Package ‘rgbif’

May 23, 2024

Title Interface to the Global Biodiversity Information Facility API
Description A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility (GBIF;
<https://www.gbif.org/developer/summary>). GBIF is a database
of species occurrence records from sources all over the globe.
rgbif includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the GBIF
tile map service to make rasters summarizing huge amounts of data.
Version 3.8.0
License MIT + file LICENSE

URL https://github.com/ropensci/rgbif (devel),

https://docs.ropensci.org/rgbif/ (documentation)

BugReports https://github.com/ropensci/rgbif/issues
LazyLoad true
Encoding UTF-8
Language en-US
Imports xml2, ggplot2, crul (>= 0.7.4), data.table, whisker, magrittr,
jsonlite (>= 1.6), oai (>= 0.2.2), tibble, lazyeval, R6, stats,
wk
Suggests testthat, png, terra, magick, protolite (>= 2.0), sf, vcr (>=
1.2.0), knitr, rmarkdown
RoxygenNote 7.2.3
X-schema.org-applicationCategory Biodiversity
X-schema.org-keywords GBIF, specimens, API, web-services, occurrences,
species, taxonomy
X-schema.org-isPartOf https://ropensci.org
NeedsCompilation no

1
2 R topics documented:

Author Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),

Damiano Oldoni [aut] (<https://orcid.org/0000-0003-3445-7562>),
Vijay Barve [ctb] (<https://orcid.org/0000-0002-4852-2567>),
Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>),
Laurens Geffert [ctb],
Dan Mcglinn [ctb] (<https://orcid.org/0000-0003-2359-3526>),
Karthik Ram [ctb] (<https://orcid.org/0000-0002-0233-1757>),
rOpenSci [fnd] (https://ropensci.org/),
John Waller [aut, cre] (<https://orcid.org/0000-0002-7302-5976>)
Maintainer John Waller <[email protected]>
Repository CRAN
Date/Publication 2024-05-23 12:20:02 UTC

R topics documented:
rgbif-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
check_wkt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
count_facet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
dataset_doi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
dataset_gridded . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
dataset_list_funs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
dataset_search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
dataset_uuid_funs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
derived_dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
downloads . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
download_predicate_dsl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
elevation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
enumeration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
gbif_bbox2wkt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
gbif_citation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
gbif_geocode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
gbif_issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
gbif_issues_lookup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
gbif_names . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
gbif_oai . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
gbif_photos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
installations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
lit_search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
map_fetch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
mvt_fetch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
name_backbone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
name_backbone_checklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
name_issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
name_lookup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
name_parse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
rgbif-package 3

name_suggest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
name_usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
occ_count . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
occ_count_ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
occ_data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
occ_download . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
occ_download_cached . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
occ_download_cancel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
occ_download_datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
occ_download_dataset_activity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
occ_download_describe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
occ_download_get . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
occ_download_import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
occ_download_list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
occ_download_meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
occ_download_queue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
occ_download_wait . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
occ_facet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
occ_get . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
occ_issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
occ_metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
occ_search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
organizations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
parsenames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
rgbif-defunct . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
rgb_country_codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
taxrank . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
wkt_parse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131

Index 133

rgbif-package Interface to the Global Biodiversity Information Facility API.

Description
rgbif: A programmatic interface to the Web Service methods provided by the Global Biodiversity
Information Facility.

About
This package gives you access to data from GBIF https://www.gbif.org/ via their API.
4 check_wkt

Documentation for the GBIF API

• summary https://www.gbif.org/developer/summary - Summary of the GBIF API
• registry https://www.gbif.org/developer/registry - Metadata on datasets, and con-
tributing organizations
• species names https://www.gbif.org/developer/species - Species names and metadata
• occurrences https://www.gbif.org/developer/occurrence - Occurrences
• maps https://www.gbif.org/developer/maps - Maps - these APIs are not implemented in
rgbif, and are meant more for intergration with web based maps.

Author(s)
Scott Chamberlain
Karthik Ram
Dan Mcglinn
Vijay Barve
John Waller

check_wkt Check input WKT

Description
Check input WKT

Usage
check_wkt(wkt = NULL, skip_validate = FALSE)

Arguments
wkt (character) one or more Well Known Text objects
skip_validate (logical) whether to skip wk::wk_problems call or not. Default: FALSE

Examples
## Not run:
check_wkt('POLYGON((30.1 10.1, 10 20, 20 60, 60 60, 30.1 10.1))')
check_wkt('POINT(30.1 10.1)')
check_wkt('LINESTRING(3 4,10 50,20 25)')

# check many passed in at once

check_wkt(c('POLYGON((30.1 10.1, 10 20, 20 60, 60 60, 30.1 10.1))',
'POINT(30.1 10.1)'))

# bad WKT
count_facet 5

# wkt <- 'POLYGON((30.1 10.1, 10 20, 20 60, 60 60, 30.1 a))'

# check_wkt(wkt)

# many wkt's, semi-colon separated, for many repeated "geometry" args

wkt <- "POLYGON((-102.2 46.0,-93.9 46.0,-93.9 43.7,-102.2 43.7,-102.2 46.0))
;POLYGON((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1))"
check_wkt(gsub("\n", '', wkt))

## End(Not run)

count_facet Facetted count occurrence search.

Description
Facetted count occurrence search.

Usage
count_facet(keys = NULL, by = "country", countries = 10, removezeros = FALSE)

Arguments
keys (numeric) GBIF keys, a vector. optional
by (character) One of georeferenced, basisOfRecord, country, or publishingCoun-
try. default: country
countries (numeric) Number of countries to facet on, or a vector of country names. default:
10
removezeros (logical) remove zeros or not? default: FALSE

Examples
## Not run:
# Select number of countries to facet on
count_facet(by='country', countries=3, removezeros = TRUE)
# Or, pass in country names
count_facet(by='country', countries='AR', removezeros = TRUE)

spplist <- c('Geothlypis trichas','Tiaris olivacea','Pterodroma axillaris',

'Calidris ferruginea','Pterodroma macroptera',
'Gallirallus australis',
'Falco cenchroides','Telespiza cantans','Oreomystis bairdi',
'Cistothorus palustris')
keys <- sapply(spplist,
function(x) name_backbone(x, rank="species")$usageKey)
count_facet(keys, by='country', countries=3, removezeros = TRUE)
count_facet(keys, by='country', countries=3, removezeros = FALSE)
count_facet(by='country', countries=20, removezeros = TRUE)
count_facet(keys, by='basisOfRecord', countries=5, removezeros = TRUE)
6 dataset

# get occurrences by georeferenced state

## across all records
count_facet(by='georeferenced')

## by keys
count_facet(keys, by='georeferenced')

# by basisOfRecord
count_facet(by="basisOfRecord")

## End(Not run)

dataset Search for more obscure dataset metadata.

Description
Search for more obscure dataset metadata.

