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Source: NEWS.md

rgbif 3.8.1

CRAN release: 2024-09-27

NEW FEATURES

BUG FIXES

DOCUMENTATION

rgbif 3.8.0

CRAN release: 2024-05-23

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

  • check_inputs()bug fixed. (#706)

DOCUMENTATION

DEPRECATED

  • gbif_citation() datasetKey methods no longer supported (#716)
  • “axe” feature in occ_data() is no longer supported. (#718)
  • occ_data() is soft deprecated and supported for legacy reasons only, and will no longer add new features.

rgbif 3.7.9

CRAN release: 2024-01-11

NEW FEATURES

There have been many additions for accessing dataset metadata.

MINOR IMPROVEMENTS

Documentation

DEPRECATED

  • There are no longer static data files in rgbif. This data is better fetched fresh from the appropriate endpoints. (#690) (#688)

  • datasets() is soft deprecated, since the interface was overloaded and confusing. See functional replacements above.

rgbif 3.7.8

CRAN release: 2023-09-11

  • rgbif has a new logo. (#679)

NEW FEATURES

MINOR IMPROVEMENTS

  • Stream error fixed (“HTTP/2 stream 15 was not closed cleanly before end of the underlying stream”). Now map_fetch(), occ_data(), occ_search(), and occ_download_wait() have curlopts = list(http_version=2), which fixes the error. This might need to be the default setting for the whole package. (#656)

  • name_suggest() now gives a warning at prevents setting the limit > 100, since this is the GBIF API max. (#657)

Documentation

New article Creating maps from occurrences, which explains how to use map_fetch().

DEPRECATED

  • occ_issues() is now deprecated, since it is difficult to maintain, and not widely used. (#651)

rgbif 3.7.7

CRAN release: 2023-04-03

MINOR IMPROVEMENTS

  • Fixes test that was causing errors on CRAN.

rgbif 3.7.6

CRAN release: 2023-03-23

BREAKING CHANGE

DEPRECATED

  • occ_count() parameters georeferenced, type, date, to, from are no longer supported and not guaranteed to work correctly. (#622)
  • occ_facet() and count_facet() are now deprecated use occ_count(facet="x") instead.

NEW FEATURES

MINOR IMPROVEMENTS

  • occ_search() now supports more multi-valued parameters. (#617)
  • Removed dependencies on randgeo and conditionz. (#624) (#625)

Documentation

New article explaining occ_count() changes and new features Getting Occurrence Counts From GBIF.

rgbif 3.7.5

CRAN release: 2023-01-05

NEW FEATURES

DOCUMENTATION

MINOR IMPROVEMENTS

  • removed sp and rgeos dependencies. (#578)

rgbif 3.7.4

CRAN release: 2022-12-06

NEW FEATURES

  • name_usage now has the ability to fetch iucn red list categories using data=iucnRedListCategory. (#547)

DOCUMENTATION

BUG FIXES

  • dataset_gridded bug fixed when inputting only one non-gridded dataset. (#546)

MINOR IMPROVEMENTS

  • New CRAN checks badge URL. (#555)
  • Update min vcr requirement to (>= 1.2.0). (#559)
  • Updated r-lib actions to v2 (#566)

rgbif 3.7.3

CRAN release: 2022-09-03

NEW FEATURES

DEPRECATED

BUG FIXES

  • occ_search fixed bug related to networkKey in the column names (#524)

rgbif 3.7.2

CRAN release: 2022-04-11

MINOR IMPROVEMENTS

  • Removing wellknown dependency and switching to wk (#512)

BUG FIXES

rgbif 3.7.1

CRAN release: 2022-03-16

BUG FIXES

rgbif 3.7.0

CRAN release: 2022-02-08

There is a new rgbif maintainer: John Waller.

