CAB International trading as CABI takes steps to prevent the transmission of viruses via e-mail, we cannot guarantee that any e-mail or attachment is free from computer viruses and you are strongly advised to undertake your own anti-virus precautions.
If you have received this communication in error, please notify us by e-mail at cabi(a)cabi.org or by telephone on +44 (0)1491 832111 and then delete the e-mail and any copies of it.
CABI is an International Organization recognised by the UK Government under Statutory Instrument 1982 No. 1071...
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