Usage
dataset(
country = NULL,
type = NULL,
identifierType = NULL,
identifier = NULL,
machineTagNamespace = NULL,
machineTagName = NULL,
machineTagValue = NULL,
modified = NULL,
query = NULL,
deleted = FALSE,
limit = NULL,
start = NULL,
curlopts = list()
)

Arguments
country The 2-letter country code (as per ISO-3166-1) of the country publishing the
dataset.
type The primary type of the dataset. Available values : OCCURRENCE, CHECK-
LIST, METADATA, SAMPLING_EVENT, MATERIAL_ENTITY.
identifierType An identifier type for the identifier parameter. Available values : URL, LSID,
HANDLER, DOI, UUID, FTP, URI, UNKNOWN, GBIF_PORTAL, GBIF_NODE,
GBIF_PARTICIPANT, GRSCICOLL_ID, GRSCICOLL_URI, IH_IRN, ROR,
GRID, CITES, SYMBIOTA_UUID, WIKIDATA, NCBI_BIOCOLLECTION.
dataset 7

identifier An identifier of the type given by the identifierType parameter.

machineTagNamespace
Filters for entities with a machine tag in the specified namespace.
machineTagName Filters for entities with a machine tag with the specified name (use in combina-
tion with the machineTagNamespace parameter).
machineTagValue
Filters for entities with a machine tag with the specified value (use in combina-
tion with the machineTagNamespace and machineTagName parameters).
modified The modified date of the dataset. Accepts ranges and a ” can be used as a
wildcard, e.g.:modified=2023-04-01,
query Simple full text search parameter. The value for this parameter can be a simple
word or a phrase. Wildcards are not supported.
deleted Logical specifying whether to return only deleted datasets.
limit Controls the number of results in the page.
start Determines the start for the search results.
curlopts options passed on to crul::HttpClient.

Details

This function allows you to search for some more obscure dataset metadata that might not be pos-
sible with dataset_search(). For example, searching through registry machinetags.

Value

A list.

Examples
## Not run:
dataset(limit=3)
dataset(country="US",limit=3)
dataset(type="CHECKLIST",limit=3)
dataset(identifierType = "URL",limit=3)
dataset(identifier = 168,limit=3)
dataset(machineTagNamespace = "metasync.gbif.org",limit=3)
dataset(machineTagName = "datasetTitle",limit=3)
dataset(machineTagValue = "Borkhart",limit=3)
dataset(modified = "2023-04-01", limit=3)
dataset(q = "dog", limit=3)
dataset(deleted=TRUE,limit=3)

## End(Not run)
8 datasets

datasets Search for datasets and dataset metadata.

Description
Search for datasets and dataset metadata.

Usage
datasets(
data = "all",
type = NULL,
uuid = NULL,
query = NULL,
id = NULL,
limit = 100,
start = NULL,
curlopts = list()
)

Arguments
data The type of data to get. One or more of: ’organization’, ’contact’, ’endpoint’,
’identifier’, ’tag’, ’machinetag’, ’comment’, ’constituents’, ’document’, ’meta-
data’, ’deleted’, ’duplicate’, ’subDataset’, ’withNoEndpoint’, or the special ’all’.
Default: all
type Type of dataset. Options: include occurrence, checklist, metadata, or sam-
pling_event.
uuid UUID of the data node provider. This must be specified if data is anything other
than all
query Query term(s). Only used when data=all
id A metadata document id.
limit Number of records to return. Default: 100. Maximum: 1000.
start Record number to start at. Default: 0. Use in combination with limit to page
through results.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Value
A list.

References
https://www.gbif.org/developer/registry#datasets
dataset_doi 9

Examples
## Not run:
datasets(limit=5)
datasets(type="occurrence", limit=10)
datasets(uuid="a6998220-7e3a-485d-9cd6-73076bd85657")
datasets(data='contact', uuid="a6998220-7e3a-485d-9cd6-73076bd85657")
datasets(data='metadata', uuid="a6998220-7e3a-485d-9cd6-73076bd85657")
datasets(data='metadata', uuid="a6998220-7e3a-485d-9cd6-73076bd85657",
id=598)
datasets(data=c('deleted','duplicate'))
datasets(data=c('deleted','duplicate'), limit=1)

# curl options
datasets(data=c('deleted','duplicate'), curlopts = list(verbose=TRUE))

## End(Not run)

dataset_doi Get a GBIF dataset from a doi

Description

Get a GBIF dataset from a doi

Usage

dataset_doi(doi = NULL, limit = 20, start = NULL, curlopts = list())

Arguments

doi the doi of the dataset you wish to lookup.

limit Controls the number of results in the page.
start Determines the offset for the search results.
curlopts options passed on to crul::HttpClient.

Details

This function allows for dataset lookup using a doi. Be aware that some doi have more than one
dataset associated with them.

Value

A list.
10 dataset_gridded

Examples
## Not run:
dataset_doi('10.15468/igasai')

## End(Not run)

dataset_gridded Check if a dataset is gridded

Description
Check if a dataset is gridded

Usage
dataset_gridded(
uuid = NULL,
min_dis = 0.05,
min_per = 50,
min_dis_count = 30,
return = "logical",
warn = TRUE
)

Arguments
uuid (vector) A character vector of GBIF datasetkey uuids.
min_dis (numeric) (default 0.02) Minimum distance in degrees to accept as gridded.
min_per (integer)(default 50%) Minimum percentage of points having same nearest neigh-
bor distance to be considered gridded.
min_dis_count (default 30) Minimum number of unique points to accept an assessment of ’grid-
dyness’.
return (character) (default "logical"). Choice of "data" will return a data.frame of more
information or "logical" will return just TRUE or FALSE indicating whether a
dataset is considered ’gridded".
warn (logical) indicates whether to warn about missing values or bad values.

Details
Gridded datasets are a known problem at GBIF. Many datasets have equally-spaced points in a
regular pattern. These datasets are usually systematic national surveys or data taken from some
atlas (“so-called rasterized collection designs”). This function uses the percentage of unique lat-
long points with the most common nearest neighbor distance to identify gridded datasets.
https://data-blog.gbif.org/post/finding-gridded-datasets/
I recommend keeping the default values for the parameters.
dataset_list_funs 11

Value
A logical vector indicating whether a dataset is considered gridded. Or if return="data", a
data.frame of more information.

Examples
## Not run:

dataset_gridded("9070a460-0c6e-11dd-84d2-b8a03c50a862")
dataset_gridded(c("9070a460-0c6e-11dd-84d2-b8a03c50a862",
"13b70480-bd69-11dd-b15f-b8a03c50a862"))

## End(Not run)

dataset_list_funs List datasets that are deleted or have no endpoint.

Description
List datasets that are deleted or have no endpoint.

Usage
dataset_duplicate(limit = 20, start = NULL, curlopts = list())

dataset_noendpoint(limit = 20, start = NULL, curlopts = list())

Arguments
limit Controls the number of results in the page.
start Determines the start for the search results.
curlopts options passed on to crul::HttpClient.

Details
Get a list of deleted datasets or datasets with no endpoint. You get the full and no parameters aside
from limit and start are accepted.

Value
A list.
12 dataset_search

Examples
## Not run:
dataset_noendpoint(limit=3)

## End(Not run)

dataset_search Search for dataset metadata.

Description
Search for dataset metadata.

