Releases: ropensci/rgbif
Releases · ropensci/rgbif
rgbif v1.0.0
NEW FEATURES
occ_issues()
now works with download data and arbitrary data.frame's (#193)- New downloads queueing tools: gains functions
occ_download_prep()
for preparing a download request without executing it, andocc_download_queue()
for kicking off many download jobs while respecting GBIF's downloads rate limits. See also internal R6 classes for dealing with queuing:DownReq
,GifQueue
. See?occ_download_queue
to get started (#266) (#305) (#311) - New function
map_fetch()
working with the GBIF maps API https://www.gbif.org/developer/maps. See?map_fetch
to get started (#238) (#269) (#284) thanks to @JanLauGe for the work on this name_lookup()
gainsorigin
parameter (#288) (#293) thanks @peterdesmet and @damianooldoniname_lookup()
andname_usage()
gain internal paging - just asocc_search()
/occ_data()
have (#291) (see also #281) thanks @damianooldoni- new import
lazyeval
, and new suggestspng
andraster
occ_search()
/occ_data()
gain parameterskip_validate
(boolean) to skip or not stkip WKT validation by thewicket
package
MINOR IMPROVEMENTS
- removed warnings about parameters that were removed in previous versions of the package (#189)
- add citation file (#189)
- updated
name_usage()
to check params that now only allow 1 value: name, language, datasetKey, rank (#287) occ_count()
losesnubKey
,catalogNumber
, andhostCountry
as those parameters are no longer accepted by GBIF
BUG FIXES
- fixed bug in
name_usage()
, was screwing something up internally (#286) - fixed bug in
occ_data()
: curl options weren't being passed through (#297) - fixed geometry usage in
occ_search()
/occ_data()
- skipping the wicket validation and constructing WKT by hand from bounding box (if bounding box given) - the validation that wicket does isn't what GBIF wants (#303) - add
fill
parameter toocc_download_import()
to pass on tofill
indata.table::fread
, and setfill=TRUE
as default. (#292) - better failure for
occ_download()
(#300) - fix bug in
occ_download()
in which a singletaxonKey
passed in was failing (#283) name_usage()
was ignoringdatasetKey
anduuid
parameters (#290)
DEFUNCT AND DEPRECATED
gbifmap()
has been removed, see the packagemapr
for similar functionality andmap_fetch()
in this package to use the GBIF map API (#298)
rgbif v0.9.9
NEW FEATURES
- Gains new functions
occ_download_datasets
andocc_download_dataset_activity
to list datasets for a download,
and list the downloads activity of a dataset (#275) (#276) - Gains a new vignette covering working with GBIF downloads
inrgbif
(#262)
MINOR IMPROVEMENTS
- Guidance added to docs for downloads functions on length of the
request body (#263) - Changed authentication details (user name, password, email) for
downloads to allow any of the options: pass in as arguments,
store as R options, store as environment variables (#187) gbif_citation()
function gains an S3 method for passing the
output ofocc_download_meta()
to it. In addition, for downloads
gbif_citation()
now returns a citation for the entire download
(including) its DOI, in addition to citations for each dataset (#274)
thanks @dnoesgaard
BUG FIXES
- Fix documentation bug in
occ_count()
:georeferenced
had a
misleading description of what the valueFALSE
did (#265) - Fixed bug in
gbifmap()
- was failing in some cases - better
error handlingn now (#271) thanks @TomaszSuchan - Fixed
occ_download_cancel_staged()
: it wasn't passing on authentication
parameters correctly (#280)
rgbif v0.9.8
NEW FEATURES
- The GBIF API supports passing in many instances of the same
parameter for some parameters on some routes. Previously we
didn't support this feature, but now we do. See the
?many-values
manual file for details. added docs to
individual functions that support this, and added additional
tests (#200) (#260) (#261) - We've removed
V8
dependency and replaced with C++ based
WKT parser packagewicket
. We still usergeos
for some
WKT parsing. rgbif functions that use wicket:gbif_bbox2wkt
,
gbif_wkt2bbox
,check_wkt
(#243) httr
replaced withcrul
for HTTP reqeusts. As part of
this change, the...