NEW FEATURES

  • derived_dataset() : New function to register a cleaned or modified dataset on GBIF for citation. (#467)
  • name_backbone_checklist() : New function that takes a list, vector, or data.frame of scientific names and asynchronously matches them to the backbone. (#475)
  • pred_isnull() : New predicate function that includes NULL values from a column in the download. (#489)
  • occ_download.print() : Now prints out much more information including a DOI and citation. (#494)

DEPRECATED

MINOR IMPROVEMENTS

  • occ_download_wait() and occ_download_meta() : now accept a class character download key directly. The keys does do not need to be class “occ_download”. (#487)
  • name_backbone() : now returns new columns “verbatim_name”, “verbatim_genus” ect. that the user has supplied. This makes it easier for the user to track what has been matched. The verbose argument also has been un-retired. If verbose=TRUE, more results will be returned in a single data.frame. (#475)
  • gbif_citation() : will now accept a download key directly.
  • occ_download_get() : Does not throw an error if the data is already present and overwrite=FALSE, it will just give a warning and return the already present dataset. This allows users to run occ_download_get(key) %>% occ_download_import() multiple times without re-downloading the same file with overwrite=TRUE.
  • download_predicate_dsl() : “publishingOrg” now added as a download key. (#496) key_lkup now includes GBIF-style uppercase keys as well. So pred("TAXON_KEY",212) and pred("taxonKey",212) will both work.

DOCUMENTATION

Wrote new articles highlighting new features and encouraging the use of occ_download() over occ_search().

New articles:

BUG FIXES

rgbif 3.6.0

CRAN release: 2021-06-02

Downloads

  • typo in download predicate functions fixed - mulitpoint -> multipoint (#460) thanks @damianooldoni for catching that
  • added three new predicate keys: stateProvince (#458), gadm (#462), and occurrenceStatus (#465)

MINOR IMPROVEMENTS

  • add two new occurrence issues: FOOTPRINT_SRS_INVALID and FOOTPRINT_WKT_INVALID (#454)
  • occ_download_import() docs: more information on data.table::fread parameters and particular ones that would be useful to sort out data read issues (#461)

BUG FIXES

  • fix occ_download_get(): downloaded files used to have a certain content type in response header we checked for, but its changed at least once even in successful responses, so that step has been removed (#464)
  • fix occ_download_import(): country code for Namibia is NA - this was turning into the R missing value NA - now fixed (#463)

rgbif 3.5.2

CRAN release: 2021-01-27

Download predicates

  • in occurrence download predicate builder checks, to better help users, give the name of the key that fails upon failure instead of just the string ‘key’ (#450)
  • occurrence download predicates: new key coordinateUncertaintyInMeters added, e.g. usage: pred_lt("coordinateUncertaintyInMeters",10000) (#449)
  • pred_and() and pred_or() slight change: now required that more than one predicate is passed to each of these functions because it doesn’t make sense to do an and or or predicate with only one predicate (#452)
  • fix for use of pred_not(pred_notnull()) (#452)

MINOR IMPROVEMENTS

  • add a new occurrence issue (TAXON_MATCH_AGGREGATE) and a new name issue (BACKBONE_MATCH_AGGREGATE) (#453)

BUG FIXES

  • remove geoaxe references in man-roxygen template doc files - not using pkg anymore here and that pkg is cran archived too (#448)

rgbif 3.5.0

CRAN release: 2021-01-13

MINOR IMPROVEMENTS

  • remove package wicket - use package wellknown instead - no user facing changes related to this (#447)
  • remove package geoaxe (to be archived on CRAN soon) - use package sf instead (#447)

BUG FIXES

  • fix to download predicate function pred_not(): it was not constructing the query correctly, fixed now. user facing change as well: it now expects a predicate to be passed, and only a single predicate as GBIF not predicate only accepts one predicate (#446)

rgbif 3.4.2

CRAN release: 2021-01-06

MINOR IMPROVEMENTS

  • Add new occurrence issue DIFFERENT_OWNER_INSTITUTION (#444)
  • re-record all test fixtures

