rgbif v1.2.0

NEW FEATURES

• pkgdown documentation site (#336) (#337) all work done by @peterdesmet
• package gains hex logo (#331) (#332) thanks @peterdesmet
• big change to elevation() function: the Google Maps API requires a form of payment up front, and so we've decided to move away from the service. elevation() now uses the Geonames service https://www.geonames.org/; it does require you to register to get a username, but its a free service. Geonames has a few different data models for elevation and can be chosen in the elevation_model parameter (#344) (#345)
• biggish change to occ_data()/occ_search() output: the data.frame in the data slot now always has the first column as the occurrence key (key), and the second column is now the scientific name (scientificName). the previously used name column still exists in the data.frame, so as not to break any user code, but is simply a duplicate of the scientificName column. in a future version of this package the name column will be dropped (#329)

MINOR IMPROVEMENTS

• README gains full list of code contributors and any folks involved in github issues (#339) (#343) thanks @peterdesmet
• update pkg citation, include all authors (#338)
• added more to occ_search()/occ_data()/occ_download() documentation on WKT (well-known text) with respect to winding order. GBIF requires counter-clockwise winding order; if you submit clockwise winding order WKT to occ_search() or occ_data() you should get data back but the WKT is treated as an exclusion, so returns data outside of that shape instead of within it; if you submit clockwise winding order WKT to occ_download() you will get no data back (#340)

BUG FIXES

• fix bug in occ_download(), was failing in certain cases because of some bad code in an internal function catch_err() (#333)
• occ_download() was not returning user name and email in it's print method (#334)
• occ_issues() was failing with occ_data() or occ_search() input when type="many" (i.e., when > 1 thing was passed in) (#341)

rgbif v1.1.0

NEW FEATURES

• tests that make HTTP requests are now cached via the vcr package so do not require an internet connection (#306) (#327)
• added name usage issues (similar to occurrence issues) data. in part fixes name_usage() problem, more work coming to allow users to use the name issues data like we allow for occurrence issues through occ_issues() (#324)

MINOR IMPROVEMENTS

• map_fetch() changes following changes in GBIF maps API: new parameters taxonKey, datasetkey, country, publishingOrg, publishingCountry and removed parameters search and id; note that this changes how queries work with this function (#319)
• added note to map_fetch() docs that style parameter does not necessarily use the style you give it. not sure why (#302)
• fixed messaging in occ_download_queue() to report an accurate number of jobs being processed; before we were just saying "kicking off first 3 requests" even if there were only 1 or 2 (#312)

BUG FIXES

• fix to occ_get() when verbatim=TRUE (#318)
• elevation() function now fails better. when the API key was invalid the function did not give an informative message; now it does (#322)

rgbif v1.0.2

MINOR IMPROVEMENTS

• significant change to occ_download_queue(): sleep time between successive calls to check on the status of download requests is now 10 seconds or greater. This shouldn't slow down your use of occ_download_queue() much because most requests should take more than the 10 seconds to be prepared (#313)
• add tests for download queue method (#315)
• explicitly @importFrom fxns used from lazyeval package to avoid check note (#316)
• remove reshape2 and maps packages from Suggests (#317)

BUG FIXES

• fix bug in name_usage(): we were screwing up parsing of issues column when single taxon keys passed in (#314)

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, and occ_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() gains origin parameter (#288) (#293) thanks @peterdesmet and @damianooldoni
• name_lookup() and name_usage() gain internal paging - just as occ_search()/occ_data() have (#291) (see also #281) thanks @damianooldoni
• new import lazyeval, and new suggests png and raster
• occ_search()/occ_data() gain parameter skip_validate (boolean) to skip or not stkip WKT validation by the wicket 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() loses nubKey, catalogNumber, and hostCountry 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 to occ_download_import() to pass on to fill in data.table::fread, and set fill=TRUE as default. (#292)
• better failure for occ_download() (#300)
• fix bug in occ_download() in which a single taxonKey passed in was failing (#283)
• name_usage() was ignoring datasetKey and uuid parameters (#290)

DEFUNCT AND DEPRECATED

• gbifmap() has been removed, see the package mapr for similar functionality and map_fetch() in this package to use the GBIF map API (#298)

rgbif v0.9.9

NEW FEATURES

• Gains new functions occ_download_datasets and occ_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
  in rgbif (#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 of occ_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 value FALSE 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 package wicket. We still use rgeos for some
  WKT parsing. rgbif functions that use wicket: gbif_bbox2wkt,
  gbif_wkt2bbox, check_wkt (#243)
• httr replaced with crul for HTTP reqeusts. As part of
  this change, the ... parameter was replaced in most functions
  by curlopts which expects a list. Some functions require
  a ... parameter for facet inputs, so ... is retained
  with the addition of curltops 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

• Fixed problem in occ_download_import() to allow import
  of csv type download in addition to darwin core archive.
  additional change to occ_download_get to add format
  attribute stating which format (#246)
• fix to occ_download_import adding fill=TRUE to
  the data.table::fread call (#257)

rgbif v0.9.7

NEW FEATURES

• occ_dowload gains new parameter body 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 of http (#244)
• Improved print method for occ_download_meta

BUG FIXES

• Fix to occ_download to structure query correctly when
  type=within and geometry used because the structure is slightly
  different than when not using geometry (#242)
• Fixed occ_download to allow OR queries for many values of a
  parameter, e.g., taxonKey=2475470,2480946 will be queried correctly
  now as essentially taxonKey=2475470 or taxonKey=2480946 (#245)

rgbif v0.9.6

BUG FIXES

• Fixed a bug in parsenames() caused by some slots in the list
  being NULL (#237)
• Fixed some failing tests: occ_facet() tests were failing due to
  changes in GBIF API (#239)
• Fixes to gbif_oai_get_records() for slight changes in oai
  dependency pkg (#236)

rgbif v0.9.5

NEW FEATURES

• occ_search() now has faceted search. This feature is not in occ_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 from occ_search(), namely facets. Note that rgbif 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 to occ_search() and
  occ_data() that if TRUE spell checks anything passed to the search
  parameter (same as q 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() and occ_data() now have ability to support
  queries where limit=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 query geometry 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 parameter typeStatus to indicate the
  specimen type status.
• When no results found, the data slot now returns NULL 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, the table view
  was outputting errors due to serving files on localhost:<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() with inherits(), no longer importing methods() (#219)
• Improved docs for registry functions. Not all options were listed
  for the data 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)