- Documented argument ‘scientificname’ in 'obis_search()' changed to 'scientificName'.
- Documented argument 'n' in 'spocc_objects()' removed
datecollectedfield flagged byridigbiomaintainers as inappropriate field--should beeventDate. Seescrubr::fix_names()(#263)
- Package
wellknownabout to be archived. Replaced withs2andwk.
as.bison()is now defunct. BISON API is being sunsetted, BISON data now available via GBIF (#252)
- Maintainer changed to Hannah L. Owens
as.ecoengine()is now defunct.ecoengineR pkg wasn't used, we used internal code, but sinceecoengineR is archived since Feb 2020, probably best to remove here (#239)
- using
wellknownnow instead ofwicketfor Well-known text manipulation (#235)
- fix failing checks (#240)
- bug fixed in ecoengine bbox - but now ecoengine removed, see above (#234)
fixnames()is now defunct. it was deprecated in a previous version. Seescrubr::fix_names()(#231)
occ()can now handle sf objects passed togeometry.spoccitself 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
- refactor
occ(): factor out functions already defined inside ofocc, add assertions for user parameters (#228) - package logo/sticker added (#188)
- Fix for ALA data source in
occ(): total records found count was always 0 because ALA changed the records found field tototalRecords - Fix for Vertnet data source in
occ(): was using an old parameterquerypassed torvertnet::searchbyterm()- changed toscientificnameinstead
- fix tests that are failing on cran checks (#225)
- fix ecoengine data option: an
ifstatement was failing because we were trying to access an element of a list that is not there sometimes, leading toNULLwhich caused theifstatement to fail
- preserve exact bytes for some tests that are failing on cran checks, taxize integration tests, and identifier based search tests (#221)
source = "inat"can now return photos. do a query as normal for inat data, and index to thephotosslot in the data.frame, that will give a nested list of data.frames for each record with links/metadata for the photos (#214) (#217)
- tests now using vcr (#209)
- add notes in section
iNaturalist notesin the?occmanual page for help with iNaturalist pagination and rate limiting (#215) - vignette title fix for docs pages (#200)
tibble::data_frame/tibble::as_data_framereplaced bytibble::tibble/tibble::as_tibblethroughout package
fixnames()is now deprecated; still useable here until the next version released; please move to usingscrubr::fix_names(#196)
- 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
?occfor details);as.obis.numericis gone and replaced withas.obis.character(#218) - fix to
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$meta$errorsspot. 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 parameterthrow_warnings(logical). By default set toTRUE(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 toFALSE, warnings are suppressed (#189) (#207)
- AntWeb has been removed from
spocc. The AntWeb API has been down for a while, and no response from maintainers (#202) (#203)
- fixes to ebird internals - a new version of
rebirdon 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)
- make pkgdown docs better: organize functions into meaningful sets (#193) (#197) (#199)
- in the
?spocc_duplicatesmanual file for duplicate records, refer toscrubrandCoordinateCleanerpackages (#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 areturnblock with detail about what's returned from the function (#208)
occ()gains new parameterdateto do date range based searches across data sources without having to know the vagaries of each data source (#181)
- fix to idigbio geometry queries (#180)
- fix
print.occdatindso 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)
- Removed javascript and V8 package import and using
wicketC++ based package instead. So you no longer need V8 which should make installation easier on some platforms. (#172)
httrreplaced withcrulfor 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
- Fix to
foo_ala()- the internal plugin forocc()that handles ALA queries: changed query from full text query usingq=foo bartoq=taxon_name="foo bar"- in addition, improved error handling as sometimesoccurrencesslot is returned in results but is empty, whereas before it seemd to always be absent if no results (#178)
- 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)
- 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)
- 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 theoccdatclass object (#171)
rvertnet, a dependency dealing with data from Vertnet, was failing on certain searches.rvertnetwas fixed and a new version on CRAN now. No changes here other than requiring the new version ofrvertnet(#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
datetimetoobserved_on. - Move all
is()toinherits(), and namespace allsetNames()calls - We are now using
rgbif::occ_data()instead ofrgbif::occ_search() - We are now using
rvertnet::searchbyterm()instead ofrgbif::vertsearch()
- 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)
occ()now allows queries that only passfromand 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 inocc(#163)
- Now using
tibblefor representing data.frames (#164) - Now using explicit
encoding="UTF-8"inhttr::content()calls to parse raw data from web requests (#160) - Now using
ridigbioas its on CRAN - was using internal fxns prior to this (#154)