parameter was replaced in most functions
bycurlopts
which expects a list. Some functions require
a...
parameter for facet inputs, so...
is retained
with the addition ofcurltops
parameter. A result of this
change is that whereas in the past parameters that were not
defined in a function that also had a...
parameter
would essentially silently ignore that undefined parameter,
but with functions where...
was removed a misspelled
or undefined parameter will cause an error with message (#256)
MINOR IMPROVEMENTS
- moved to markdown docs (#258)
- namespacing calls to base R pkgs instead of importing them
BUG FIXES
rgbif v0.9.7
NEW FEATURES
occ_dowload
gains new parameterbody
to allow users to pass in
JSON or a list for the query instead of passing in statements to
...
. See examples in?occ_dowload
.
MINOR IMPROVEMENTS
- Now using
tibble
for compact data.frame output for
occ_download_import
instead of bespoke internal solution (#240) - Moved all GBIF API requests to use
https
instead ofhttp
(#244) - Improved print method for
occ_download_meta
BUG FIXES
- Fix to
occ_download
to structure query correctly when
type=within
andgeometry
used because the structure is slightly
different than when not usinggeometry
(#242) - Fixed
occ_download
to allowOR
queries for many values of a
parameter, e.g.,taxonKey=2475470,2480946
will be queried correctly
now as essentiallytaxonKey=2475470
ortaxonKey=2480946
(#245)
rgbif v0.9.6
rgbif v0.9.5
NEW FEATURES
occ_search()
now has faceted search. This feature is not inocc_data()
as that function focuses on getting occurrence data quickly, so will not
do get facet data. This means that a new slot is available in the output
object fromocc_search()
, namelyfacets
. Note thatrgbif
has had
faceted search for the species search route (name_lookup()
) and the
registry search route (dataset_search()
) for quite a while. (#215)- new function (
occ_facet()
) to facilitate retrieving only
facet data, so no occurrence data is retrieved. (#215) (#229) - A suite of new parameters added to
occ_search()
and
occ_data()
following addition the GBIF search API:subgenusKey
,
repatriated
,phylumKey
,kingdomKey
,
classKey
,orderKey
,familyKey
,genusKey
,establishmentMeans
,
protocol
,license
,organismId
,publishingOrg
,stateProvince
,
waterBody
,locality
(#216) (#224) - New parameter
spellCheck
added toocc_search()
and
occ_data()
that ifTRUE
spell checks anything passed to thesearch
parameter (same asq
parameter on GBIF API; which is a full text
search) (#227) - New function
occ_spellcheck
to spell check search terms, returns
TRUE
if no spelling problems, or a list with info on suggestions
if not. - Both
occ_search()
andocc_data()
now have ability to support
queries wherelimit=0
, which for one should be possible and not
fail as we did previously, and second, this makes it so that you
can do faceted searches (See above) and not have to wait for occurrence
records to be returned. (#222) MULTIPOLYGON
well known text features now supported in the GBIF
API. Previously, you could not querygeometry
with more than
one polygon (POLYGON
), but now you can. (#222)
MINOR IMPROVEMENTS
- Improved docs for
occ_count()
, especially for the set of
allowed parameter options that the GBIF count API supports occ_count()
gains new parametertypeStatus
to indicate the
specimen type status.- When no results found, the
data
slot now returnsNULL
instead
of a character string
BUG FIXES
- Fixes to
gbif_photos()
: 1) Mapbox URLs to their JS and CSS assets
were out of date, and API key needed. 2) In RStudio, thetable
view
was outputting errors due to serving files onlocalhost:<port>
instead of simply opening the file; fixed now by checking platform
and using simple open file command appropriate for the OS. (#228) (#235)
rgbif v0.9.4
NEW FEATURES
- Now using
tibble
in most of the package when the output is
a data.frame (#204) - New vignette Taxonomic Names for discussing some common names
problems users may run into, and some strategies for dealing with
