occ_download_sql() for downloading
occurrence data using SQL queries. (#752)occ_download_cached() bug fixed. (#748)occ_search() terms. (#698)occ_download_describe() for getting
information about download formats. (#721)constituentKey to name_lookup().
(#729)gbifId downloads (#711)check_inputs()bug fixed. (#706)gbif_citation() datasetKey methods no longer supported
(#716)occ_data() is no longer supported.
(#718)occ_data() is soft deprecated and supported for legacy
reasons only, and will no longer add new features.There have been many additions for accessing dataset metadata.
dataset_export() downloads all of the results of a
dataset_search().
New functions for getting dataset metadata from a datasetkey
(uuid) : dataset_get(), dataset_process(),
dataset_networks(), dataset_constituents(),
dataset_comment(), dataset_contact(),
dataset_endpoint(), dataset_identifier(),
dataset_machinetag(), dataset_tag(),
dataset_metrics().
New function for getting more obscure dataset metadata, such as
machineTags: dataset().
New functions for listing dataset metadata :
dataset_noendpoint(),
dataset_duplicate().
dataset_doi() gets dataset metadata from the
dataset’s doi.
occ_count(). (#686)There are no longer static data files in rgbif. This data is better fetched fresh from the appropriate endpoints. (#690) (#688)
datasets() is soft deprecated, since the interface
was overloaded and confusing. See functional replacements
above.
map_fetch() now returns a base map as a
magick::magick-image. This allows for the creation of high
quality images from the GBIF maps API. (#675)occ_download() terms added to key lookup. (#661)
(#589)pred_default() is an occ_download() pred
function that allows users to easily filter out commonly unwanted
occurrence records. (#611)Stream error fixed (“HTTP/2 stream 15 was not closed cleanly
before end of the underlying stream”). Now map_fetch(),
occ_data(), occ_search(), and
occ_download_wait() have
curlopts = list(http_version=2), which fixes the error.
This might need to be the default setting for the whole package.
(#656)
name_suggest() now gives a warning at prevents
setting the limit > 100, since this is the GBIF API max.
(#657)
New article Creating
maps from occurrences, which explains how to use
map_fetch().
occ_issues() is now deprecated, since it is difficult
to maintain, and not widely used. (#651)occ_count() parameter type is now
deprecated and will no longer work correctly. Please see
occ_count_country(), occ_count_pub_country(),
occ_count_year(), occ_count_basis_of_record()
for replacements. (#622)occ_count() parameters georeferenced,
type, date, to, from
are no longer supported and not guaranteed to work correctly.
(#622)occ_facet() and count_facet() are now
deprecated use occ_count(facet="x") instead.lit_search() now supports searching the GBIF literature
API. (#591)occ_count() now supports almost all
occ_search() queries. (#622)occ_count() now supports the facets interface through
occ_count(facet="x"). (#622)organizations() (aka publishers) now supports the use
of getting lists of publishers by country. (#606)occ_download() and occ_search() now
support downloading and getting occurrences a certain distance from
known country/area centroids via the parameter
distanceFromCentroidInMeters. (#594)occ_search() now supports more multi-valued parameters.
(#617)randgeo and
conditionz. (#624) (#625)New article explaining occ_count() changes and new
features Getting
Occurrence Counts From GBIF.
name_backbone_checklist() now accepts
strict=TRUE, meaning that only non-fuzzy matches are
returned. (#565)name_backbone_checklist() now accepts default values
for high taxonomy, such as kingdom, phylum, family, ect. (#515)name_backbone_checklist() now returns a column
is_alternative when verbose=TRUE, which lets
the user know if a name was originally considered to be an alternative
choice by the name matcher. (#515)sp and rgeos dependencies.