- There was a problem in the ebird parser where it wasn't processing
results from ebird with no data. A problem with
has_coordsalso fixed. (#161)
- Using
data.table::setDF()instead ofdata.frame()to set adata.tablestyle table to adata.frame - Added many more tests to make it less likely errors will occur
- Added
vertnetas an option toocc_options()to get the options for passing tovertoptsinocc()
- 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 toocc(), but nonetheless, not good (#159)
- New import
data.tablefor fast list to data.frame
- Fix to ecoengine spatial search - internally we were not making the bounding box correctly - fixed now (#158)
- New function
as.vertnet()to coerce various inputs (e.g., result fromocc(),occ2df(), or a key itself) to occurrence data objects (#142) occ()gains two parametersstartandpageto facilitate paging through results across data sources, instead of having to page individually for each data source. Some sources use thestartparameter, while others use thepageparameter. See Paging section in?occfor details on Paging (#140)
- Added Code of Conduct
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 multiplegeometryelements 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)
- Added iDigBio as a new data source in
spocc(#136) (#124)
- 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)
- 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 -
Datetimevariable changed todatetime - Fixed bug in vertnet data source -
occurrenceIDvariable changed tooccurrenceid
- Mapping functions all gone, and put into a new package
spoccutils(#132) occ()gains new parameterhas_coords- a global parameter (except for ebird and bison) to return only records with lat/long data. (#128)type(#134) andrank(#133) parameters dropped fromocc()- 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. Thekeyfield 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 fromocc()or individual occurrence keys and gets detailed occurrence data.
- Now importing packages:
jsonlite,V8,utils, andmethods. No longer importing:ggmap,maptools,rworldmap,sp,rgeos,RColorBrewer,rgdal, andleafletR. Pkgs removed mostly due to splitting off some functionality intospoccutils. 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.
- Fixes to being able to pass curl options on to each data source's functions (#107)
- Improved documentation for bounding boxes, their expected format, etc. (#96)
- Remove dependency on the following packages:
assertthat,plyr,data.table, andXML(#102) - Using package
gistrnow to post interactive geojson maps on GitHub gists (#100) rgbifnow must bev0.7.7or greater (the latest version on CRAN).- Removed the startup message.
- Duplicate, but not working correctly, function
occ2sp()removed. The functionocc_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
\donttestto\dontrunin examples as requested by CRAN maintainers (#99)
- 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 toocc_names(). - New
summary()method for theoccdatS3object that is output fromocc()(#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)
- All latitude/longitude column headers are now changed to latitude and longitude, whereas they use to vary from
latitude,decimalLatitude,Latitude,lat, anddecimal_latitude. (#91) - Default is 500 now for the
limitparameter inocc()(#78) - You can now pass in
limitto each functions options parameter, and it will work. Each data source can have a different parameter internally fromlimit, but now internally withinspocc, we allow you to uselimitso 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 parameterwhereto print either in the console or to open man file in the IDE, or prints to console in command line R.
occ()gains new parametercalloptsto pass on curl debugging options tohttr::GET()(#35)wkt_vis()now by default plots a well known text area (WKT) on an interactive mapbox map in your default browser. New parameterwhichallows 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, adata.framewas printed. Now the data is assigned the objectoccdatind(short for occdat individual). occ()now uses a print method for theoccdatindclass, adopted fromdplyrthat prints a briefdata.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 anocc()call remains the same. (#69) (#74)
- Added
whiskeras a package import to use in thewkt_vis()function. (#70) - Mapping functions now all accept the same input. Previously
mapggplot()accepted the output ofocc(), of classoccdat, while the other two functions for mapping,mapleaflet()andmapgist()accepted adata.frame. Now all three functions accept the output ofocc(), an object of classoccdat. (#75) - The
metaslot in each returned object (indexed byobject$meta) contains spots forreturnedandfound, to designate number of records returned, and number of records found. (#64)
- Fixed bug in AntWeb output, where there was supposed to be a column titled
name. (#71)
- Can now do geometry only queries. See examples in
occ(). - In addition, you can pass in sp objects of SpatialPolygons or SpatialPolygonsDataFrame classes.
- There were quite a few changes in one of the key packages that
spoccdepends on:rgbif. A number of input and output parameter names changed. A new version ofrgbifwas 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. Usesggmapto 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)
- 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.
- Initial release to CRAN