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datecollected field flagged by ridigbio maintainers as inappropriate field–should be eventDate. See scrubr::fix_names() (#263)wellknown about to be archived. Replaced with s2 and wk.as.bison() is now defunct. BISON API is being sunsetted, BISON data now available via GBIF (#252)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 totalRecordsocc(): was using an old parameter query passed to rvertnet::searchbyterm() - changed to scientificname insteadif 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 failsource = "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)ala (#98)obis (#155)occ2df() more robust to varied inputs - allowing for users that may on purpose or not have a subset of the data source slots normally in the occdat class object (#171)rvertnet, a dependency dealing with data from Vertnet, was failing on certain searches. rvertnet was fixed and a new version on CRAN now. No changes here other than requiring the new version of rvertnet (#168)datetime to observed_on.is() to inherits(), and namespace all setNames() callsrgbif::occ_data() instead of rgbif::occ_search()rvertnet::searchbyterm() instead of rgbif::vertsearch()occ() now allows queries that only pass from and one of the data source opts params (e.g., gbifopts) - allows specifying any options passed down to the internal functions used to do data queries without having to use the other params in occ (#163)tibble for representing data.frames (#164)encoding="UTF-8" in httr::content() calls to parse raw data from web requests (#160)ridigbio as its on CRAN - was using internal fxns prior to this (#154)has_coords also fixed. (#161)data.table::setDF() instead of data.frame() to set a data.table style table to a data.framevertnet as an option to occ_options() to get the options for passing to vertopts in occ()print.occdatind() - which in last version introduced a bug in this print method - wasn’t fatal as only applied to empty slots in the output of a call to occ(), but nonetheless, not good (#159)data.table for fast list to data.frameas.vertnet() to coerce various inputs (e.g., result from occ(), occ2df(), or a key itself) to occurrence data objects (#142)occ() gains two parameters start and page to facilitate paging through results across data sources, instead of having to page individually for each data source. Some sources use the start parameter, while others use the page parameter. See Paging section in ?occ for details on Paging (#140)wkt_vis() now works with WKT polygons with multipe polygons, e.g., spocc::wkt_vis("POLYGON((-125 38.4, -121.8 38.4, -121.8 40.9, -125 40.9, -125 38.4), (-115 22.4, -111.8 22.4, -111.8 30.9, -115 30.9, -115 22.4))") (#147)print.occdatind() to print more helpful info when a geometry search is used as opposed to a taxonomy based search (#149)print.occdatind() to not fail when first element not present; proceeds to next slot with data (#143)occ() failed when multiple geometry elements passed in along with taxonomic names (#146)occ2df() for combining outputs to not fail when AntWeb doesn’t give back dates (#144) (#145) - thanks @timcdlucasocc2df() to not fail when date field missing (#141)spocc (#136) (#124)occ() function. Each data source is taken care of in a separate package or set of wrapper functions, and the man file now details what API parameters are being queried (#138)Datetime variable changed to datetimeoccurrenceID variable changed to occurrenceidspoccutils (#132)occ() gains new parameter has_coords - a global parameter (except for ebird and bison) to return only records with lat/long data. (#128)type (#134) and rank (#133) parameters dropped from occ()occ() is printed, we now include a message that total count of records found (not returned) is not completely known if ebird is included, because eBird does not include data on records found on their servers with requests to their API (#111)as.*() (e.g., as.gbif) for most data sources. These functions take in occurrence keys or sets of keys, and retrieve detailed occurrence record data for each key (#112)occ2df() now returns more fields. This function collapses all essential fields that are easy to get in all data sources: name, lat, long, prov, date, key. The key field is the occurrence key for each record, which you can use to keep track of individual records, get more data on the record, etc. (#103) (#108)inspect() - takes output from occ() or individual occurrence keys and gets detailed occurrence data.jsonlite, V8, utils, and methods. No longer importing: ggmap, maptools, rworldmap, sp, rgeos, RColorBrewer, rgdal, and leafletR. Pkgs removed mostly due to splitting off some functionality into spoccutils. related issues: (#131) (#132)methods, utils (#120)occ2df() (#106)wkt_vis() now only has an option to view a WKT shape in the browser.assertthat, plyr, data.table, and XML (#102)gistr now to post interactive geojson maps on GitHub gists (#100)rgbif now must be v0.7.7 or greater (the latest version on CRAN).occ2sp() removed. The function occ_to_sp() function is the working version. (#97)\donttest to \dontrun in examples as requested by CRAN maintainers (#99)occ_names() to search only for taxonomic names. The goal here is to use ths function if there is some question about what names you want to use to search for occurrences with. (#84). Suggested by @jarioksaocc_names_options() to quickly get parameter options to pass to occ_names().summary() method for the occdat S3 object that is output from occ() (#83)spocc (README, vignette, occ() documentation file, at package startup), we make it clear that there could be duplicate records returned in certain scenarios. And a new documentation page detailing what to watch out for: ?spocc_duplicates. (#77)latitude, decimalLatitude, Latitude, lat, and decimal_latitude. (#91)limit parameter in occ() (#78)limit to each functions options parameter, and it will work. Each data source can have a different parameter internally from limit, but now internally within spocc, we allow you to use limit so you don’t have to know what the data source specific parameter is. (#81)occ_options() gains new parameter where to print either in the console or to open man file in the IDE, or prints to console in command line R.occ() gains new parameter callopts to pass on curl debugging options to httr::GET() (#35)wkt_vis() now by default plots a well known text area (WKT) on an interactive mapbox map in your default browser. New parameter which allows you to choose the interactive map or a static ggplot2 map. (#70)occ() gains new class. In the previous version of this package, a data.frame was printed. Now the data is assigned the object occdatind (short for occdat individual).occ() now uses a print method for the occdatind class, adopted from dplyr that prints a brief data.frame, with columns wrapped to fit the width of your console, and additional columns not printed given at bottom with their class type. Note that the print behavior for the resulting object of an occ() call remains the same. (#69) (#74)whisker as a package import to use in the wkt_vis() function. (#70)mapggplot() accepted the output of occ(), of class occdat, while the other two functions for mapping, mapleaflet() and mapgist() accepted a data.frame. Now all three functions accept the output of occ(), an object of class occdat. (#75)meta slot in each returned object (indexed by object$meta) contains spots for returned and found, to designate number of records returned, and number of records found. (#64)name. (#71)occ().spocc depends on: rgbif. A number of input and output parameter names changed. A new version of rgbif was pushed to CRAN. (#56)clean_spocc() started (not finished yet) to attempt to clean data. For example, one use case is removing impossible lat/long values (i.e., longitue values greater than absolute 180). Another, not implemented yet, is to remove points that are not in the country or habitat your points are supposed to be in. (#44)fixnames() to trim species names with optional input parameters to make data easier to use for mapping.wkt_vis() to visualize a WKT (well-known text) area on a map. Uses ggmap to pull down a Google map so that the visualization has some geographic and natural earth context. We’ll soon introduce an interactive version of this function that will bring up a small Shiny app to draw a WKT area, then return those coordinates to your R session. (#34)These binaries (installable software) and packages are in development.
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