rgbif v0.9.3

NEW FEATURES

• occ_data() and occ_search() gain ability to more flexibly deal with inputs to the
  geometry parameter. Previously, long WKT strings passed to occ_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 the geom_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 the geoaxe package to chop up the input WKT polygon into many, with toggles in the
  new parameters geom_size and geom_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 names geom1, 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 of expect_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 with xml2 (#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(), and parsenames() (#191)
• Changes to httr usage to comply with changes in httr >= v1.1.0: now setting
  encoding explicitly to UTF-8 and parsing all data manually, using the internal
  function function(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 importing oai 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 header X-USER-AGENT in case the useragent
  header gets stripped somewhere along the line (#185)
• New function gbif_citation() helps get citations for datasets
  eith using the occurrence search API via occ_search() or the
  downloads API via occ_downlad() (#178) (#179)

MINOR IMPROVEMENTS

• Using importFrom instead of import in all cases now.
• Parameter collectorName changed to recordedBy (#184)

BUG FIXES

• Fix to occ_download_meta() print method to handle 1 or more predicate results (#186)
• Fix to occ_issues() to work with return=data and return=all occ_search() output (#188)

rgbif v0.8.9

MINOR IMPROVEMENTS

• Updated terraformer.js javascript code included in the package
  along with an update in that codebase (#156)
• The email parameter now NULL by default in the function
  occ_download(), so that if not provided or not set in options,
  then function fails. (#173)
• Additional explanation added to the ?downloads help file.
• Added internal checks to elevation() to check for coordinates that
  are impossible (e.g., latitude > 90), not complete (e.g., lat given,
  long not given), or points at 0,0 (just warns, doesn't stop). (#176)
  thanks @luisDVA
• General code tidying across package

BUG FIXES

• A route changed for getting images for a taxon within the /species
  route, fix to function name_usage() (#174)
• Fix to occ_search() to remove a block of code to do synonym checking.
  This block of code was used if the parameter scientificName was passed,
  and checked if the name given was a synonym; if yes, we used the accepted
  name according to the GBIF backbone taxonomy; if no, we proceeded with the
  name given by the user. We removed the block of code because the GBIF
  API now essentially does this behind the scenes server side. See
  https://github.com/gbif/gbif-api for examples. (#175)

rgbif 0.8.8

MINOR IMPROVEMENTS

• Additional tests added for gbif_photos() and gbif_names() (#170)

BUG FIXES

• Fixed a few tests that were not passing on CRAN.

rgbif v0.8.6

NEW FEATURES

• New set of functions with names occ_download*() for working with the GBIF download API. This is the same service as using the GBIF website, but via an API. See ?downloads. (#154) (#167)

MINOR IMPROVEMENTS

• Explicitly import non-base R pkg functions, so importing from utils, methods, and stats (#166)

BUG FIXES

• Fixed problem with httr v1 where empty list not allowed to pass to
  the query parameter in GET (#163)

rgbif 0.8.4

NEW FEATURES

• New functions for the /enumerations GBIF API route: enumeration()
  and enumeration_country(). Many parts of the GBIF API make use of
  enumerations, i.e. controlled vocabularies for specific topics - and are
  available via these functions. (#152)

IMPROVEMENTS

• elevation() now requires an API key (#148)
• The V8 package an Import now, used to do WKT read/create with use of
  the Javascript library Terraformer (http://terraformer.io/). Replaces
  packages sp and rgeos, which are no longer imported (#155)
• Changed occ_search() parameter spatialIssues to
  hasGeospatialIssues (#151)
• Added note to docs about difference between /search and /count
  services, and how they work. (#150)
• Added tests for habitat parameter in name_lookup() (#149)
• Dropped plyr from Imports (#159)
• Dropped stringr from Imports (#160)
• Dropped maps and grid packages from Imports (#161)

BUG FIXES

• Looping over records with limit and start parameters was in some
  cases resulting in duplicate records returned. Problem fixed. (#157)

v0.8.0

IMPROVEMENTS

• All example moved to \dontrun (#139)
• README fixes for html (#141)
• Fixed documentation in occ_search() to give correct values for default and max limit
  and start parameters (#145)
• Changed internal GET helper function to properly pass on error message (#144)
• Replaced assertthat::assert_that() with stopifnot() to have one less dependency (#134)
• Fixed occ_search() to allow ability to query by only publishingCountry, that is, with no
  other parameters if desired (#137)

BUG FIXES

• Fixed bug in internal GET() helper function to just pass NULL to the query parameter when
  the list of length 0 passed, since it caused requests to fail in some cases.
• Fix to name_lookup() to force a logical entry for certain parameters - before this fix
  if the correct logical param was not passed, the GBIF API went with its default parameter (#135)
• Fixed bug in name_backbone() due to change in namelkupparser() helper function - fixes
  parsing for verbose output (#136)
• Fixed some broken URLs in occ_search() documentation (#140)

v0.7.7

rgbif 0.7.7

NEW FEATURES

• New function occ_issues() to subset data from occ_search() based on GBIF issues. (#) (#122)
• Related to the last bullet, GBIF issues now are returned by default in occ_search() results, and are intentionally moved to the beginning of the column order of the data to be more obvious. (#102)
• occ_search() now returns all data fields by default. The default setting for the fields parameter is all - but can be changed. See ?occ_search
• New function gbif_names() to view highlighted terms in name results from a call to name_lookup(). (#114)
• New functions: occ_issues_lookup() to lookup GBIF issues based on code name or full issue name, and gbif_issues() to print the entire issues table.