BUG FIXES

rgbif 3.4

MINOR IMPROVEMENTS

  • Documentation: clarify for occ_search() and occ_data() what parameters accept many values and which do not; in addition, we clarify which parameters accept multiple values in the same HTTP request, and those that accept multiple values but apply each in separate HTTP requests. See also ?many-values manual file (#369)
  • gbif_issues() gains 9 new occurrence issues (#435)
  • for occ_search() and occ_data(), basisOfRecord parameter now supports multiple values, both in one request and in different requests, depending on input format (see “Multiple values passed to a parameter” section in ?occ_search) (#437)
  • remove vignettes from cran to avoid cran checks - still available on our docs site (#438)
  • occ_download_get(): GBIF slightly altered download behavior - we now explicitly follow any redirects to get a download (#439)
  • print.occ_download_meta (used when you run occ_download_meta()) was printing NA for number of results found if no results were ready yet - now prints 0 instead of NA (#440)

BUG FIXES

  • count_facet() fixes: fixed internal fxn for count_facet for parsing results, was dropping values for facets; added assertions to check parameter types input by user for the fxn; changed so that keys and basisofrecord can be passed together (#436)

rgbif 3.3

MINOR IMPROVEMENTS

  • added two new occurrence issues to gbif_issues(): GEOREFERENCED_DATE_INVALID and GEOREFERENCED_DATE_UNLIKELY (#430)

BUG FIXES

  • fixed an error in occ_data() caused by GBIF adding a new field of data to the output of /occurrence/search/: gadm. cleaned up internals of occ_data() to drop gadm, and other fields that are complex and take time to parse (use occ_search() if you want all the data fields) (#427)
  • gbif_names() fix: was ending up with invalid URLs to GBIF species pages because we had taxon keys with leading spaces somehow. now all leading and trailing spaces in taxon keys removed before making URLs (#429)

rgbif 3.2

MINOR IMPROVEMENTS

  • gbif_issues() changes: three new occurrence issues added; one name issue removed that’s deprecated (#423)
  • gbif_citation() rights field was empty unless pulling from a downloaded file; now fill in with license key; also a fix for when occurrence key passed to the function (#424)
  • establishmentMeans now supported in occ_download/pred (#420)

BUG FIXES

rgbif 3.1

MINOR IMPROVEMENTS

BUG FIXES

rgbif 3.0

BREAKING CHANGE

  • Many functions (occ_search, occ_get, name_usage, name_lookup, name_suggest, name_backbone, and dataset_search) have a return parameter to toggle what is returned from the function call. To simplify rgbif maintenance, we’ve deprecated the return parameter. We’ve left it in each of the functions, but it no longer does anything, other than raising a warning if used. This means that function calls to these functions now always return the same data structure, making it easier to reason about for the user, as well as for us developers trying to make sure the package works as expected under a variety of conditions. If you have been using the return parameter, do the same function call as before, but now index to the output you need. This is a breaking change, thus the major version bump (#413)

NEW FEATURES

  • new function occ_download_cached(), which takes the same input as occ_download(), but instead of starting a query, it checks if you’ve recently made the same request (with configureable settings for what “recent” means). This can save time when you’re doing occurrence download requests that you may have done in the recent past (#308)

MINOR IMPROVEMENTS

  • configured package to be able to use two different base urls, api.gbif-uat.org and api.gbif.org. We have only used the latter previously, but now can configure rgbif to use the former, mostly for testing purposes (#398)
  • occ_download_import() gains encoding parameter that is passed down to data.table::fread to make it very clear that encoding can be configured (even though you could have before via ...) (#414)