Usage
dataset_export(
query = NULL,
type = NULL,
publishingCountry = NULL,
subtype = NULL,
license = NULL,
keyword = NULL,
publishingOrg = NULL,
hostingOrg = NULL,
endorsingNodeKey = NULL,
decade = NULL,
projectId = NULL,
hostingCountry = NULL,
networkKey = NULL,
doi = NULL
)

dataset_search(
query = NULL,
type = NULL,
publishingCountry = NULL,
subtype = NULL,
license = NULL,
keyword = NULL,
publishingOrg = NULL,
hostingOrg = NULL,
endorsingNodeKey = NULL,
decade = NULL,
projectId = NULL,
hostingCountry = NULL,
networkKey = NULL,
doi = NULL,
dataset_search 13

facet = NULL,
facetLimit = NULL,
facetOffset = NULL,
facetMincount = NULL,
facetMultiselect = NULL,
limit = 100,
start = NULL,
description = FALSE,
curlopts = list()
)

dataset_suggest(
query = NULL,
type = NULL,
publishingCountry = NULL,
subtype = NULL,
license = NULL,
keyword = NULL,
publishingOrg = NULL,
hostingOrg = NULL,
endorsingNodeKey = NULL,
decade = NULL,
projectId = NULL,
hostingCountry = NULL,
networkKey = NULL,
doi = NULL,
limit = 100,
start = NULL,
description = FALSE,
curlopts = list()
)

Arguments

query Simple full text search parameter. The value for this parameter can be a simple
word or a phrase. Wildcards are not supported.
type The primary type of the dataset. Available values: "OCCURRENCE", "CHECK-
LIST", "METADATA", "SAMPLING_EVENT", "MATERIAL_ENTITY".
publishingCountry
Filters datasets by their owning organization’s country given as a ISO 639-1 (2
letter) country code.
subtype The sub-type of the dataset.The sub-type of the dataset. Available values: "TAX-
ONOMIC_AUTHORITY", "NOMENCLATOR_AUTHORITY", "INVENTORY_THEMATIC",
"INVENTORY_REGIONAL", "GLOBAL_SPECIES_DATASET", "DERIVED_FROM_OCCURRENCE
"SPECIMEN", "OBSERVATION".
license The dataset’s licence. Available values: "CC0_1_0", "CC_BY_4_0", "CC_BY_NC_4_0",
"UNSPECIFIED", "UNSUPPORTED".
14 dataset_search

keyword Filters datasets by a case insensitive plain text keyword. The search is done on
the merged collection of tags, the dataset keywordCollections and temporalCov-
erages.
publishingOrg Filters datasets by their publishing organization UUID key.
hostingOrg Filters datasets by their hosting organization UUID key
endorsingNodeKey
Node UUID key that endorsed this dataset’s publisher.
decade Filters datasets by their temporal coverage broken down to decades. Decades are
given as a full year, e.g. 1880, 1960, 2000, etc, and will return datasets wholly
contained in the decade as well as those that cover the entire decade or more.
Ranges can be used like this "1800,1900".
projectId Filter or facet based on the project ID of a given dataset. A dataset can have
a project id if it is the result of a project. Multiple datasets can have the same
project id.
hostingCountry Filters datasets by their hosting organization’s country given as a ISO 639-1 (2
letter) country code.
networkKey Filters network UUID associated to a dataset.
doi DOI of the dataset.
facet A facet name used to retrieve the most frequent values for a field.
facetLimit Facet parameters allow paging requests using the parameters facetOffset and
facetLimit.
facetOffset Facet parameters allow paging requests using the parameters facetOffset and
facetLimit
facetMincount Used in combination with the facet parameter.
facetMultiselect
Used in combination with the facet parameter.
limit Controls the number of results in the page. Using too high a value will be over-
written with the default maximum threshold, depending on the service. Sensible
defaults are used so this may be omitted.
start Determines the offset for the search results. A limit of 20 and offset of 40 will
get the third page of 20 results. Some services have a maximum offset.
description Logical whether to return descriptions.
curlopts options passed on to crul::HttpClient.

Details
dataset_search() searches and returns metadata on GBIF datasets from the registry. This func-
tion does not search occurrence data, only metadata on the datasets that contain may contain occur-
rence data. It also searches over other dataset types, such checklist and metadata datasets. Only a
sample of results is returned.
dataset_export() function will download a tibble of the results of a dataset_search(). This
function is primarily useful if you want the full results of a dataset_search().
Use dataset_search(facet="x",limit=0)$facets to get simple group by counts for different
parameters.
dataset_search 15

Value

A list for dataset_search(). A tibble for dataset_export().

References

https://techdocs.gbif.org/en/openapi/v1/registry#/Datasets/searchDatasets

Examples
## Not run:
# search metadata on all datasets and return a sample
dataset_search()
# dataset_export() # download info on all +90K datasets

dataset_search(publishingCountry = "US")
dataset_search(type = "OCCURRENCE")
dataset_search(keyword = "bird")
dataset_search(subtype = "TAXONOMIC_AUTHORITY")
dataset_search(license = "CC0_1_0")
dataset_search(query = "frog")
dataset_search(publishingCountry = "UA")
dataset_search(publishingOrg = "e2e717bf-551a-4917-bdc9-4fa0f342c530")
dataset_search(hostingOrg = "7ce8aef0-9e92-11dc-8738-b8a03c50a862")
dataset_search(decade="1890,1990",limit=5)
dataset_search(projectId = "GRIIS")
dataset_search(hostingCountry = "NO")
dataset_search(networkKey = "99d66b6c-9087-452f-a9d4-f15f2c2d0e7e")
dataset_search(doi='10.15468/aomfnb')

# search multiple values

dataset_search(projectId = "GRIIS;BID-AF2020-140-REG")
dataset_search(hostingCountry = "NO;SE")
dataset_search(doi="10.15468/aomfnb;10.15468/igasai")

# multiple filters
dataset_search(license = "CC0_1_0",subtype = "TAXONOMIC_AUTHORITY")
# dataset_export(license = "CC0_1_0",subtype = "TAXONOMIC_AUTHORITY")

# using dataset export to get all datasets

dataset_export(decade="1800,1900")
dataset_export(projectId="GRIIS")

# get simple group by counts

dataset_search(facet="type",limit=0,facetLimit=5)$facets
dataset_search(facet="publishingCountry",limit=0,facetLimit=5)$facets
dataset_search(facet="license",limit=0,facetLimit=5, facetMincount=10000)

## End(Not run)
16 dataset_uuid_funs

dataset_uuid_funs Get dataset metadata using a datasetkey

Description
Get dataset metadata using a datasetkey

Usage
dataset_get(uuid = NULL, curlopts = list())

dataset_process(uuid = NULL, limit = 20, start = NULL, curlopts = list())

dataset_networks(uuid = NULL, limit = 20, start = NULL, curlopts = list())

dataset_constituents(uuid = NULL, limit = 20, start = NULL, curlopts = list())

dataset_comment(uuid = NULL, curlopts = list())

dataset_contact(uuid = NULL, curlopts = list())

dataset_endpoint(uuid = NULL, curlopts = list())

dataset_identifier(uuid = NULL, curlopts = list())

dataset_machinetag(uuid = NULL, curlopts = list())

dataset_tag(uuid = NULL, curlopts = list())

dataset_metrics(uuid = NULL, curlopts = list())

Arguments
uuid A GBIF datasetkey uuid.
curlopts options passed on to crul::HttpClient.
limit Number of records to return.
start Record number to start at.

Details
dataset_metrics() can only be used with checklist type datasets.