(#578)name_usage now has the ability to fetch iucn red list
categories using data=iucnRedListCategory. (#547)name_backbone_checklist updated definition of
verbose argument. (#564)dataset_gridded bug fixed when inputting only one
non-gridded dataset. (#546)occ_data() and
occ_search() (#530)occ_download() terms to key lookup
(#541)dataset_gridded() (#516)network_constituents() (#527)gbif_geocode() (#521)networks() is deprecated and called
network() instead. (#527)parsenames() is deprecated and called
name_parse() for better alignment with other
name_* functions. (#504)occ_search fixed bug related to networkKey in the
column names (#524)wellknown dependency and switching to
wk (#512)name_backbone_checklist() : bug fix related two square
brackets in url (#509)name_backbone_checklist() : bug fixes (#501)
(#505)There is a new rgbif maintainer: John Waller.
derived_dataset() : New function to register a cleaned
or modified dataset on GBIF for citation. (#467)name_backbone_checklist() : New function that takes a
list, vector, or data.frame of scientific names and asynchronously
matches them to the backbone. (#475)pred_isnull() : New predicate function that includes
NULL values from a column in the download. (#489)occ_download.print() : Now prints out much more
information including a DOI and citation. (#494)gbif_citation.gbif() : it is no longer considered best
practice to generate a citation from occ_search() or
occ_data(). We recommend occ_download() or
derived_dataset() instead. (#494)occ_download_wait() and
occ_download_meta() : now accept a class character download
key directly. The keys does do not need to be class “occ_download”.
(#487)name_backbone() : now returns new columns
“verbatim_name”, “verbatim_genus” ect. that the user has supplied. This
makes it easier for the user to track what has been matched. The verbose
argument also has been un-retired. If verbose=TRUE, more
results will be returned in a single data.frame. (#475)gbif_citation() : will now accept a download key
directly.occ_download_get() : Does not throw an error if the
data is already present and overwrite=FALSE, it will just
give a warning and return the already present dataset. This allows users
to run occ_download_get(key) %>% occ_download_import()
multiple times without re-downloading the same file with
overwrite=TRUE.download_predicate_dsl() : “publishingOrg” now added as
a download key. (#496) key_lkup now includes GBIF-style
uppercase keys as well. So pred("TAXON_KEY",212) and
pred("taxonKey",212) will both work.Wrote new articles highlighting new features and encouraging the use
of occ_download() over occ_search().
New articles:
occ_download_import() : fixed bug related to select
argument. (#479)map_fetch() : fixed bug related to sp::CRS
(#497)mulitpoint
-> multipoint (#460) thanks @damianooldoni for catching thatstateProvince (#458),
gadm (#462), and occurrenceStatus (#465)FOOTPRINT_SRS_INVALID
and FOOTPRINT_WKT_INVALID (#454)occ_download_import() docs: more information on
data.table::fread parameters and particular ones that would
be useful to sort out data read issues (#461)occ_download_get(): downloaded files used to have a
certain content type in response header we checked for, but its changed
at least once even in successful responses, so that step has been
removed (#464)occ_download_import(): country code for Namibia is
NA - this was turning into the R missing value
NA - now fixed (#463)coordinateUncertaintyInMeters added, e.g. usage:
pred_lt("coordinateUncertaintyInMeters",10000) (#449)pred_and() and pred_or() slight change:
now required that more than one predicate is passed to each of these
functions because it doesn’t make sense to do an and or
or predicate with only one predicate (#452)pred_not(pred_notnull()) (#452)TAXON_MATCH_AGGREGATE) and
a new name issue (BACKBONE_MATCH_AGGREGATE) (#453)pred_not(): it was
not constructing the query correctly, fixed now. user facing change as
well: it now expects a predicate to be passed, and only a single
predicate as GBIF not predicate only accepts one predicate (#446)DIFFERENT_OWNER_INSTITUTION
(#444)occ_search() (#443)occ_search() and
occ_data() what parameters accept many values and which do
not; in addition, we clarify which parameters accept multiple values in
the same HTTP request, and those that accept multiple values but apply
each in separate HTTP requests. See also ?many-values
manual file (#369)gbif_issues() gains 9 new occurrence issues (#435)occ_search() and occ_data(),
basisOfRecord parameter now supports multiple values, both
in one request and in different requests, depending on input format (see
“Multiple values passed to a parameter” section in
?occ_search) (#437)occ_download_get(): GBIF slightly altered download
behavior - we now explicitly follow any redirects to get a download
(#439)print.occ_download_meta (used when you run
occ_download_meta()) was printing NA for
