rgbif v3.7.1

BUG FIXES

• name_backbone_checklist() : bug fixes (#501) (#505)

rgbif v3.7.0

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

• gbif_citation.gbif() : it is no longer considered best practice to generate a citation from occ_search() or occ_data(). We recommend occ_download() or derived_dataset() instead. (#494)

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", "verabtim_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:

• Citing GBIF Mediated Data
• Set Up Your GBIF Username and Password
• Getting Occurrence Data From GBIF
• Downloading A Long Species List
• Working With Taxonomic Names

BUG FIXES

• occ_download_import() : fixed bug related to select argument. (#479)
• map_fetch() : fixed bug related to sp::CRS (#497)

rgbif v3.6.0

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 v3.5.2

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 v3.5.0

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 v3.4.2

MINOR IMPROVEMENTS

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

BUG FIXES

• fix bug in occ_search() (#443)

rgbif v3.4.0

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 v3.3.0

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 v3.2.0

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

• fix for occ_download_get(): response content-type header changed recently, fixed (#422)

rgbif v3.1.0

MINOR IMPROVEMENTS

• finally delete code originally extracted from plyr::rbind.fill - use data.table::rbindlist in all cases (#417)
• fix failing test on cran for dataset_search() (#418)
• fix xd refs note on cran (non-file package anchored links) for curl pkg function (#419)

BUG FIXES

• occ_download_cancel_staged() fix: was broken cause we were indexing to a column in a table with [,"key"] (#416)