Value
A tibble or a list.
derived_dataset 17

References
https://techdocs.gbif.org/en/openapi/v1/registry

Examples
## Not run:
dataset_get("38b4c89f-584c-41bb-bd8f-cd1def33e92f")
dataset_process("38b4c89f-584c-41bb-bd8f-cd1def33e92f",limit=3)
dataset_networks("3dab037f-a520-4bc3-b888-508755c2eb52")
dataset_constituents("7ddf754f-d193-4cc9-b351-99906754a03b",limit=3)
dataset_comment("2e4cc37b-302e-4f1b-bbbb-1f674ff90e14")
dataset_contact("7ddf754f-d193-4cc9-b351-99906754a03b")
dataset_endpoint("7ddf754f-d193-4cc9-b351-99906754a03b")
dataset_identifier("7ddf754f-d193-4cc9-b351-99906754a03b")
dataset_machinetag("7ddf754f-d193-4cc9-b351-99906754a03b")
dataset_tag("c47f13c1-7427-45a0-9f12-237aad351040")
dataset_metrics("7ddf754f-d193-4cc9-b351-99906754a03b")

## End(Not run)

derived_dataset Register a derived dataset for citation.

Description
Register a derived dataset for citation.

Usage
derived_dataset(
citation_data = NULL,
title = NULL,
description = NULL,
source_url = NULL,
gbif_download_doi = NULL,
user = NULL,
pwd = NULL,
curlopts = list()
)

derived_dataset_prep(
citation_data = NULL,
title = NULL,
description = NULL,
source_url = NULL,
gbif_download_doi = NULL,
user = NULL,
pwd = NULL,
18 derived_dataset

curlopts = list()
)

Arguments
citation_data (required) A data.frame with two columns. The first column should be GBIF
datasetkey uuids and the second column should be occurrence counts from
each of your datasets, representing the contribution of each dataset to your final
derived dataset.
title (required) The title for your derived dataset.
description (required) A description of the dataset. Perhaps describing how it was created.
source_url (required) A link to where the dataset is stored.
gbif_download_doi
(optional) A DOI from an original GBIF download.
user (required) Your GBIF username.
pwd (required) Your GBIF password.
curlopts a list of arguments to pass to curl.

Value
A list.

Usage
Create a citable DOI for a dataset derived from GBIF mediated occurrences.
Use-case (1) your dataset was obtained with occ_search() and never returned a citable DOI, but
you want to cite the data in a research paper.
Use-case (2) your dataset was obtained using occ_download() and you got a DOI, but the data
underwent extensive filtering using CoordinateCleaner or some other cleaning pipeline. In this
case be sure to fill in your original gbif_download_doi.
Use-case (3) your dataset was generated using a GBIF cloud export but you want a DOI to cite in
your research paper.
Use derived_dataset to create a custom citable meta-data description and most importantly a
DOI link between an external archive (e.g. Zenodo) and the datasets involved in your research or
analysis.
All fields (except gbif_download_doi) are required for the registration to work.
We recommend that you run derived_dataset_prep() to check registration details before making
it final with derived_dataset().

Authentication
Some rgbif functions require your GBIF credentials.
For the user and pwd parameters, you can set them in one of three ways:
1. Set them in your .Renviron/.bash_profile (or similar) file with the names GBIF_USER,
GBIF_PWD, and GBIF_EMAIL
derived_dataset 19

2. Set them in your .Rprofile file with the names gbif_user and gbif_pwd.
3. Simply pass strings to each of the parameters in the function call.

We strongly recommend the first option - storing your details as environment variables - as it’s the
most widely used way to store secrets.
You can edit your .Renviron with usethis::edit_r_environ().
After editing, your .Renviron file should look something like this...
GBIF_USER="jwaller"
GBIF_PWD="fakepassword123"
GBIF_EMAIL="[email protected]"

See ?Startup for help.

References
https://data-blog.gbif.org/post/derived-datasets/ https://www.gbif.org/derived-dataset/
about

Examples
## Not run:
data <- data.frame(
datasetKey = c(
"3ea36590-9b79-46a8-9300-c9ef0bfed7b8",
"630eb55d-5169-4473-99d6-a93396aeae38",
"806bf7d4-f762-11e1-a439-00145eb45e9a"),
count = c(3, 1, 2781)
)

## If output looks ok, run derived_dataset to register the dataset

derived_dataset_prep(
citation_data = data,
title = "Test for derived dataset",
description = "This data was filtered using a fake protocol",
source_url = "https://zenodo.org/record/4246090#.YPGS2OgzZPY"
)

# derived_dataset(
# citation_data = data,
# title = "Test for derived dataset",
# description = "This data was filtered using a fake protocol",
# source_url = "https://zenodo.org/record/4246090#.YPGS2OgzZPY"
# )

## Example with occ_search and dplyr

# library(dplyr)

# citation_data <- occ_search(taxonKey=212, limit=20)$data %>%

# group_by(datasetKey) %>%
# count()
20 downloads

# # You would still need to upload your data to Zenodo or something similar
# derived_dataset_prep(
# citation_data = citation_data,
# title="Bird data downloaded for test",
# description="This data was downloaded using rgbif::occ_search and was
# later uploaded to Zenodo.",
# source_url="https://zenodo.org/record/4246090#.YPGS2OgzZPY",
# gbif_download_doi = NULL,
# )

## End(Not run)

downloads Downloads interface

Description
GBIF provides two ways to get occurrence data: through the /occurrence/search route (see
occ_search()), or via the /occurrence/download route (many functions, see below). occ_search()
is more appropriate for smaller data, while occ_download*() functions are more appropriate for
larger data requests.

Settings
You’ll use occ_download() to kick off a download. You’ll need to give that function settings
from your GBIF profile: your user name, your password, and your email. These three settings are
required to use the function. You can specify them in one of three ways:

• Pass them to occ_download as parameters

• Use R options: As options either in the current R session using the options() function, or by
setting them in your .Rprofile file, after which point they’ll be read in automatically
• Use environment variables: As env vars either in the current R session using the Sys.setenv()
function, or by setting them in your .Renviron/.bash_profile or similar files, after which
point they’ll be read in automatically

BEWARE
You can not perform that many downloads, so plan wisely. See Rate limiting below.

Rate limiting
If you try to launch too many downloads, you will receive an 420 "Enhance Your Calm" response.
If there is less then 100 in total across all GBIF users, then you can have 3 running at a time. If
there are more than that, then each user is limited to 1 only. These numbers are subject to change.
downloads 21

Functions

• occ_download() - Start a download

• occ_download_prep() - Prepare a download request
• occ_download_queue() - Start many downloads in a queue
• occ_download_cached() - Check for downloads already in your GBIF account
• occ_download_wait() - Re-run occ_download_meta() until ready
• occ_download_meta() - Get metadata progress on a single download
• occ_download_list() - List your downloads
• occ_download_cancel() - Cancel a download
• occ_download_cancel_staged() - Cancels any jobs with status RUNNING or PREPARING
• occ_download_get() - Retrieve a download
• occ_download_import() - Import a download from local file system
• occ_download_datasets() - List datasets for a download
• occ_download_dataset_activity() - Lists the downloads activity of a dataset
Download query composer methods:
See download_predicate_dsl

Query length

GBIF has a limit of 12,000 characters for a download query. This means that you can have a pretty
long query, but at some point it may lead to an error on GBIF’s side and you’ll have to split your
query into a few.