BUG FIXES

  • fix tibble construction (#412)

rgbif 2.3

CRAN release: 2020-05-28

MINOR IMPROVEMENTS

  • max records you can return for /occurrence/search route is now 100,000 (used in occ_data() and occ_search()). updated docs throughout accordingly (#405)
  • improved docs in occ_download_queue() for how we determine when a job is done. see new section “When is a job done?” (#409)
  • print methods print.occ_download_prep and print.occ_download improved. previously well-known text strings were printed in their entirety. now they are handled to only print so many characters; also applies to any download predicate string that’s long (#407)
  • occ_download_get() now supports using a progress bar by passing in httr::progress() (#402)
  • occ_data() and occ_search() gain two new parameters: recordedByID and identifiedByID (#403)

BUG FIXES

rgbif 2.2

MINOR IMPROVEMENTS

  • add a section Download status to the ?downloads manual file listing all the different download status states a download can have and what they mean (#390)
  • fix gbif_issues/gbif_issues_lookup: added four missing occurrence issues to the package (COORDINATE_PRECISION_INVALID, COORDINATE_UNCERTAINTY_METERS_INVALID, INDIVIDUAL_COUNT_INVALID, and INTERPRETATION_ERROR) (#400)
  • doing real tests now for occ_download() via vcr (#396)

BUG FIXES

  • fix name_lookup(): we were attempting to rearrange columns when no results found, leading to an error (#399)

rgbif 2.1

DEFUNCT

MINOR IMPROVEMENTS

  • docs fix for occ_data(): remove ... parameter definition as it wasn’t used in the function (#394)

BUG FIXES

  • download predicate fxns fix: “within” wasnt being handled properly (#393) thanks @damianooldoni

rgbif 2.0

NEW FEATURES

MINOR IMPROVEMENTS

BUG FIXES

rgbif 1.4.0

CRAN release: 2019-10-30

NEW FEATURES

  • gains new function mvt_fetch() for fetching Map Vector Tiles (MVT). mvt used to be an option in map_fetch(), but we only returned raw bytes for that option. With mvt_fetch() we now leverage the protolite package, which parses MVT files, to give back an sf object (#373) thanks to @jeroen for the protolite work to make this work
  • associated with above, map_fetch() loses the format = ".mvt" option; and thus now only returns a RasterLayer
  • occ_issues() and name_issues() reworked. Both now use the same underlying internal logic, with occ_issues pulling metadata specfic to occurrence issues and name_issues pulling metadata specific to name issues. name_issues used to only be a data.frame of name issues, but can now be used similarly to occ_issues; you can pass the output of name_usage() to name_issues to filter/parse name results by their associated name issues. Associated with this, new function gbif_issues_lookup can be used to lookup either occurrence or name issues by their full name or code (#363) (#364)

MINOR IMPROVEMENTS

  • fix examples and tests that had WKT in the wrong winding order (#361)
  • parsing GBIF issues in the output of name_usage() wasn’t working (#328) (#363) (#364)
  • name_lookup() gains an additional parameters issue for filtering name results by name issues (#335) (#363) (#364)
  • fixed definitions of x, y, z parameters in map_fetch() manual file (#375)
  • added examples to gbif_citation() manual file for accessing many citations (#379)
  • fixed a test for occ_download_queue() (#365)
  • name_* function outpus have changed, so be aware if you’re using those functions

BUG FIXES

  • fixed issue with map_fetch(): when srs was EPSG:3857, the extent we set was incorrectly set as raster::extent(-180, 180, -85.1, 85.1). Now the extent is raster::extent(-20037508, 20037508, -20037508, 20037508 (#366) (#367) thanks @dmcglinn for reporting and @mdsumner for fixing!
  • fix for Windows platforms for gbif_citation() for occ_download_get objects. we weren’t correctly creating the path to a file on windows (#359)
  • fix to print.gbif_data (#370) (#371)
  • occ_download() was erroring with a useless error when users try to use the fxn with the same parameter input types as occ_search/occ_data; when this happens now there is a useful error message (#381)
  • fix to occ_download(): when type = "in" was used, we weren’t creating the JSON correctly, fixed now (#362)

rgbif 1.3.0

CRAN release: 2019-05-08

NEW FEATURES

  • occ_download() and occ_download_prep() gain a new parameter format for specifying the type of download. options are DWCA (default), SIMPLE_CSV, or SPECIES_LIST. SIMPLE_CSV and SPECIES_LIST are csv formats, while DWCA is the darwin core format (#352)
  • now throughout the package you can pass NA in addition to NULL for a missing parameter - both are removed before being sent to GBIF (#351)

