spocc v1.2.3

spocc 1.2.3

Documentation

• Documented argument ‘scientificname’ in 'obis_search()' changed to 'scientificName'.
• Documented argument 'n' in 'spocc_objects()' removed

DEFUNCT

• datecollected field flagged by ridigbio maintainers as inappropriate field--should be eventDate. See scrubr::fix_names() (#263)

spocc v1.2.1

DEFUNCT

• as.bison() is now defunct. BISON API is being sunsetted, BISON data now available
  via GBIF (#252)

Documentation

• Maintainer changed to Hannah L. Owens

spocc v1.2.0

DEFUNCT

• as.ecoengine() is now defunct. ecoengine R pkg wasn't used, we used internal code, but since ecoengine R is archived since Feb 2020, probably best to remove here (#239)

MINOR IMPROVEMENTS

• using wellknown now instead of wicket for Well-known text manipulation (#235)

BUG FIXES

• fix failing checks (#240)
• bug fixed in ecoengine bbox - but now ecoengine removed, see above (#234)

spocc v1.1.0

DEFUNCT

• fixnames() is now defunct. it was deprecated in a previous version. See scrubr::fix_names() (#231)

NEW FEATURES

• occ() can now handle sf objects passed to geometry. spocc itself does not import/suggest sf, but uses some code donated by Michael Sumner to pull out well known text (WKT) needed for spatially defined queries

MINOR IMPROVEMENTS

• refactor occ(): factor out functions already defined inside of occ, add assertions for user parameters (#228)
• package logo/sticker added (#188)

BUG FIXES

• Fix for ALA data source in occ(): total records found count was always 0 because ALA changed the records found field to totalRecords
• Fix for Vertnet data source in occ(): was using an old parameter query passed to rvertnet::searchbyterm() - changed to scientificname instead

spocc v1.0.8

BUG FIXES

• fix tests that are failing on cran checks (#225)
• fix ecoengine data option: an if statement was failing because we were trying to access an element of a list that is not there sometimes, leading to NULL which caused the if statement to fail

spocc v1.0.2

BUG FIXES

• preserve exact bytes for some tests that are failing on cran checks, taxize integration tests, and identifier based search tests (#221)

spocc v1.0.0

NEW FEATURES

• source = "inat" can now return photos. do a query as normal for inat data, and index to the photos slot in the data.frame, that will give a nested list of data.frames for each record with links/metadata for the photos (#214) (#217)

MINOR IMPROVEMENTS

• tests now using vcr (#209)
• add notes in section iNaturalist notes in the ?occ manual page for help with iNaturalist pagination and rate limiting (#215)
• vignette title fix for docs pages (#200)
• tibble::data_frame/tibble::as_data_frame replaced by tibble::tibble/tibble::as_tibble throughout package

DEPRECATED

• fixnames() is now deprecated; still useable here until the next version released; please move to using scrubr::fix_names (#196)

BUG FIXES

• fix inat data source for occ() queries: change from http to https for the inat base url (#213)
• inat fixes: use rbind fill approach for combining rows of data to fill missing columns safely; work with newer version of their API; unnest lat/lon results into tidy column in resulting data.frame (#215)
• OBIS API changed; changed internals for OBIS data in line with the new API; note that pagination for OBIS has changed (see ?occ for details); as.obis.numeric is gone and replaced with as.obis.character (#218)
• fix to fixnames(), coerce taxon name to character in case the name is factor class (#211)

spocc v0.9.0

NEW FEATURES

• occ() now attempts to collect errors from requests that fail and puts these error messages (character strings) in the $meta$errors spot. We can not always collect errors, and some data providers do not error well: they do not provide a meaningful error message other than that there was an error. (#189) (#207)
• occ() gains new parameter throw_warnings (logical). By default set to TRUE (matches previous behavior) and throws warnings about errors that occur and when no results found for a query. We now prefix each warning with the data provider so you can match up an error or warning with a data provider and (hopefully) query. If set to FALSE, warnings are suppressed (#189) (#207)

DEFUNCT

• AntWeb has been removed from spocc. The AntWeb API has been down for a while, and no response from maintainers (#202) (#203)

BUG FIXES

• fixes to ebird internals - a new version of rebird on CRAN requires a few changes in parameters used. Importantly, ebird now wants species codes instead of full scientific names, but we internally attempt to handle this, so users still just pass scientific names (#205)

DOCUMENTATION

• make pkgdown docs better: organize functions into meaningful sets (#193) (#197) (#199)
• in the ?spocc_duplicates manual file for duplicate records, refer to scrubr and CoordinateCleaner packages (#198)
• in inspect() manual file, clarify what the function does (#194)
• now we document better when we use one or the other function for BISON data source (#204)
• occ() gains a return block with detail about what's returned from the function (#208)

spocc v0.8.0

NEW FEATURES

• occ() gains new parameter date to do date range based searches across data sources without having to know the vagaries of each data source (#181)

BUG FIXES

• fix to idigbio geometry queries (#180)
• fix print.occdatind so that empty data.frame's don't throw tibble warnings (#184)
• fix to internal method for standardizing dates stand_dates() due to ALA giving back a timestamp now (#182) (#185)
• vertnet fixes (#179)
• fix to geometry bounding box queries (#187) thanks @timcdlucas
• fix to output of list names for gbif data source when using taxonomic IDs, was resulting in booleans, should be the taxonomic IDs (#191)

spocc v0.7.0

NEW FEATURES

• Removed javascript and V8 package import and using
  wicket C++ based package instead. So you no longer need V8
  which should make installation easier on some platforms. (#172)

MINOR IMPROVEMENTS

• httr replaced with crul for HTTP reqeusts (#174)
• Moved to using markdown for docs. The only thing you should
  notice that's different now is doing curl options is slightly
  different - it's just curl::curl_options() (#176)
• All as.*() functions can now pass on curl options to the
  http client (#177)
• Bumped minimum versions for a number of dependencies

BUG FIXES

• Fix to foo_ala() - the internal plugin for occ() that
  handles ALA queries: changed query from full text query using
  q=foo bar to q=taxon_name="foo bar" - in addition, improved
  error handling as sometimes occurrences slot is returned in
  results but is empty, whereas before it seemd to always be
  absent if no results (#178)