v0.6.2

rgbif 0.6.2

BUG FIXES

• gbifmap() was throwing an error because it was looking for two variables latitude and longitude, which had been changed to decimalLatitude and decimalLongitude, respectively, in other functions in this package. Fixed. (#81)
• occ_get() was updated to include changes in the GBIF API for this endpoint. The fix included fixing the parser for verbatim results, see rgbif::gbifparser_verbatim. (#83)
• Fixed bugs in elevation() - it was expecting column names to be latitude and longitude, whereas inputs from other rgbif functions have changed to decimalLatitude and decimalLongitude.
• Fixed bug in count_facet() introduced b/c GBIF no longer accepts hostCountry or nubKey parameters.

IMPROVEMENTS

• gist(), stylegeojson(), and togeojson() functions now listed as deprecated. Their functionality moved to the spocc package (http://cran.r-project.org/web/packages/spocc/index.html). These functions will be removed from this package in a future version. (#82)
• Added a quick sanity test for gbifmap().
• Added tests for occ_get() for when verbatim=TRUE, which gives back different data than when verbatim=FALSE.

Files:

• rgbif_0.6.2.tar.gz (source)
• rgbif_0.6.2.zip (windows binary)
• rgbif_0.6.2.tgz (osx binary)

v0.6.0

rgbif 0.6.0

BUG FIXES

• A number of variables changed names to better follow the Darwin Core standard. latitude is now decimalLatitude. longitude is now decimalLongitude. clazz is now class. Code in this package changed to accomodate these changes. date is now eventDate. georeferenced is now hasCoordinate. Beware of these changes in your own code using rgbif - find and replace for these should be easy.
• Changed altitude parameter in occ_search() to elevation - should have been elevation the whole time.
• occ_count() function with parameter changes: nubKey parameter in changed to taxonKey. New parameter protocol. Parameter catalogNumber gone. Parameter hostCountry gone. These parameters are still in the function definition, but if called they throw a useful warning telling you the correct parameter names. (#76)
• Fixed bug in name_lookup() function that was labeling facet outputs incorrectly. (#77)

IMPROVEMENTS

• Better checking and parsing of response data from GBIF: Across all functions, we now check that the response content type is application/json, then parse JSON ourselves using RJSONIO::fromJSON (instead of httr doing it).
• Across all functions, we now return all potenital character class columns as character class (instead of factor), by passing stringsAsFactors = FALSE to all data.frame() calls.
• Now using assertthat package in various places to give better error messages when the wrong input is passed to a function.
• Four parameters have name changes in the occ_search() function. These parameters are still in the function definition, but if called they throw a useful warning telling you the correct parameter names. (#75)
• Updated docs in name_usage, name_backbone, name_lookup, and name_suggest functions.
• sourceId parameter in name_usage() function doesn't work so error message is thrown when used.

NEW FEATURES

• New function check_wkt() to check that well known text string is the right format. (#68)
• New dataset typestatus to look up possible specimen typeStatus values. See #74 for more information.
• GBIF added some new parameters for use in the occ_search() function. scientificName: search for a species by name (instead of taxonKey). continent: search by continent. lastInterpreted: search by last time GBIF modified the record. recordNumber: search by the data collector's specimen record number - this is different from the GBIF record number. typeStatus: search by specimen type status. (#74)
• Note that given the new parameters many more options are available for implicit faceted search in which you can pass many values in a vector to do multiple searches like parameterName = c(x, y, z). These parameters are: taxonKey, scientificName, datasetKey, catalogNumber, collectorName, geometry, country, recordNumber, search, institutionCode, collectionCode, decimalLatitude, decimalLongitude, depth, year, typeStatus, lastInterpreted, and continent. This isn't faceted search server side - this is just looping your different values of the parameter against the GBIF API.
• Range queries are a new feature in the GBIF API. Some parameters in occ_search() now support range queries: decimalLatitude,decimalLongitude,depth,elevation,eventDate,lastInterpreted,month, and year. Do a range query for example by depth=50,100 to ask for occurrences where depth was recorded between 50 and 100 meters. Note that this syntax depth=c(50,100) will perform two separate searches, one for depth=50 and one for depth=100. (#71)

v0.5.0

All changes since v0.3

rgbif 0.5.0

IMPROVEMENTS

• Changed name of country_codes() function to gbif_country_codes() to avoid conflicts with other packages.
• Replaced sapply() with vapply() throughout the package as it is more robust and can be faster.
• Added a startup message to the package.
• gbifmap() now plots a map with ggplot2::coord_fixed(ratio=1) so that you don't get wonky maps.
• occ_count() now accepts a call to query publishingCountry with a single parameter (country), to list occurrence counts by publishing country.
• occ_get() and occ_search() lose parameter minimal, and in its place gains parameter fields, in which you can request fields='minimal' to get just name, taxon key, lat and long. Or set to 'all' to get all fields, or selection the fields you want by passing in a vector of field names.

BUG FIXES

• Updated base url for the GIBF parser function parsenames()
• isocodes dataset now with documentation.

NEW FEATURES

• New function count_facet() to do facetted count search, as GBIF doesn't allow faceted searches against the count API.
• New function elevation() to get elevation data for a data.frame of lat/long points, or a list of lat/long points. This function uses the Google Elevation API (https://developers.google.com/maps/documentation/elevation/).
• New function installations() to get metadata on installations.

rgbif 0.4.1

BUG FIXES

• Improved handling of limit parameter in occ_search() so that the correct number of occurrences are returned.
• Fixed various tests that were broken.

IMPROVEMENTS

• Added missing limit argument in datasets() function man file, also function gains start and callopts parameters.

v0.4.0

All changes since v0.3.0

rgbif 0.4.0

IMPROVEMENTS

• Data object isocodes gains new column gbif_names, the GBIF specific names for countries.
• Added in deprecation messages throughtout package for functions and arguments that are deprecated.
• tests moved to tests/testthat from inst/tests.
• Vignettes now in vignettes/ directory.

NEW FEATURES

• New function dataset_suggest(), a quick autocomplete service that returns up to 20 datasets.
• New function name_backbone() looks up names against the GBIF backbone taxonomy.
• New function name_suggest(), a quick autocomplete service that returns up to 20 name usages.
• New function occ_metadata() to search dataset metadata.
• New function parsenames() that parses taxonomic names and returns their components.

rgbif 0.3.9

IMPROVEMENTS

• Added back in functions, and .Rd files, from old version or rgbif that interacts with the old GBIF API.
• Updated vignette to work with new GBIF API and fxns.

NEW FEATURES

• Added functions to interact with the new GBIF API, notably: country_codes(), dataset_metrics(), dataset_search(), datasets(), name_lookup(), gbifmap(), gist(), name_lookup(), name_usage(), networks(), nodes(), occ_count(), occ_get(), occ_search(), organizations(), stylegeojson(), togeojson(). See the README for a crosswalk from old functions to new ones.

BUG FIXES

• test files moved from inst/tests/ to tests/testthat/

rgbif 0.3.2

BUG FIXES

• Removed georeferencedonly parameter - is deprecated in the GBIF API