number of results found if no results were ready yet - now prints
0 instead of NA (#440)count_facet() fixes: fixed internal fxn for
count_facet for parsing results, was dropping values for
facets; added assertions to check parameter types input by user for the
fxn; changed so that keys and basisofrecord can be passed together
(#436)gbif_issues():
GEOREFERENCED_DATE_INVALID and
GEOREFERENCED_DATE_UNLIKELY (#430)occ_data() caused by GBIF adding a
new field of data to the output of /occurrence/search/:
gadm. cleaned up internals of occ_data() to drop gadm, and
other fields that are complex and take time to parse (use
occ_search() if you want all the data fields) (#427)gbif_names() fix: was ending up with invalid URLs to
GBIF species pages because we had taxon keys with leading spaces
somehow. now all leading and trailing spaces in taxon keys removed
before making URLs (#429)gbif_issues() changes: three new occurrence issues
added; one name issue removed that’s deprecated (#423)gbif_citation() rights field was empty unless pulling
from a downloaded file; now fill in with license key; also
a fix for when occurrence key passed to the function (#424)establishmentMeans now supported in
occ_download/pred (#420)occ_download_get(): response content-type
header changed recently, fixed (#422)plyr::rbind.fill - use data.table::rbindlist
in all cases (#417)dataset_search()
(#418)occ_download_cancel_staged() fix: was broken cause we
were indexing to a column in a table with [,"key"]
(#416)occ_search, occ_get,
name_usage, name_lookup,
name_suggest, name_backbone, and
dataset_search) have a return parameter to
toggle what is returned from the function call. To simplify rgbif
maintenance, we’ve deprecated the return parameter. We’ve
left it in each of the functions, but it no longer does anything, other
than raising a warning if used. This means that function calls to these
functions now always return the same data structure, making it easier to
reason about for the user, as well as for us developers trying to make
sure the package works as expected under a variety of conditions. If you
have been using the return parameter, do the same function
call as before, but now index to the output you need. This is a breaking
change, thus the major version bump (#413)occ_download_cached(), which takes the
same input as occ_download(), but instead of starting a
query, it checks if you’ve recently made the same request (with
configureable settings for what “recent” means). This can save time when
you’re doing occurrence download requests that you may have done in the
recent past (#308)api.gbif-uat.org and api.gbif.org. We have
only used the latter previously, but now can configure rgbif to use the
former, mostly for testing purposes (#398)occ_download_import() gains encoding
parameter that is passed down to data.table::fread to make
it very clear that encoding can be configured (even though you could
have before via ...) (#414)/occurrence/search route
is now 100,000 (used in occ_data() and
occ_search()). updated docs throughout accordingly
(#405)occ_download_queue() for how we
determine when a job is done. see new section “When is a job done?”
(#409)print.occ_download_prep and
print.occ_download improved. previously well-known text
strings were printed in their entirety. now they are handled to only
print so many characters; also applies to any download predicate string
that’s long (#407)occ_download_get() now supports using a progress bar by
passing in httr::progress() (#402)occ_data() and occ_search() gain two new
parameters: recordedByID and identifiedByID
(#403)occ_download_queue: an empty
occ_download_meta() lead to problems; now removing any
NULL’s from a list of occ_download_meta()
outputs before further work (#408)occ_download_queue: we were not accounting for
job status “cancelled” (#409)occ_download_import() fix: fill parameter
was set to TRUE by default, changed to FALSE.
improved docs for this fxn on passing down parameters to
data.table::fread (#404)?downloads manual file listing all the different download
status states a download can have and what they mean (#390)gbif_issues/gbif_issues_lookup: added
four missing occurrence issues to the package
(COORDINATE_PRECISION_INVALID, COORDINATE_UNCERTAINTY_METERS_INVALID,
INDIVIDUAL_COUNT_INVALID, and INTERPRETATION_ERROR) (#400)occ_download() via vcr
(#396)name_lookup(): we were attempting to rearrange
columns when no results found, leading to an error (#399)spellCheck parameter has been removed from the
occurrence routes; thus, the occ_spellcheck() function is
now defunct - and the parameter spellCheck has been removed
from occ_data() and occ_search() (#397)occ_data(): remove ...
parameter definition as it wasn’t used in the function (#394)occ_download()
has changed in a breaking fashion (thus the major version bump). After
installation, see ?download_predicate_dsl. Much more
complex queries are now possible with occ_download().
