NEWS.md

In spocc: Interface to Species Occurrence Data Sources

spocc 1.2.2

DEFUNCT

• Package wellknown about to be archived. Replaced with s2 and wk.

spocc 1.2.1

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 1.2.0

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 1.1.0

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 1.0.8

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 1.0.2

BUG FIXES

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

spocc 1.0.0

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 0.9.0

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 0.8.0

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 0.7.0

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)

spocc 0.6.0

NEW FEATURES

• Added a new data source: Atlas of Living Australia (ALA), under the abbreviation ala (#98)
• Added a new data source: Ocean Biogeographic Information System (OBIS), under the abbreviation obis (#155)

MINOR IMPROVEMENTS

• Added note to docs and minor tweak to internal methods to account for max results from iDigBio of 100,000. Now when you request more than 100K, you should get a warning saying as much (#169)

BUG FIXES

• Made 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)

spocc 0.5.4

MINOR IMPROVEMENTS

• 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)
• Fix to internal INAT parsers to handle JSON data output instead of CSV output. And fix to internal date parsing; INAT changed field for date from datetime to observed_on.
• Move all is() to inherits(), and namespace all setNames() calls
• We are now using rgbif::occ_data() instead of rgbif::occ_search()
• We are now using rvertnet::searchbyterm() instead of rgbif::vertsearch()

BUG FIXES

• Fixes to iDigBio internal plugin - we were dropping scientificname if geometry was passed by the user. Fixed now. (#167)
• Fixed bug in GBIF internal plugin - when more than 1 result given back (e.g., multiple searches were done, resulting in a list of objects) we weren't parsing the output correctly. Fixed now. (#166)

spocc 0.5.0

NEW FEATURES

• 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)

MINOR IMPROVEMENTS

• Now using tibble for representing data.frames (#164)
• Now using explicit encoding="UTF-8" in httr::content() calls to parse raw data from web requests (#160)
• Now using ridigbio as its on CRAN - was using internal fxns prior to this (#154)

BUG FIXES

• There was a problem in the ebird parser where it wasn't processing results from ebird with no data. A problem with has_coords also fixed. (#161)

spocc 0.4.5

MINOR IMPROVEMENTS

• Using data.table::setDF() instead of data.frame() to set a data.table style table to a data.frame
• Added many more tests to make it less likely errors will occur
• Added vertnet as an option to occ_options() to get the options for passing to vertopts in occ()

BUG FIXES

• Fix to 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)

spocc 0.4.4

MINOR IMPROVEMENTS

• New import data.table for fast list to data.frame

BUG FIXES

• Fix to ecoengine spatial search - internally we were not making the bounding box correctly - fixed now (#158)

spocc 0.4.0

NEW FEATURES

• New function as.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)

MINOR IMPROVEMENTS

• Added Code of Conduct

BUG FIXES

• 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)
• Fix to print.occdatind() to print more helpful info when a geometry search is used as opposed to a taxonomy based search (#149)
• Fix to print.occdatind() to not fail when first element not present; proceeds to next slot with data (#143)
• Fixed problem where occ() failed when multiple geometry elements passed in along with taxonomic names (#146)
• Fix to occ2df() for combining outputs to not fail when AntWeb doesn't give back dates (#144) (#145) - thanks @timcdlucas
• Fix to occ2df() to not fail when date field missing (#141)

spocc 0.3.2

NEW FEATURES

• Added iDigBio as a new data source in spocc (#136) (#124)

MINOR IMPROVEMENTS

• Added much more detail on what parameters in child packages are being used inside of the 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)

BUG FIXES

• Fixed bug where when latitude/longitude columns missing, caused problems downstream in printing outputs, etc. Now we put in NA's when those columns missing (#139)
• Fixed bug in inat data source - Datetime variable changed to datetime
• Fixed bug in vertnet data source - occurrenceID variable changed to occurrenceid

spocc 0.3.0

NEW FEATURES

• Mapping functions all gone, and put into a new package spoccutils (#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()
• When object returned by 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)
• New functions 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)
• New data source: VertNet (#110)
• 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)
• New function inspect() - takes output from occ() or individual occurrence keys and gets detailed occurrence data.

MINOR IMPROVEMENTS

• Now importing packages: 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)
• Now importing explicitly all non-base R functions that we use: now importing methods, utils (#120)
• We now attempt to standardize dates across all data sources, and return that in the output of a call to occ2df() (#106)
• wkt_vis() now only has an option to view a WKT shape in the browser.

BUG FIXES

• Fixes to being able to pass curl options on to each data source's functions (#107)

spocc 0.2.4

MINOR IMPROVEMENTS

• Improved documentation for bounding boxes, their expected format, etc. (#96)
• Remove dependency on the following packages: assertthat, plyr, data.table, and XML (#102)
• Using package 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).
• Removed the startup message.

BUG FIXES

• Duplicate, but not working correctly, function occ2sp() removed. The function occ_to_sp() function is the working version. (#97)
• Fixed bug where some records returned form GBIF did not have lat/long column headers, and we internally rearranged columns, which caused complete stop when that happened. Fixed now. (#101)
• Changed all \donttest to \dontrun in examples as requested by CRAN maintainers (#99)

spocc 0.2.2

NEW FEATURES

• Added new function 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 @jarioksa
• New function occ_names_options() to quickly get parameter options to pass to occ_names().
• New summary() method for the occdat S3 object that is output from occ() (#83)
• In many places in 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)

MINOR IMPROVEMENTS

• All latitude/longitude column headers are now changed to latitude and longitude, whereas they use to vary from latitude, decimalLatitude, Latitude, lat, and decimal_latitude. (#91)
• Default is 500 now for the limit parameter in occ() (#78)
• You can now pass in 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)
• There is a now a startup message to give information on the package (#79)
• 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.

spocc 0.2.0

NEW FEATURES

• 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)
• Individual data sources 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)

MINOR IMPROVEMENTS

• Added whisker as a package import to use in the wkt_vis() function. (#70)
• Mapping functions now all accept the same input. Previously 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)
• The 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)

BUG FIXES

• Fixed bug in AntWeb output, where there was supposed to be a column titled name. (#71)

spocc 0.1.4

NEW FEATURES

• Can now do geometry only queries. See examples in occ().
• In addition, you can pass in sp objects of SpatialPolygons or SpatialPolygonsDataFrame classes.

spocc 0.1.2

NEW FEATURES

• There were quite a few changes in one of the key packages that spocc depends on: rgbif. A number of input and output parameter names changed. A new version of rgbif was pushed to CRAN. (#56)
• New function 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)
• New function fixnames() to trim species names with optional input parameters to make data easier to use for mapping.
• New function 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)

MINOR IMPROVEMENTS

• Added a CONTRIBUTING.md file to the github repo to help guide contributions (#61)
• Packages that require a certain version are forced to be X version or greater. Thes are rinat (>= 0.1.1), rbison (>= 0.3.2), rgbif (>= 0.6.2), ecoengine (>= 1.3), rebird (>= 0.1.1), AntWeb (>= 0.6.1), and leafletR (>= 0.2-0). This should help avoid problems.
• General improvement to function documentation.

spocc 0.1.0

• Initial release to CRAN

spocc documentation built on March 31, 2023, 9:59 p.m.