gbif new deployment and “georeferenced” parameter

[sghignone]

Hello everybody, sorry but I'm very new to spocc, so forgive me for being eventually not precise... Yesterday I started playing with spocc, and everything was ok in morning (april, 9). After a while nothing was working (see below the error). Today I heard GBIF developpers, and they told me that yesterday they deployed a new version of our portal, and that, in this new version, the “georeferenced” parameter has been renamed to HAS_COORDINATE. Are you aware of this? Which is the affected libraries update schedule, if any? Thanks a lot. Regards, Stefano

The error:

library("spocc") spp <- c('Danaus plexippus','Accipiter striatus','Pinus contorta') dat <- occ(query = spp, from = 'gbif', gbifopts = list(georeferenced=TRUE)) Error in data.frame(name = name, key = key, rank = row.names(name), row.names = NULL) : arguments imply differing number of rows: 6, 7

[sckott]

Hi @sghignone - Thanks for the heads up! We didn't know about this change. I will get this fixed asap, probably by 1030 PST or so.

[sckott]

hey again @sghignone - Looks like the field names have changed,, e,.g,

• latitude -> decimalLatitude
• longitude -> decimalLongitude
• clazz -> class (thought class was a reserved word in a sql database)

Pushing fix soon - this needs a fix in the rgbif package, which is used within spocc, so you'll need to update both pkgs

[sckott]

@sghignone the hasCoordinate field is an additional field that is related to the georeferenced parameter - see http://www.gbif.org/developer/occurrence#p_hasCoordinate

so fi you say hasCoordinate=TRUE, you get records that have data for both lat and long, whereas georeferenced=TRUE requires data in one of lat or long, but doesn't require data in both fields

[sckott]

woops, mean to reference this issue from rgbif commit ropensci/rgbif#70

[sckott]

A new version of rgbif is on CRAN http://cran.r-project.org/web/packages/rgbif/index.html

Closing