TL;DR: you now construct queries with functions like
pred("taxonKey", 3119195) rather than passing in strings
like taxonKey = 3119195, and
pred_gt("elevation", 5000) instead of
"elevation > 5000" (#362)occ_download_wait() to re-run
occ_download_meta() until the download is ready - kinda
like occ_download_queue() but for a single download
(#389)occ_download_dataset_activity() gains pagination
parameters limit and start to paginate through
results (#382)gbif_citation() now works with the output of
occ_data() in addition to the other existing inputs it
accepts (#392)occ_download() manual file (#387)gbif_citation() tests needed preserve body bytes for
vcr (#384)occ_count() and count_facet():
isGeoreferenced/georeferenced variable needed booleans converted to
lowercase before being sent to GBIF (#385) (#386)mvt_fetch() for fetching Map Vector
Tiles (MVT). mvt used to be an option in map_fetch(), but
we only returned raw bytes for that option. With
mvt_fetch() we now leverage the protolite
package, which parses MVT files, to give back an sf object (#373) thanks
to @jeroen for the
protolite work to make this workmap_fetch() loses the
format = ".mvt" option; and thus now only returns a
RasterLayerocc_issues() and name_issues() reworked.
Both now use the same underlying internal logic, with occ_issues pulling
metadata specfic to occurrence issues and name_issues pulling metadata
specific to name issues. name_issues used to only be a data.frame of
name issues, but can now be used similarly to occ_issues; you can pass
the output of name_usage() to name_issues to filter/parse
name results by their associated name issues. Associated with this, new
function gbif_issues_lookup can be used to lookup either
occurrence or name issues by their full name or code (#363) (#364)name_usage()
wasn’t working (#328) (#363) (#364)name_lookup() gains an additional parameters
issue for filtering name results by name issues (#335)
(#363) (#364)x, y, z
parameters in map_fetch() manual file (#375)gbif_citation() manual file for
accessing many citations (#379)occ_download_queue() (#365)name_* function outpus have changed, so be aware if
you’re using those functionsmap_fetch(): when srs was
EPSG:3857, the extent we set was incorrectly set as
raster::extent(-180, 180, -85.1, 85.1). Now the extent is
raster::extent(-20037508, 20037508, -20037508, 20037508
(#366) (#367) thanks @dmcglinn for reporting and @mdsumner for fixing!gbif_citation() for
occ_download_get objects. we weren’t correctly creating the
path to a file on windows (#359)print.gbif_data (#370) (#371)occ_download() was erroring with a useless error when
users try to use the fxn with the same parameter input types as
occ_search/occ_data; when this happens now
there is a useful error message (#381)occ_download(): when type = "in"
was used, we weren’t creating the JSON correctly, fixed now (#362)occ_download() and occ_download_prep()
gain a new parameter format for specifying the type of
download. options are DWCA (default), SIMPLE_CSV, or SPECIES_LIST.
SIMPLE_CSV and SPECIES_LIST are csv formats, while DWCA is the darwin
core format (#352)NA in addition
to NULL for a missing parameter - both are removed before
being sent to GBIF (#351)tibble::as_data_frame/tibble::data_frame with
tibble::as_tibble (#350)key and gbifID in the output of
occ_data/occ_search/occ_get have
been changed so that both are character class (strings) to match how
GBIF encodes them (#349)occ_download: fail with useful message when user
does not pass in queries as character class (#347)occ_download: fail with useful message now when
user/pwd/email not found or given (#348)elevation() function: the Google Maps API
requires a form of payment up front, and so we’ve decided to move away
from the service. elevation() now uses the Geonames service
https://www.geonames.org/; it does require you to
register to get a username, but its a free service. Geonames has a few
different data models for elevation and can be chosen in the
elevation_model parameter (#344) (#345)occ_data()/occ_search()
output: the data.frame in the data slot now always has the
first column as the occurrence key (key), and the second
column is now the scientific name (scientificName). the
previously used name column still exists in the data.frame,
so as not to break any user code, but is simply a duplicate of the
scientificName column. in a future version of this package
the name column will be dropped (#329)occ_search()/occ_data()/occ_download()
documentation on WKT (well-known text) with respect to winding order.