Download status

The following statuses can be found with any download:

• PREPARING: just submitted by user and awaiting processing (typically only a few seconds)
• RUNNING: being created (takes typically 1-15 minutes)
• FAILED: something unexpected went wrong
• KILLED: user decided to abort the job while it was in PREPARING or RUNNING phase
• SUCCEEDED: The download was created and the user was informed
• FILE_ERASED: The download was deleted according to the retention policy, see https://www.gbif.org/faq?question=for
how-long-will-does-gbif-store-downloads
22 download_predicate_dsl

download_predicate_dsl
Download predicate DSL (domain specific language)

Description

Download predicate DSL (domain specific language)

Usage

pred(key, value)

pred_gt(key, value)

pred_gte(key, value)

pred_lt(key, value)

pred_lte(key, value)

pred_not(...)

pred_like(key, value)

pred_within(value)

pred_isnull(key)

pred_notnull(key)

pred_or(..., .list = list())

pred_and(..., .list = list())

pred_in(key, value)

pred_default()

Arguments

key (character) the key for the predicate. See "Keys" below
value (various) the value for the predicate
..., .list For pred_or() or pred_and(), one or more objects of class occ_predicate,
created by any pred* function
download_predicate_dsl 23

predicate methods and their equivalent types

pred* functions are named for the ’type’ of operation they do, following the terminology used by
GBIF, see https://www.gbif.org/developer/occurrence#predicates
Function names are given, with the equivalent GBIF type value (e.g., pred_gt and greaterThan)
The following functions take one key and one value:
• pred: equals
• pred_lt: lessThan
• pred_lte: lessThanOrEquals
• pred_gt: greaterThan
• pred_gte: greaterThanOrEquals
• pred_like: like
The following function is only for geospatial queries, and only accepts a WKT string:
• pred_within: within
The following function is only for stating the you don’t want a key to be null, so only accepts one
key:
• pred_notnull: isNotNull
The following function is only for stating that you want a key to be null.
• pred_isnull : isNull
The following two functions accept multiple individual predicates, separating them by either "and"
or "or":
• pred_and: and
• pred_or: or
The not predicate accepts one predicate; that is, this negates whatever predicate is passed in, e.g.,
not the taxonKey of 12345:
• pred_not: not
The following function is special in that it accepts a single key but many values; stating that you
want to search for all the values:
• pred_in: in
The following function will apply commonly used defaults.
• pred_default
Using pred_default() is equivalent to running:

pred_and(
pred("HAS_GEOSPATIAL_ISSUE",FALSE),
pred("HAS_COORDINATE",TRUE),
pred("OCCURRENCE_STATUS","PRESENT"),
pred_not(pred_in("BASIS_OF_RECORD",
c("FOSSIL_SPECIMEN","LIVING_SPECIMEN")))
)
24 download_predicate_dsl

What happens internally

Internally, the input to pred* functions turns into JSON to be sent to GBIF. For example ...
pred_in("taxonKey", c(2480946, 5229208)) gives:

{
"type": "in",
"key": "TAXON_KEY",
"values": ["2480946", "5229208"]
}

pred_gt("elevation", 5000) gives:

{
"type": "greaterThan",
"key": "ELEVATION",
"value": "5000"
}

pred_or(pred("taxonKey", 2977832), pred("taxonKey", 2977901)) gives:

{
"type": "or",
"predicates": [
{
"type": "equals",
"key": "TAXON_KEY",
"value": "2977832"
},
{
"type": "equals",
"key": "TAXON_KEY",
"value": "2977901"
}
]
}

Keys
Acceptable arguments to the key parameter are (with the version of the key in parens that must
be sent if you pass the query via the body parameter; see below for examples). You can also use
the ’ALL_CAPS’ version of a key if you prefer. Open an issue in the GitHub repository for this
package if you know of a key that should be supported that is not yet.
• taxonKey (TAXON_KEY)
• acceptedTaxonKey (ACCEPTED_TAXON_KEY)
• kingdomKey (KINGDOM_KEY)
• phylumKey (PHYLUM_KEY)
download_predicate_dsl 25

• classKey (CLASS_KEY)
• orderKey (ORDER_KEY)
• familyKey (FAMILY_KEY)
• genusKey (GENUS_KEY)
• subgenusKey (SUBGENUS_KEY)
• speciesKey (SPECIES_KEY)
• scientificName (SCIENTIFIC_NAME)
• country (COUNTRY)
• publishingCountry (PUBLISHING_COUNTRY)
• hasCoordinate (HAS_COORDINATE)
• hasGeospatialIssue (HAS_GEOSPATIAL_ISSUE)
• typeStatus (TYPE_STATUS)
• recordNumber (RECORD_NUMBER)
• lastInterpreted (LAST_INTERPRETED)
• modified (MODIFIED)
• continent (CONTINENT)
• geometry (GEOMETRY)
• basisOfRecord (BASIS_OF_RECORD)
• datasetKey (DATASET_KEY)
• datasetID/datasetId (DATASET_ID)
• eventDate (EVENT_DATE)
• catalogNumber (CATALOG_NUMBER)
• otherCatalogNumbers (OTHER_CATALOG_NUMBERS)
• year (YEAR)
• month (MONTH)
• decimalLatitude (DECIMAL_LATITUDE)
• decimalLongitude (DECIMAL_LONGITUDE)
• elevation (ELEVATION)
• depth (DEPTH)
• institutionCode (INSTITUTION_CODE)
• collectionCode (COLLECTION_CODE)
• issue (ISSUE)
• mediatype (MEDIA_TYPE)
• recordedBy (RECORDED_BY)
• recordedById/recordedByID (RECORDED_BY_ID)
• establishmentMeans (ESTABLISHMENT_MEANS)
• coordinateUncertaintyInMeters (COORDINATE_UNCERTAINTY_IN_METERS)
26 download_predicate_dsl

• gadm (GADM_GID) (for the Database of Global Administrative Areas)

• level0Gid (GADM_LEVEL_0_GID)
• level1Gid (GADM_LEVEL_1_GID)
• level2Gid (GADM_LEVEL_2_GID)
• level3Gid (GADM_LEVEL_3_GID)
• stateProvince (STATE_PROVINCE)
• occurrenceStatus (OCCURRENCE_STATUS)
• publishingOrg (PUBLISHING_ORG)
• occurrenceId/occurrenceID (OCCURRENCE_ID)
• eventId/eventID (EVENT_ID)
• parentEventId/parentEventID (PARENT_EVENT_ID)
• identifiedBy (IDENTIFIED_BY)
• identifiedById/identifiedByID (IDENTIFIED_BY_ID)
• license (LICENSE)
• locality(LOCALITY)
• pathway (PATHWAY)
• preparations (PREPARATIONS)
• networkKey (NETWORK_KEY)
• organismId/organismID (ORGANISM_ID)
• organismQuantity (ORGANISM_QUANTITY)
• organismQuantityType (ORGANISM_QUANTITY_TYPE)
• protocol (PROTOCOL)
• relativeOrganismQuantity (RELATIVE_ORGANISM_QUANTITY)
• repatriated (REPATRIATED)
• sampleSizeUnit (SAMPLE_SIZE_UNIT)
• sampleSizeValue (SAMPLE_SIZE_VALUE)
• samplingProtocol (SAMPLING_PROTOCOL)
• verbatimScientificName (VERBATIM_SCIENTIFIC_NAME)
• taxonID/taxonId (TAXON_ID)
• taxonomicStatus (TAXONOMIC_STATUS)
• waterBody (WATER_BODY)
• iucnRedListCategory (IUCN_RED_LIST_CATEGORY)
• degreeOfEstablishment (DEGREE_OF_ESTABLISHMENT)
• isInCluster (IS_IN_CLUSTER)
• lifeStage (LIFE_STAGE)
• distanceFromCentroidInMeters (DISTANCE_FROM_CENTROID_IN_METERS)
• gbifId (GBIF_ID)
elevation 27