IMPROVEMENTS

• Completely replaced RCurl with httr
• Completely replaced RJSONIO with jsonlite. Should see slight performance in JSON parsing with jsonlite.
• Default number of records in occ_search() now 500; was 25. (#113)
• Vignette for old version of GBIF API removed.
• New vignette for cleaning data via GBIF issues added. (#132)
• Functions for working with old GBIF API removed, now defunct. (#116)
• Now better parsing for some functions (organizations(), datasets(), networks(), nodes(), installations()) to data.frames when possible. (#117)
• Added further help to warn users when searching on ranges in latitude or longitude in occ_search() (#123)
• callopts parameter changed to ... throughout all functions. Now pass on options to httr as named lists or functions. (#130)
• Beware that GBIF data is becoming Darwin Core compliant - so many parameters throughout this package have changed from sentence_case to camelCase.
• dataset_search() and dataset_suggest() gain new parameter publishingOrg
• Default for limit parameter changed to 100 for dataset functions: dataset_search(), dataset_suggest(), and datasets().
• Default for limit parameter changed to 100 for registry functions: installations(), networks(), organizations, and nodes().
• Parameter changes in networks(): name, code, modifiedsince, startindex, and maxresults gone; new parameters query, identifier, identifierType, limit, and start
• Parameter changes in nodes(): new parameters identifier, identifierType, limit, and start

BUG FIXES

• occ_search() failed sometimes on species that were not found. Fixed. (#112)
• Added better handling of some server errors to pass on to user. (#115) (#118)
• Fixed incorrect parsing for some cases in occ_search() (#119)
• Fixed bad parsing on output from name_lookup() (#120)
• Fixed single map option in gbif_photos() that caused map with no data. (#121)
• Fixed some parameter names in name_() functions according to changes in the GBIF API spec, and fixed documentation to align with GBIF API changes, and added note about maximum limit. (#124) (#127) (#129) Thanks to @willgearty !
• Fixed internals of occ_search() so that user can pass in multiple values to the issue parameter. (#107)
• Fixed URL to tutorial on ropensci website (#105) Thanks @fxi !

v0.7.0

rgbif 0.7.0

NEW FEATURES

• occ_search() now has a dplyr like summary output when return='all'. See ?occ_search for examples. You can still easily access all data, by indexing to meta, hierarchy, data, or media via e.g., $data, ['data'], or [['data']]. (#95) See example below:

occ_search(taxonKey=key, fields=c('name','basisOfRecord','protocol'))

Records found [8330] 
Records returned [20] 
No. unique hierarchies [1] 
No. media records [20] 
Args [taxonKey=2433407, limit=20, fields=name,basisOfRecord,protocol] 
First 10 rows of data

               name    protocol     basisOfRecord
1  Ursus americanus DWC_ARCHIVE HUMAN_OBSERVATION
2  Ursus americanus DWC_ARCHIVE HUMAN_OBSERVATION
3  Ursus americanus DWC_ARCHIVE HUMAN_OBSERVATION
4  Ursus americanus DWC_ARCHIVE HUMAN_OBSERVATION
5  Ursus americanus DWC_ARCHIVE HUMAN_OBSERVATION
6  Ursus americanus DWC_ARCHIVE HUMAN_OBSERVATION
7  Ursus americanus DWC_ARCHIVE HUMAN_OBSERVATION
8  Ursus americanus DWC_ARCHIVE HUMAN_OBSERVATION
9  Ursus americanus DWC_ARCHIVE HUMAN_OBSERVATION
10 Ursus americanus DWC_ARCHIVE HUMAN_OBSERVATION
..              ...         ...               ...

• Media now returned from the GBIF API. Thus, in occ_search(), we now return a media slot in the output list by default.
• New function gbif_photos() to view media files (photos in the wild or of museum specimens). Two options are available, which='map' creates a single map which presents the image when the user clicks on the point, and which='table' in which a table has one row for each image, presenting the image and an interactive map with the single point. (#88) See screenshots at bottom.
• Two new packages are imported: sp and whisker

IMPROVEMENTS

• GBIF updated their API, now at v1. URL endpoints in rgbif changed accordingly. (#92)
• GBIF switched to using 2-letter country codes. Take note. (#90)
• GBIF switched all parameters to camelCase from under_score style - changed accordingly in rgbif.
• Using package custom version of plyr::compact() instead of importing from plyr.
• In name_lookup() removed facet_only parameter as it doesn't do anything - use limit=0 instead. Further, added two new slots of output: hierarchy and names (for common/vernacular names) (#96). The output can be determined by user via the return parameter.
• In name_suggest(), if the field higherClassificationMap is selected to be returned via the fields parameter, a list is returned with a data frame, and a list of the hierarchies separately. If higherClassificationMap is not selected, only a data frame is returned.
• occ_search() gains new parameters mediatype and issue (#93), with detailed list of possible options for the issue parameter. Gains new examples for searching for images, examples of calls that will throw errors.
• Updated the vignette.

BUG FIXES

• Added better error message to check_wkt().
• facet_only parameter removed from dataset_search() function as it doesn't do anything - use limit=0 instead.
• Fixed some examples that didn't work correctly.

New gbif_photos() function

which='table'

which='map'