GBIF requires counter-clockwise winding order; if you submit clockwise
winding order WKT to occ_search() or
occ_data() you should get data back but the WKT is treated
as an exclusion, so returns data outside of that shape instead of within
it; if you submit clockwise winding order WKT to
occ_download() you will get no data back (#340)occ_download(), was failing in certain cases
because of some bad code in an internal function
catch_err() (#333)occ_download() was not returning user name and email in
it’s print method (#334)occ_issues() was failing with occ_data()
or occ_search() input when type="many" (i.e.,
when > 1 thing was passed in) (#341)vcr package so do not require an internet connection (#306)
(#327)name_usage() problem, more work coming to allow users
to use the name issues data like we allow for occurrence issues through
occ_issues() (#324)map_fetch() changes following changes in GBIF maps API:
new parameters taxonKey, datasetkey,
country, publishingOrg,
publishingCountry and removed parameters
search and id; note that this changes how
queries work with this function (#319)map_fetch() docs that style
parameter does not necessarily use the style you give it. not sure why
(#302)occ_download_queue() to report an
accurate number of jobs being processed; before we were just saying
“kicking off first 3 requests” even if there were only 1 or 2
(#312)occ_get() when verbatim=TRUE
(#318)elevation() function now fails better. when the API key
was invalid the function did not give an informative message; now it
does (#322)occ_download_queue(): sleep time
between successive calls to check on the status of download requests is
now 10 seconds or greater. This shouldn’t slow down your use of
occ_download_queue() much because most requests should take
more than the 10 seconds to be prepared (#313)@importFrom fxns used from
lazyeval package to avoid check note (#316)reshape2 and maps packages from
Suggests (#317)name_usage(): we were screwing up parsing of
issues column when single taxon keys passed in (#314)occ_issues() now works with download data and arbitrary
data.frame’s (#193)occ_download_prep() for preparing a download request
without executing it, and occ_download_queue() for kicking
off many download jobs while respecting GBIF’s downloads rate limits.
See also internal R6 classes for dealing with queuing:
DownReq, GifQueue. See
?occ_download_queue to get started (#266) (#305)
(#311)map_fetch() working with the GBIF maps API
https://www.gbif.org/developer/maps. See
?map_fetch to get started (#238) (#269) (#284) thanks to
@JanLauGe for the
work on thisname_lookup() gains origin parameter
(#288) (#293) thanks @peterdesmet and @damianooldoniname_lookup() and name_usage() gain
internal paging - just as
occ_search()/occ_data() have (#291) (see also
#281) thanks @damianooldonilazyeval, and new suggests png
and rasterocc_search()/occ_data() gain parameter
skip_validate (boolean) to skip or not stkip WKT validation
by the wicket packagename_usage() to check params that now only
allow 1 value: name, language, datasetKey, rank (#287)occ_count() loses nubKey,
catalogNumber, and hostCountry as those
parameters are no longer accepted by GBIFname_usage(), was screwing something up
internally (#286)occ_data(): curl options weren’t being
passed through (#297)occ_search()/occ_data() - skipping the wicket
validation and constructing WKT by hand from bounding box (if bounding
box given) - the validation that wicket does isn’t what GBIF wants
(#303)fill parameter to
occ_download_import() to pass on to fill in
data.table::fread, and set fill=TRUE as
default. (#292)occ_download() (#300)occ_download() in which a single
taxonKey passed in was failing (#283)name_usage() was ignoring datasetKey and
uuid parameters (#290)gbifmap() has been removed, see the package
mapr for similar functionality and map_fetch()
in this package to use the GBIF map API (#298)occ_download_datasets and
occ_download_dataset_activity to list datasets for a
download, and list the downloads activity of a dataset (#275)
(#276)rgbif (#262)gbif_citation() function gains an S3 method for passing
the output of occ_download_meta() to it. In addition, for
downloads gbif_citation() now returns a citation for the
entire download (including) its DOI, in addition to citations for each
dataset (#274) thanks @dnoesgaardocc_count():
georeferenced had a misleading description of what the
value FALSE did (#265)gbifmap() - was failing in some cases -
better error handlingn now (#271) thanks @TomaszSuchanocc_download_cancel_staged(): it wasn’t passing
on authentication parameters correctly (#280)?many-values
manual file for details. added docs to individual functions that support
this, and added additional tests (#200) (#260) (#261)V8 dependency and replaced with C++ based
WKT parser package wicket. We still use rgeos
for some WKT parsing. rgbif functions that use wicket:
gbif_bbox2wkt, gbif_wkt2bbox,
check_wkt (#243)httr replaced with crul for HTTP reqeusts.