References
Download predicates docs: https://www.gbif.org/developer/occurrence#predicates

See Also
Other downloads: occ_download_cached(), occ_download_cancel(), occ_download_dataset_activity(),
occ_download_datasets(), occ_download_get(), occ_download_import(), occ_download_list(),
occ_download_meta(), occ_download_queue(), occ_download_wait(), occ_download()

Examples
pred("taxonKey", 3119195)
pred_gt("elevation", 5000)
pred_gte("elevation", 5000)
pred_lt("elevation", 1000)
pred_lte("elevation", 1000)
pred_within("POLYGON((-14 42, 9 38, -7 26, -14 42))")
pred_and(pred_within("POLYGON((-14 42, 9 38, -7 26, -14 42))"),
pred_gte("elevation", 5000))
pred_or(pred_lte("year", 1989), pred("year", 2000))
pred_and(pred_lte("year", 1989), pred("year", 2000))
pred_in("taxonKey", c(2977832, 2977901, 2977966, 2977835))
pred_in("basisOfRecord", c("MACHINE_OBSERVATION", "HUMAN_OBSERVATION"))
pred_not(pred("taxonKey", 729))
pred_like("catalogNumber", "PAPS5-560%")
pred_notnull("issue")
pred("basisOfRecord", "LITERATURE")
pred("hasCoordinate", TRUE)
pred("stateProvince", "California")
pred("hasGeospatialIssue", FALSE)
pred_within("POLYGON((-14 42, 9 38, -7 26, -14 42))")
pred_or(pred("taxonKey", 2977832), pred("taxonKey", 2977901),
pred("taxonKey", 2977966))
pred_in("taxonKey", c(2977832, 2977901, 2977966, 2977835))

elevation Get elevation for lat/long points from a data.frame or list of points.

Description
Uses the GeoNames web service

Usage
elevation(
input = NULL,
latitude = NULL,
longitude = NULL,
latlong = NULL,
28 elevation

elevation_model = "srtm3",
username = Sys.getenv("GEONAMES_USER"),
key,
curlopts,
...
)

Arguments
input A data.frame of lat/long data. There must be columns decimalLatitude and dec-
imalLongitude.
latitude A vector of latitude’s. Must be the same length as the longitude vector.
longitude A vector of longitude’s. Must be the same length as the latitude vector.
latlong A vector of lat/long pairs. See examples.
elevation_model
(character) one of srtm3 (default), srtm1, astergdem, or gtopo30. See "Elevation
models" below for more
username (character) Required. An GeoNames user name. See Details.
key, curlopts defunct. see docs
... curl options passed on to crul::verb-GET see curl::curl_options() for curl
options

Value
A new column named elevation_geonames in the supplied data.frame or a vector with elevation
of each location in meters. Note that data from GBIF can already have a column named elevation,
thus the column we add is named differently.

GeoNames user name

To get a GeoNames user name, register for an account at http://www.geonames.org/login - then you
can enable your account for the GeoNames webservice on your account page (http://www.geonames.org/manageaccount).
Once you are enabled to use the webservice, you can pass in your username to the username
parameter. Better yet, store your username in your .Renviron file, or similar (e.g., .zshrc or
.bash_profile files) and read it in via Sys.getenv() as in the examples below. By default we do
Sys.getenv("GEONAMES_USER") for the username parameter.

Elevation models
• srtm3:
– sample area: ca 90m x 90m
– result: a single number giving the elevation in meters according to srtm3, ocean areas
have been masked as "no data" and have been assigned a value of -32768
• srtm1:
– sample area: ca 30m x 30m
elevation 29

– result: a single number giving the elevation in meters according to srtm1, ocean areas
have been masked as "no data" and have been assigned a value of -32768
• astergdem (Aster Global Digital Elevation Model V2 2011):
– sample area: ca 30m x 30m, between 83N and 65S latitude
– result: a single number giving the elevation in meters according to aster gdem, ocean
areas have been masked as "no data" and have been assigned a value of -32768
• gtopo30:
– sample area: ca 1km x 1km
– result: a single number giving the elevation in meters according to gtopo30, ocean areas
have been masked as "no data" and have been assigned a value of -9999

References

GeoNames http://www.geonames.org/export/web-services.html

Examples
## Not run:
user <- Sys.getenv("GEONAMES_USER")

occ_key <- name_suggest('Puma concolor')$key[1]

dat <- occ_search(taxonKey = occ_key, limit = 300, hasCoordinate = TRUE)
head( elevation(dat$data, username = user) )

# Pass in a vector of lat's and a vector of long's

elevation(latitude = dat$data$decimalLatitude[1:10],
longitude = dat$data$decimalLongitude[1:10],
username = user, verbose = TRUE)

# Pass in lat/long pairs in a single vector

pairs <- list(c(31.8496,-110.576060), c(29.15503,-103.59828))
elevation(latlong=pairs, username = user)

# Pass on curl options

pairs <- list(c(31.8496,-110.576060), c(29.15503,-103.59828))
elevation(latlong=pairs, username = user, verbose = TRUE)

# different elevation models

lats <- dat$data$decimalLatitude[1:5]
lons <- dat$data$decimalLongitude[1:5]
elevation(latitude = lats, longitude = lons, elevation_model = "srtm3")
elevation(latitude = lats, longitude = lons, elevation_model = "srtm1")
elevation(latitude = lats, longitude = lons, elevation_model = "astergdem")
elevation(latitude = lats, longitude = lons, elevation_model = "gtopo30")

## End(Not run)
30 enumeration

enumeration Enumerations.

Description

Many parts of the GBIF API make use of enumerations, i.e. controlled vocabularies for specific
topics - and are available via these functions

Usage

enumeration(x = NULL, curlopts = list())

enumeration_country(curlopts = list())

Arguments

x A given enumeration.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Value

enumeration returns a character vector, while enumeration_country returns a data.frame.

Examples

## Not run:
# basic enumeration
enumeration()
enumeration("NameType")
enumeration("MetadataType")
enumeration("TypeStatus")

# country enumeration
enumeration_country()

# curl options
enumeration(curlopts = list(verbose=TRUE))

## End(Not run)
gbif_bbox2wkt 31

gbif_bbox2wkt Convert a bounding box to a Well Known Text polygon, and a WKT to
a bounding box

Description
Convert a bounding box to a Well Known Text polygon, and a WKT to a bounding box

Usage
gbif_bbox2wkt(minx = NA, miny = NA, maxx = NA, maxy = NA, bbox = NULL)

gbif_wkt2bbox(wkt = NULL)

Arguments
minx (numeric) Minimum x value, or the most western longitude
miny (numeric) Minimum y value, or the most southern latitude
maxx (numeric) Maximum x value, or the most eastern longitude
maxy (numeric) Maximum y value, or the most northern latitude
bbox (numeric) A vector of length 4, with the elements: minx, miny, maxx, maxy
wkt (character) A Well Known Text object.

