Species occurrence data toolkit for R
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)wellknown now instead of wicket for Well-known text manipulation (#235)fixnames() is now defunct. it was deprecated in a previous version. See scrubr::fix_names() (#231)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 queriesocc(): factor out functions already defined inside of occ, add assertions for user parameters (#228)occ(): total records found count was always 0 because ALA changed the records found field to totalRecords
occ(): was using an old parameter query passed to rvertnet::searchbyterm() - changed to scientificname insteadsource = "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)iNaturalist notes in the ?occ manual page for help with iNaturalist pagination and rate limiting (#215)tibble::data_frame/tibble::as_data_frame replaced by tibble::tibble/tibble::as_tibble throughout packagefixnames() is now deprecated; still useable here until the next version released; please move to using scrubr::fix_names (#196)occ() queries: change from http to https for the inat base url (#213)?occ for details); as.obis.numeric is gone and replaced with as.obis.character (#218)fixnames(), coerce taxon name to character in case the name is factor class (#211)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)spocc. The AntWeb API has been down for a while, and no response from maintainers (#202) (#203)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)?spocc_duplicates manual file for duplicate records, refer to scrubr and CoordinateCleaner packages (#198)inspect() manual file, clarify what the function does (#194)occ() gains a return block with detail about what's returned from the function (#208)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)print.occdatind so that empty data.frame's don't throw tibble warnings (#184)stand_dates() due to ALA giving back a timestamp now (#182) (#185)wicket C++ based package instead. So you no longer need V8
which should make installation easier on some platforms. (#172)httr replaced with crul for HTTP reqeusts (#174)curl::curl_options() (#176)as.*() functions can now pass on curl options to the
http client (#177)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)