taxonomic names when using GBIF (#208) (#209)
MINOR IMPROVEMENTS
- Replaced
is()
withinherits()
, no longer importingmethods()
(#219) - Improved docs for registry functions. Not all options were listed
for thedata
parameter, now they are (#210) - Fixed documentation error in
gbifmap()
man file (#212) thanks to @rossmounce
BUG FIXES
- Fixed bug in internal parser within
occ_download()
, in which
strings to parse were not being parsed correctly if spaces weren't in
the right place, should be more robust now, and added tests (#217). Came
from https://discuss.ropensci.org/t/rgbif-using-geometry-in-occ-download/395 - The parameter
type
was being silently ignored in a number of
registry functions. fixed that. (#211)
rgbif v0.9.3
NEW FEATURES
occ_data()
andocc_search()
gain ability to more flexibly deal with inputs to the
geometry
parameter. Previously, long WKT strings passed toocc_search()
or
occ_data()
would fail because URIs can only be so long. Another option is to use
the download API (see?downloads
). This version adds the ability to choose what to
do with long WKT strings via thegeom_big
parameter:asis
(same as previous version),
bbox
which detects if a WKT sting is likely too long, and creates a bounding box from the
WKT string then once data is retrived, clips the result to the original WKT string;axe
uses thegeoaxe
package to chop up the input WKT polygon into many, with toggles in the
new parametersgeom_size
andgeom_n
. (#197) (#199)- As part of this change, when >1 geometry value passed, or if
geom_big="axe"
, then
named elements of the output get namesgeom1
,geom2
,geom3
, etc. instead of the
input WKT strings - this is because WKT strings can be very long, and make for very
awkward named access to elements. The original WKT strings can still be accessed via
attr(result, "args")$geometry
MINOR IMPROVEMENTS
- code tidying throughout the package
BUG FIXES
- Fix parsing bug in
name_usage()
function, see commit e88cf01cc11cb238d44222346eaeff001c0c637e - Fix to tests to use new
testthat
fxn names, e.g.,expect_gt()
instead ofexpect_more_than()
- Fix to
occ_download()
to parse error correctly when empty body passed from
GBIF (#202)
gbif v0.9.2
NEW FEATURES
- New function
occ_data()
- its primary purpose to perform faster data requests. Whereas
occ_search()
gives you lots of data, including taxonomic hierarchies and media records,
occ_data()
only gives occurrence data. (#190)
MINOR IMPROVEMENTS
- Replaced
XML
withxml2
(#192) - Speed ups to the following functions due to use of
data.table::rbindlist()
for
fast list to data.frame coercion:name_lookup()
,name_backbone()
,name_suggest()
,
name_usage()
, andparsenames()
(#191) - Changes to
httr
usage to comply with changes inhttr >= v1.1.0
: now setting
encoding explicitly toUTF-8
and parsing all data manually, using the internal
functionfunction(x) content(x, "text", encoding = "UTF-8")
(#195)
BUG FIXES
- Fix to internal function
move_col()
to not fail on fields that don't exist.
Was failing sometimes when no latitude or longitude columns were returned. (#196)
rgbif v0.9.0
NEW FEATURES
- New set of functions (
gbif_oai_*()
) for working with
GBIF registry OAI-PMH service. Now importingoai
package to
make working with GBIF's OAI-PMH service easier (#183) - Added code of conduct (#180)
- Now sending user-agent header with all requests from this
package to GBIF's servers indicating what version of rgbif
and that it's an ropensci package. Looks like
r-curl/0.9.4 httr/1.0.0 rOpenSci(rgbif/0.9.0)
, with whatever
versions of each package you're using. We also pass a user-agent
string with the headerX-USER-AGENT
in case theuseragent
header gets stripped somewhere along the line (#185) - New function
gbif_citation()
helps get citations for datasets
eith using the occurrence search API viaocc_search()
or the
downloads API viaocc_downlad()
(#178) (#179)
MINOR IMPROVEMENTS
- Using
importFrom
instead ofimport
in all cases now. - Parameter
collectorName
changed torecordedBy
(#184)