MINOR IMPROVEMENTS

  • replace tibble::as_data_frame/tibble::data_frame with tibble::as_tibble (#350)
  • key and gbifID in the output of occ_data/occ_search/occ_get have been changed so that both are character class (strings) to match how GBIF encodes them (#349)
  • fix some test fixtures to use preserve exact bytes so that cran checks on debian clang devel don’t fail (#355)

BUG FIXES

  • fix to occ_download: fail with useful message when user does not pass in queries as character class (#347)
  • fix to occ_download: fail with useful message now when user/pwd/email not found or given (#348)

rgbif 1.2.0

CRAN release: 2019-02-26

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

rgbif 1.1.0

CRAN release: 2018-10-19

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 1.0.2

CRAN release: 2018-07-06

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 1.0.0

CRAN release: 2018-07-03

NEW FEATURES

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

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 0.9.9

CRAN release: 2017-11-12

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

rgbif 0.9.8

CRAN release: 2017-04-18

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 0.9.7

CRAN release: 2017-01-21

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 0.9.6

CRAN release: 2016-12-06

BUG FIXES

rgbif 0.9.5

CRAN release: 2016-10-06

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 0.9.4

CRAN release: 2016-06-29

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

BUG FIXES

rgbif 0.9.3

CRAN release: 2016-03-29

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 retrieved, 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

rgbif 0.9.2

CRAN release: 2016-02-02

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

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 0.9.0

CRAN release: 2015-11-25

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

rgbif 0.8.9

CRAN release: 2015-10-07

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

CRAN release: 2015-07-24

MINOR IMPROVEMENTS

BUG FIXES

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

rgbif 0.8.6

CRAN release: 2015-07-03

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

CRAN release: 2015-06-08

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)

rgbif 0.8.0

CRAN release: 2015-03-09

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)

rgbif 0.7.7

CRAN release: 2014-11-07

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 !

rgbif 0.7.0

CRAN release: 2014-07-31

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)
  • 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)
  • 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.

rgbif 0.6.3

IMPROVEMENTS

  • Added functions gbif_bbox2wkt() and gbif_wkt2bbox() to convert a bounding box to wkt and a wkt object to a bounding box, respectively. Copied from the spocc package. Prefixes to fxn names will avoid conflicts.
  • Now spitting out more informative error messages when WKT strings passed in are not properly formed, either from rgeos::readWKT or from the returned response from GBIF.

rgbif 0.6.2

CRAN release: 2014-04-24

BUG FIXES

  • gbifmap() was throwing an error because it was looking for two variables latitude and longitude, which had been changed to decimalLatitude and decimalLongitude, respectively, in other functions in this package. Fixed. (#81)
  • occ_get() was updated to include changes in the GBIF API for this endpoint. The fix included fixing the parser for verbatim results, see rgbif::gbifparser_verbatim. (#83)
  • Fixed bugs in elevation() - it was expecting column names to be latitude and longitude, whereas inputs from other rgbif functions have changed to decimalLatitude and decimalLongitude.
  • Fixed bug in count_facet() introduced b/c GBIF no longer accepts hostCountry or nubKey parameters.