As part of this change, the ... parameter was replaced in
most functions by curlopts which expects a list. Some
functions require a ... parameter for facet inputs, so
... is retained with the addition of curltops
parameter. A result of this change is that whereas in the past
parameters that were not defined in a function that also had a
... parameter would essentially silently ignore that
undefined parameter, but with functions where ... was
removed a misspelled or undefined parameter will cause an error with
message (#256)occ_download_import() to allow import
of csv type download in addition to darwin core archive. additional
change to occ_download_get to add format
attribute stating which format (#246)occ_download_import adding
fill=TRUE to the data.table::fread call
(#257)occ_dowload gains new parameter body to
allow users to pass in JSON or a list for the query instead of passing
in statements to .... See examples in
?occ_dowload.tibble for compact data.frame output for
occ_download_import instead of bespoke internal solution
(#240)https instead of
http (#244)occ_download_metaocc_download to structure query correctly when
type=within and geometry used because the
structure is slightly different than when not using
geometry (#242)occ_download to allow OR queries for
many values of a parameter, e.g., taxonKey=2475470,2480946
will be queried correctly now as essentially
taxonKey=2475470 or taxonKey=2480946
(#245)parsenames() caused by some slots in the
list being NULL (#237)occ_facet() tests were
failing due to changes in GBIF API (#239)gbif_oai_get_records() for slight changes in
oai dependency pkg (#236)occ_search() now has faceted search. This feature is
not in occ_data() as that function focuses on getting
occurrence data quickly, so will not do get facet data. This means that
a new slot is available in the output object from
occ_search(), namely facets. Note that
rgbif has had faceted search for the species search route
(name_lookup()) and the registry search route
(dataset_search()) for quite a while. (#215)occ_facet()) to facilitate retrieving
only facet data, so no occurrence data is retrieved. (#215) (#229)occ_search() and
occ_data() following addition the GBIF search API:
subgenusKey, repatriated,
phylumKey, kingdomKey, classKey,
orderKey, familyKey, genusKey,
establishmentMeans, protocol,
license, organismId,
publishingOrg, stateProvince,
waterBody, locality (#216) (#224)spellCheck added to
occ_search() and occ_data() that if
TRUE spell checks anything passed to the
search parameter (same as q parameter on GBIF
API; which is a full text search) (#227)occ_spellcheck to spell check search
terms, returns TRUE if no spelling problems, or a list with
info on suggestions if not.occ_search() and occ_data() now have
ability to support queries where limit=0, which for one
should be possible and not fail as we did previously, and second, this
makes it so that you can do faceted searches (See above) and not have to
wait for occurrence records to be returned. (#222)MULTIPOLYGON well known text features now supported in
the GBIF API. Previously, you could not query geometry with
more than one polygon (POLYGON), but now you can.
(#222)occ_count(), especially for the set
of allowed parameter options that the GBIF count API supportsocc_count() gains new parameter typeStatus
to indicate the specimen type status.data slot now returns
NULL instead of a character stringgbif_photos(): 1) Mapbox URLs to their JS and
CSS assets were out of date, and API key needed. 2) In RStudio, the
table view was outputting errors due to serving files on
localhost:<port> instead of simply opening the file;
fixed now by checking platform and using simple open file command
appropriate for the OS. (#228) (#235)tibble in most of the package when the output
is a data.frame (#204)is() with inherits(), no longer
importing methods() (#219)data parameter, now they are (#210)gbifmap() man file (#212)
thanks to @rossmounceocc_download(), in
which strings to parse were not being parsed correctly if spaces weren’t
in the right place, should be more robust now, and added tests (#217).