Value
gbif_bbox2wkt returns an object of class charactere, a Well Known Text string of the form ’POLY-
GON((minx miny, maxx miny, maxx maxy, minx maxy, minx miny))’.
gbif_wkt2bbox returns a numeric vector of length 4, like c(minx, miny, maxx, maxy)

Examples
## Not run:
# Convert a bounding box to a WKT
## Pass in a vector of length 4 with all values
gbif_bbox2wkt(bbox=c(-125.0,38.4,-121.8,40.9))

## Or pass in each value separately

gbif_bbox2wkt(minx=-125.0, miny=38.4, maxx=-121.8, maxy=40.9)

# Convert a WKT object to a bounding box

wkt <- "POLYGON((-125 38.4,-125 40.9,-121.8 40.9,-121.8 38.4,-125 38.4))"
gbif_wkt2bbox(wkt)

## End(Not run)
32 gbif_citation

gbif_citation Get citation for datasets used

Description

Get citation for datasets used

Usage

gbif_citation(x)

Arguments

x (character) Result of call to occ_download_get(), occ_download_meta().

Details

The function is deprecated for use with occ_search() and occ_data() results, and is deprecated
for use with datasetKeys and gbifids. Instead, we encourage you to use derived_dataset() in-
stead.
occ_download_get() and occ_download_meta() results are still supported.

Value

list with S3 class assigned, used by a print method to pretty print citation information. Though you
can unclass the output or just index to the named items as needed.

Examples
## Not run:
# Downloads
## occ_download_get()
# d1 <- occ_download(pred("country", "BG"), pred_gte("year", 2020))
# occ_download_meta(d1) # wait until status = succeeded
# d1 <- occ_download_get(d1, overwrite = TRUE)
# gbif_citation(d1)

## occ_download_meta()
# key <- "0000122-171020152545675"
# res <- occ_download_meta(key)
# gbif_citation(res)

## End(Not run)
gbif_geocode 33

gbif_geocode Geocode lat-lon point(s) with GBIF’s set of geo-polygons (experimen-

tal)

Description
Geocode lat-lon point(s) with GBIF’s set of geo-polygons (experimental)

Usage
gbif_geocode(latitude = NULL, longitude = NULL)

Arguments
latitude a vector of numeric latitude values between -90 and 90.
longitude a vector of numeric longitude values between -180 and 180.

Value
A data.frame of results from the GBIF gecoding service.
• latitude : The input latitude
• longitude : The input longitude
• index : The original input rownumber
• id : The polygon id from which the geocode comes from
• type : One of the following : "Political" (county codes), "IHO" (marine regions), "SeaVox"
(marine regions), "WGSRPD" (tdwg regions), "EEZ", (in national waters) or "GADM0","GADM1","GADM2","GADM
• title : The name of the source polygon
• distance : distance to the polygon boarder
This function uses the GBIF geocoder API which is not guaranteed to be stable and is undocu-
mented. As such, this may return different data over time, may be rate-limited or may stop working
if GBIF change the service. Use this function with caution.

References
http://gadm.org/ http://marineregions.org/ http://www.tdwg.org/standards/ http://api.gbif.org/
v1/geocode/reverse?lat=0&lng=0

Examples
## Not run:
# one pair
gbif_geocode(0,0)
# or multiple pairs of points
gbif_geocode(c(0,50),c(0,20))
34 gbif_issues_lookup

## End(Not run)

gbif_issues List all GBIF issues and their codes.

Description
Returns a data.frame of all GBIF issues with the following columns:
• code: issue short code, e.g. gass84
• code: issue full name, e.g. GEODETIC_DATUM_ASSUMED_WGS84
• description: issue description
• type: issue type, either related to occurrence or name

Usage
gbif_issues()

Source
https://gbif.github.io/gbif-api/apidocs/org/gbif/api/vocabulary/OccurrenceIssue.html https://gbif.github.io/gbif-
api/apidocs/org/gbif/api/vocabulary/NameUsageIssue.html

gbif_issues_lookup Lookup issue definitions and short codes

Description
Lookup issue definitions and short codes

Usage
gbif_issues_lookup(issue = NULL, code = NULL)

Arguments
issue Full name of issue, e.g, CONTINENT_COUNTRY_MISMATCH
code An issue short code, e.g. ’ccm’

Examples
gbif_issues_lookup(issue = 'CONTINENT_COUNTRY_MISMATCH')
gbif_issues_lookup(code = 'ccm')
gbif_issues_lookup(issue = 'COORDINATE_INVALID')
gbif_issues_lookup(code = 'cdiv')
gbif_names 35

gbif_names View highlighted terms in name results from GBIF.

Description

View highlighted terms in name results from GBIF.

Usage

gbif_names(input, output = NULL, browse = TRUE)

Arguments

input Input output from occ_search

output Output folder path. If not given uses temporary folder.
browse (logical) Browse output (default: TRUE)

Examples

## Not run:
# browse=FALSE returns path to file
gbif_names(name_lookup(query='snake', hl=TRUE), browse=FALSE)

(out <- name_lookup(query='canada', hl=TRUE, limit=5))

gbif_names(out)
gbif_names(name_lookup(query='snake', hl=TRUE))
gbif_names(name_lookup(query='bird', hl=TRUE))

# or not highlight
gbif_names(name_lookup(query='bird', limit=200))

## End(Not run)

gbif_oai GBIF registry data via OAI-PMH

Description

GBIF registry data via OAI-PMH

36 gbif_oai

Usage
gbif_oai_identify(...)

gbif_oai_list_identifiers(
prefix = "oai_dc",
from = NULL,
until = NULL,
set = NULL,
token = NULL,
as = "df",
...
)

gbif_oai_list_records(
prefix = "oai_dc",
from = NULL,
until = NULL,
set = NULL,
token = NULL,
as = "df",
...
)

gbif_oai_list_metadataformats(id = NULL, ...)

gbif_oai_list_sets(token = NULL, as = "df", ...)

gbif_oai_get_records(ids, prefix = "oai_dc", as = "parsed", ...)

Arguments
... Curl options passed on to httr::GET
prefix (character) A string to specify the metadata format in OAI-PMH requests issued
to the repository. The default ("oai_dc") corresponds to the mandatory OAI
unqualified Dublin Core metadata schema.
from (character) string giving datestamp to be used as lower bound for datestamp-
based selective harvesting (i.e., only harvest records with datestamps in the given
range). Dates and times must be encoded using ISO 8601. The trailing Z must be
used when including time. OAI-PMH implies UTC for data/time specifications.
until (character) Datestamp to be used as an upper bound, for datestamp-based selec-
tive harvesting (i.e., only harvest records with datestamps in the given range).
set (character) A set to be used for selective harvesting (i.e., only harvest records in
the given set).
token (character) a token previously provided by the server to resume a request where
it last left off. 50 is max number of records returned. We will loop for you
internally to get all the records you asked for.
gbif_photos 37

as (character) What to return. One of "df" (for data.frame; default), "list" (get a
list), or "raw" (raw text). For gbif_oai_get_records, one of "parsed" or "raw"
id, ids (character) The OAI-PMH identifier for the record. Optional.

Details
These functions only work with GBIF registry data, and do so via the OAI-PMH protocol (https://www.openarchives.org/OAI/

Value
raw text, list or data.frame, depending on requested output via as parameter

Examples
## Not run:
gbif_oai_identify()

today <- format(Sys.Date(), "%Y-%m-%d")

gbif_oai_list_identifiers(from = today)
gbif_oai_list_identifiers(set = "country:NL")

gbif_oai_list_records(from = today)
gbif_oai_list_records(set = "country:NL")

gbif_oai_list_metadataformats()
gbif_oai_list_metadataformats(id = "9c4e36c1-d3f9-49ce-8ec1-8c434fa9e6eb")

gbif_oai_list_sets()
gbif_oai_list_sets(as = "list")

gbif_oai_get_records("9c4e36c1-d3f9-49ce-8ec1-8c434fa9e6eb")
ids <- c("9c4e36c1-d3f9-49ce-8ec1-8c434fa9e6eb",
"e0f1bb8a-2d81-4b2a-9194-d92848d3b82e")
gbif_oai_get_records(ids)

## End(Not run)

gbif_photos View photos from GBIF.