IMPROVEMENTS

rgbif 0.6.0

CRAN release: 2014-04-17

BUG FIXES

  • A number of variables changed names to better follow the Darwin Core standard. latitude is now decimalLatitude. longitude is now decimalLongitude. clazz is now class. Code in this package changed to accomodate these changes. date is now eventDate. georeferenced is now hasCoordinate. Beware of these changes in your own code using rgbif - find and replace for these should be easy.
  • Changed altitude parameter in occ_search() to elevation - should have been elevation the whole time.
  • occ_count() function with parameter changes: nubKey parameter in changed to taxonKey. New parameter protocol. Parameter catalogNumber gone. Parameter hostCountry gone. These parameters are still in the function definition, but if called they throw a useful warning telling you the correct parameter names. (#76)
  • Fixed bug in name_lookup() function that was labeling facet outputs incorrectly. (#77)

IMPROVEMENTS

  • Better checking and parsing of response data from GBIF: Across all functions, we now check that the response content type is application/json, then parse JSON ourselves using RJSONIO::fromJSON (instead of httr doing it).
  • Across all functions, we now return all potential character class columns as character class (instead of factor), by passing stringsAsFactors = FALSE to all data.frame() calls.
  • Now using assertthat package in various places to give better error messages when the wrong input is passed to a function.
  • Four parameters have name changes in the occ_search() function. These parameters are still in the function definition, but if called they throw a useful warning telling you the correct parameter names. (#75)
  • Updated docs in name_usage, name_backbone, name_lookup, and name_suggest functions.
  • sourceId parameter in name_usage() function doesn’t work so error message is thrown when used.

NEW FEATURES

  • New function check_wkt() to check that well known text string is the right format. (#68)
  • New dataset typestatus to look up possible specimen typeStatus values. See #74 for more information.
  • GBIF added some new parameters for use in the occ_search() function. scientificName: search for a species by name (instead of taxonKey). continent: search by continent. lastInterpreted: search by last time GBIF modified the record. recordNumber: search by the data collector’s specimen record number - this is different from the GBIF record number. typeStatus: search by specimen type status. (#74)
  • Note that given the new parameters many more options are available for implicit faceted search in which you can pass many values in a vector to do multiple searches like parameterName = c(x, y, z). These parameters are: taxonKey, scientificName, datasetKey, catalogNumber, collectorName, geometry, country, recordNumber, search, institutionCode, collectionCode, decimalLatitude, decimalLongitude, depth, year, typeStatus, lastInterpreted, and continent. This isn’t faceted search server side - this is just looping your different values of the parameter against the GBIF API.
  • Range queries are a new feature in the GBIF API. Some parameters in occ_search() now support range queries: decimalLatitude,decimalLongitude,depth,elevation,eventDate,lastInterpreted,month, and year. Do a range query for example by depth=50,100 to ask for occurrences where depth was recorded between 50 and 100 meters. Note that this syntax depth=c(50,100) will perform two separate searches, one for depth=50 and one for depth=100. (#71)

rgbif 0.5.0

CRAN release: 2014-02-16

IMPROVEMENTS

  • Changed name of country_codes() function to gbif_country_codes() to avoid conflicts with other packages.
  • Replaced sapply() with vapply() throughout the package as it is more robust and can be faster.
  • Added a startup message to the package.
  • gbifmap() now plots a map with ggplot2::coord_fixed(ratio=1) so that you don’t get wonky maps.
  • occ_count() now accepts a call to query publishingCountry with a single parameter (country), to list occurrence counts by publishing country.
  • occ_get() and occ_search() lose parameter minimal, and in its place gains parameter fields, in which you can request fields=‘minimal’ to get just name, taxon key, lat and long. Or set to ‘all’ to get all fields, or selection the fields you want by passing in a vector of field names.

BUG FIXES

  • Updated base url for the GIBF parser function parsenames()
  • isocodes dataset now with documentation.

NEW FEATURES

  • New function count_facet() to do facetted count search, as GBIF doesn’t allow faceted searches against the count API.
  • New function elevation() to get elevation data for a data.frame of lat/long points, or a list of lat/long points. This function uses the Google Elevation API (https://developers.google.com/maps/documentation/elevation/).
  • New function installations() to get metadata on installations.

rgbif 0.4.1

BUG FIXES

  • Improved handling of limit parameter in occ_search() so that the correct number of occurrences are returned.
  • Fixed various tests that were broken.