Came from
https://discuss.ropensci.org/t/rgbif-using-geometry-in-occ-download/395type was being silently ignored in a
number of registry functions. fixed that. (#211)occ_data() and occ_search() gain ability
to more flexibly deal with inputs to the geometry
parameter. Previously, long WKT strings passed to
occ_search() or occ_data() would fail because
URIs can only be so long. Another option is to use the download API (see
?downloads). This version adds the ability to choose what
to do with long WKT strings via the geom_big parameter:
asis (same as previous version), bbox which
detects if a WKT sting is likely too long, and creates a bounding box
from the WKT string then once data is retrieved, clips the result to the
original WKT string; axe uses the geoaxe
package to chop up the input WKT polygon into many, with toggles in the
new parameters geom_size and geom_n. (#197)
(#199)geom_big="axe", then named elements of the output get names
geom1, geom2, geom3, etc. instead
of the input WKT strings - this is because WKT strings can be very long,
and make for very awkward named access to elements. The original WKT
strings can still be accessed via
attr(result, "args")$geometryname_usage() function, see commit e88cf01cc11cb238d44222346eaeff001c0c637etestthat fxn names, e.g.,
expect_gt() instead of expect_more_than()occ_download() to parse error correctly when
empty body passed from GBIF (#202)occ_data() - its primary purpose to
perform faster data requests. Whereas occ_search() gives
you lots of data, including taxonomic hierarchies and media records,
occ_data() only gives occurrence data. (#190)XML with xml2 (#192)data.table::rbindlist() for fast list to data.frame
coercion: name_lookup(), name_backbone(),
name_suggest(), name_usage(), and
parsenames() (#191)httr usage to comply with changes in
httr >= v1.1.0: now setting encoding explicitly to
UTF-8 and parsing all data manually, using the internal
function function(x) content(x, "text", encoding = "UTF-8")
(#195)move_col() to not fail on
fields that don’t exist. Was failing sometimes when no latitude or
longitude columns were returned. (#196)gbif_oai_*()) for working with
GBIF registry OAI-PMH service. Now importing oai package to
make working with GBIF’s OAI-PMH service easier (#183)r-curl/0.9.4 httr/1.0.0 rOpenSci(rgbif/0.9.0), with
whatever versions of each package you’re using. We also pass a
user-agent string with the header X-USER-AGENT in case the
useragent header gets stripped somewhere along the line
(#185)gbif_citation() helps get citations for
datasets eith using the occurrence search API via
occ_search() or the downloads API via
occ_downlad() (#178) (#179)importFrom instead of import in all
cases now.collectorName changed to
recordedBy (#184)occ_download_meta() print method to handle 1 or
more predicate results (#186)occ_issues() to work with
return=data and return=all
occ_search() output (#188)terraformer.js javascript code included in the
package along with an update in that codebase (#156)email parameter now NULL by default in
the function occ_download(), so that if not provided or not
set in options, then function fails. (#173)?downloads help
file.elevation() to check for
coordinates that are impossible (e.g., latitude > 90), not complete
(e.g., lat given, long not given), or points at 0,0 (just
warns, doesn’t stop). (#176) thanks @luisDVA/species route, fix to function name_usage()
(#174)occ_search() to remove a block of code to do
synonym checking. This block of code was used if the parameter
scientificName was passed, and checked if the name given
was a synonym; if yes, we used the accepted name according to the GBIF
backbone taxonomy; if no, we proceeded with the name given by the user.
We removed the block of code because the GBIF API now essentially does
this behind the scenes server side. See https://github.com/gbif/gbif-api
for examples. (#175)gbif_photos() and
gbif_names() (#170)occ_download*() for
working with the GBIF download API. This is the same service as using
the GBIF website, but via an API. See ?downloads. (#154)
(#167)utils, methods, and stats
(#166)httr v1 where empty
list not allowed to pass to the query parameter in
GET (#163)/enumerations GBIF API route:
enumeration() and enumeration_country(). Many
parts of the GBIF API make use of enumerations, i.e. controlled
vocabularies for specific topics - and are available via these
functions. (#152)elevation() now requires an API key (#148)V8 package an Import now, used to do WKT
read/create with use of the Javascript library Terraformer
(http://terraformer.io/). Replaces packages sp and
rgeos, which are no longer imported (#155)occ_search() parameter
spatialIssues to hasGeospatialIssues
(#151)/search and
/count services, and how they work. (#150)name_lookup()
(#149)plyr from Imports (#159)stringr from Imports (#160)maps and grid packages from
Imports (#161)limit and start
parameters was in some cases resulting in duplicate records returned.
Problem fixed. (#157)\dontrun (#139)occ_search() to give correct
values for default and max limit and start parameters (#145)GET helper function to properly pass
on error message (#144)assertthat::assert_that() with
stopifnot() to have one less dependency (#134)occ_search() to allow ability to query by only
publishingCountry, that is, with no other parameters if desired
(#137)GET() helper function to just
pass NULL to the query parameter when the list
of length 0 passed, since it caused requests to fail in some cases.name_lookup() to force a logical entry for
certain parameters - before this fix if the correct logical param was
not passed, the GBIF API went with its default parameter (#135)name_backbone() due to change in
namelkupparser() helper function - fixes parsing for
verbose output (#136)occ_search() documentation
(#140)occ_issues() to subset data from
occ_search() based on GBIF issues. (#) (#122)occ_search() results, and are intentionally moved to the
beginning of the column order of the data to be more obvious.