IMPROVEMENTS

  • Added missing limit argument in datasets() function man file, also function gains start and callopts parameters.

rgbif 0.4.0

CRAN release: 2013-11-20

IMPROVEMENTS

  • Data object isocodes gains new column gbif_names, the GBIF specific names for countries.
  • Added in deprecation messages throughout package for functions and arguments that are deprecated.
  • tests moved to tests/testthat from inst/tests.
  • Vignettes now in vignettes/ directory.

NEW FEATURES

  • New function dataset_suggest(), a quick autocomplete service that returns up to 20 datasets.
  • New function name_backbone() looks up names against the GBIF backbone taxonomy.
  • New function name_suggest(), a quick autocomplete service that returns up to 20 name usages.
  • New function occ_metadata() to search dataset metadata.
  • New function parsenames() that parses taxonomic names and returns their components.

rgbif 0.3.9

IMPROVEMENTS

  • Added back in functions, and .Rd files, from old version or rgbif that interacts with the old GBIF API.
  • Updated vignette to work with new GBIF API and fxns.

NEW FEATURES

  • Added functions to interact with the new GBIF API, notably: country_codes(), dataset_metrics(), dataset_search(), datasets(), name_lookup(), gbifmap(), gist(), name_lookup(), name_usage(), networks(), nodes(), occ_count(), occ_get(), occ_search(), organizations(), stylegeojson(), togeojson(). See the README for a crosswalk from old functions to new ones.

BUG FIXES

  • test files moved from inst/tests/ to tests/testthat/

rgbif 0.3.2

BUG FIXES

  • Removed georeferencedonly parameter - is deprecated in the GBIF API

rgbif 0.3.0

CRAN release: 2013-07-19

IMPROVEMENTS

  • Added S3 objects: Output from calls to occurrencelist() and occurrence list_many() now of class gbiflist, and output from calls to densitylist() now of class gbifdens.
  • Slight changes to gbifmaps() function.
  • url parameter in all functions moved into the function itself as the base GBIF API url doesn’t need to be specified by user.
  • Vignette added.

NEW FEATURES

  • Added function country_codes() to look up 2 character ISO country codes for use in searches.
  • Added function occurrencelist_many() to handle searches of many species.
  • Added functions togeojson() and stylegeosjon() to convert a data.frame with lat/long columns to geojson file format, and to add styling to data.frames before using togeojson() .
  • occurrencelist() and occurrencelist_many() gain argument fixnames, which lets user change species names in output data.frame according to a variety of scenarios.
  • taxonsearch() gains argument accepted_status to accept only those names that have a status of accepted. In addition, this function has significant changes, and examples, to improve performance.

rgbif 0.2.0

CRAN release: 2013-03-01

IMPROVEMENTS

  • Improved code style, and simplified code in some functions.

NEW FEATURES

  • occurrencelist() now handles scientific notation when maxresults are given in that form.
  • occurencelist() now can retrieve any number of records; was previously a max of 1000 records.

BUG FIXES

  • Demo “List” was returning incorrect taxon names - corrected now.
  • Removed unused parameter ‘latlongdf’ in occurencelist().

rgbif 0.1.5

CRAN release: 2012-12-04

IMPROVEMENTS

  • Changed all functions to use RCurl instead of httr as httr was presenting some problems.
  • Two function, capwords and gbifxmlToDataFrame, added with documentation as internal functions.

NEW FEATURES

  • Added function density_spplist to get a species list or data.frame of species and their counts for any degree cell.
  • Added function densitylist to access to records showing the density of occurrence records from the GBIF Network by one-degree cell.
  • Added function gbifmap to make a simple map to visualize GBIF data.
  • Added function occurrencecount to count taxon concept records matching a range of filters.

DEPRECATED

  • gbifdatause removed, was just a function to return the data sharing agreement from GBIF.

rgbif 0.1.0

NEW FEATURES

  • released to CRAN