(#102)occ_search() now returns all data fields by default.
The default setting for the fields parameter is
all - but can be changed. See ?occ_searchgbif_names() to view highlighted terms in
name results from a call to name_lookup(). (#114)occ_issues_lookup() to lookup GBIF
issues based on code name or full issue name, and
gbif_issues() to print the entire issues table.RCurl with httrRJSONIO with jsonlite.
Should see slight performance in JSON parsing with
jsonlite.occ_search() now 500; was
25. (#113)organizations(),
datasets(), networks(), nodes(),
installations()) to data.frames when possible. (#117)occ_search() (#123)callopts parameter changed to ...
throughout all functions. Now pass on options to httr as
named lists or functions. (#130)dataset_search() and dataset_suggest()
gain new parameter publishingOrglimit parameter changed to 100 for dataset
functions: dataset_search(),
dataset_suggest(), and datasets().limit parameter changed to 100 for registry
functions: installations(), networks(),
organizations, and nodes().networks(): name,
code, modifiedsince, startindex,
and maxresults gone; new parameters query,
identifier, identifierType,
limit, and startnodes(): new parameters
identifier, identifierType,
limit, and startocc_search() failed sometimes on species that were not
found. Fixed. (#112)occ_search()
(#119)name_lookup()
(#120)gbif_photos() that caused
map with no data. (#121)name_() functions
according to changes in the GBIF API spec, and fixed documentation to
align with GBIF API changes, and added note about maximum limit. (#124)
(#127) (#129) Thanks to @willgearty !occ_search() so that user can pass
in multiple values to the issue parameter. (#107)occ_search() now has a dplyr like summary
output when return='all'. See ?occ_search for
examples. You can still easily access all data, by indexing to
meta, hierarchy, data, or
media via e.g., $data, ['data'],
or [['data']]. (#95)occ_search(), we now return a media slot in the output list
by default.gbif_photos() to view media files (photos
in the wild or of museum specimens). Two options are available,
which='map' creates a single map which presents the image
when the user clicks on the point, and which='table' in
which a table has one row for each image, presenting the image and an
interactive map with the single point. (#88)sp and
whiskerrgbif changed accordingly. (#92)camelCase from
under_score style - changed accordingly in
rgbif.plyr::compact() instead
of importing from plyr.name_lookup() removed facet_only
parameter as it doesn’t do anything - use limit=0 instead.
Further, added two new slots of output: hierarchy and
names (for common/vernacular names) (#96). The output can
be determined by user via the return parameter.name_suggest(), if the field
higherClassificationMap is selected to be returned via the
fields parameter, a list is returned with a data frame, and
a list of the hierarchies separately. If
higherClassificationMap is not selected, only a data frame
is returned.occ_search() gains new parameters
mediatype and issue (#93), with detailed list
of possible options for the issue parameter. Gains new
examples for searching for images, examples of calls that will throw
errors.check_wkt().facet_only parameter removed from
dataset_search() function as it doesn’t do anything - use
limit=0 instead.gbif_bbox2wkt() and
gbif_wkt2bbox() to convert a bounding box to wkt and a wkt
object to a bounding box, respectively. Copied from the
spocc package. Prefixes to fxn names will avoid
conflicts.rgeos::readWKT or from the returned response from
GBIF.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)elevation() - it was expecting column
names to be latitude and longitude, whereas inputs from other
rgbif functions have changed to decimalLatitude and
decimalLongitude.count_facet() introduced b/c GBIF no
longer accepts hostCountry or nubKey parameters.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)gbifmap().occ_get() for when
verbatim=TRUE, which gives back different data than when
verbatim=FALSE.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.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)name_lookup() function that was labeling
facet outputs incorrectly. (#77)application/json, then parse JSON ourselves using
RJSONIO::fromJSON (instead of httr doing it).stringsAsFactors = FALSE to all data.frame()
calls.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)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.check_wkt() to check that well known text
string is the right format. (#68)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)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.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)DEPRECATED