Description
View photos from GBIF.

Usage
gbif_photos(input, output = NULL, which = "table", browse = TRUE)
38 installations

Arguments
input Input output from occ_search
output Output folder path. If not given uses temporary folder.
which One of map or table (default).
browse (logical) Browse output (default: TRUE)

Details
The max number of photos you can see when which="map" is ~160, so cycle through if you have
more than that.

BEWARE
The maps in the table view may not show up correctly if you are using RStudio

Examples
## Not run:
res <- occ_search(mediaType = 'StillImage', limit = 100)
gbif_photos(res)
gbif_photos(res, which='map')

res <- occ_search(scientificName = "Aves", mediaType = 'StillImage',

limit=150)
gbif_photos(res)
gbif_photos(res, output = '~/barfoo')

## End(Not run)

installations Installations metadata.

Description
Installations metadata.

Usage
installations(
data = "all",
uuid = NULL,
query = NULL,
identifier = NULL,
identifierType = NULL,
limit = 100,
start = NULL,
curlopts = list()
)
installations 39

Arguments

data The type of data to get. One or more of: ’contact’, ’endpoint’, ’dataset’, ’com-
ment’, ’deleted’, ’nonPublishing’, or the special ’all’. Default: 'all'
uuid UUID of the data node provider. This must be specified if data is anything other
than ’all’.
query Query nodes. Only used when data='all'. Ignored otherwise.
identifier The value for this parameter can be a simple string or integer, e.g. identifier=120.
This parameter doesn’t seem to work right now.
identifierType Used in combination with the identifier parameter to filter identifiers by identi-
fier type. See details. This parameter doesn’t seem to work right now.
limit Number of records to return. Default: 100. Maximum: 1000.
start Record number to start at. Default: 0. Use in combination with limit to page
through results.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Details

identifierType options:

• DOI No description.
• FTP No description.
• GBIF_NODE Identifies the node (e.g: DK for Denmark, sp2000 for Species 2000).
• GBIF_PARTICIPANT Participant identifier from the GBIF IMS Filemaker system.
• GBIF_PORTAL Indicates the identifier originated from an auto_increment column in the por-
tal.data_provider or portal.data_resource table respectively.
• HANDLER No description.
• LSID Reference controlled by a separate system, used for example by DOI.
• SOURCE_ID No description.
• UNKNOWN No description.
• URI No description.
• URL No description.
• UUID No description.

References

https://www.gbif.org/developer/registry#installations
40 lit_search

Examples
## Not run:
installations(limit=5)
installations(query="france", limit = 25)
installations(uuid="b77901f9-d9b0-47fa-94e0-dd96450aa2b4")
installations(data='contact', uuid="2e029a0c-87af-42e6-87d7-f38a50b78201")
installations(data='endpoint', uuid="b77901f9-d9b0-47fa-94e0-dd96450aa2b4")
installations(data='dataset', uuid="b77901f9-d9b0-47fa-94e0-dd96450aa2b4")
installations(data='deleted', limit = 25)
installations(data='deleted', limit=2)
installations(data=c('deleted','nonPublishing'), limit=2)
installations(identifierType='DOI', limit=2)

# Pass on curl options

installations(data='deleted', curlopts = list(verbose=TRUE))

## End(Not run)

lit_search Search for literature that cites GBIF mediated data

Description
Search for literature that cites GBIF mediated data

Usage
lit_search(
q = NULL,
countriesOfResearcher = NULL,
countriesOfCoverage = NULL,
literatureType = NULL,
relevance = NULL,
year = NULL,
topics = NULL,
datasetKey = NULL,
publishingOrg = NULL,
peerReview = NULL,
openAccess = NULL,
downloadKey = NULL,
doi = NULL,
journalSource = NULL,
journalPublisher = NULL,
flatten = TRUE,
limit = NULL,
curlopts = list()
)

lit_count(...)
lit_search 41

Arguments
q (character) Simple full text search parameter. The value for this parameter can
be a simple word or a phrase. Wildcards are not supported.
countriesOfResearcher
(character) Country of institution with which author is affiliated, e.g. DK (for
Denmark). Country codes are listed in enumeration_country().
countriesOfCoverage
(character) Country of focus of study, e.g. BR (for Brazil). Country codes are
listed in enumeration_country().
literatureType (character) Type of literature ("JOURNAL", "BOOK_SECTION", "WORK-
ING_PAPER", "REPORT", "GENERIC", "THESIS", "CONFERENCE_PROCEEDINGS",
"WEB_PAGE").
relevance (character) How is the publication relate to GBIF. See details ("GBIF_USED",
"GBIF_MENTIONED", "GBIF_PUBLISHED", "GBIF_CITED", "GBIF_CITED",
"GBIF_PUBLISHED", "GBIF_ACKNOWLEDGED", "GBIF_AUTHOR").
year (integer) Year of publication.
topics (character) Topic of publication.
datasetKey (character) GBIF dataset uuid referenced in publication.
publishingOrg (character) Publisher uuid whose dataset is referenced in publication.
peerReview (logical) Has publication undergone peer-review?
openAccess (logical) Is publication Open Access?
downloadKey (character) Download referenced in publication.
doi (character) Digital Object Identifier (DOI).
journalSource (character) Journal of publication.
journalPublisher
(character) Publisher of journal.
flatten (logical) should any lists in the resulting data be flattened into comma-seperated
strings?
limit how many records to return. limit=NULL will fetch up to 10,000.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options for
curl options.
... additional parameters passed to lit_search

Details
This function enables you to search for literature indexed by GBIF, including peer-reviewed papers,
citing GBIF datasets and downloads. The literature API powers the literature search on GBIF.
The GBIF Secretariat maintains an ongoing literature tracking programme, which identifies research
uses and citations of biodiversity information accessed through GBIF’s global infrastructure.
In the literature database, relevance refers to how publications relate to GBIF following these defi-
nitions:
42 lit_search

• GBIF_USED : makes substantive use of data in a quantitative analysis (e.g. ecological niche
modelling)
• GBIF_CITED : cites a qualitative fact derived in data (e.g. a given species is found in a given
country)
• GBIF_DISCUSSED : discusses GBIF as an infrastructure or the use of data
• GBIF_PRIMARY : GBIF is the primary source of data (no longer applied)
• GBIF_ACKNOWLEDGED : acknowledges GBIF (but doesn’t use or cite data)
• GBIF_PUBLISHED : describes or talks about data published to GBIF
• GBIF_AUTHOR : authored by GBIF staff
• GBIF_MENTIONED : unspecifically mentions GBIF or the GBIF portal
• GBIF_FUNDED : funded by GBIF or a GBIF-managed funding programme

The following arguments can take multiple values:

• relevance
• countriesOfResearcher
• countriesOfCoverage
• literatureType
• topics
• datasetKey
• publishingOrg
• downloadKey
• doi
• journalSource
• journalPublisher

If flatten=TRUE, then data will be returned as flat data.frame with no complex column types (i.e.
no lists or data.frames).
limit=NULL will return up to 10,000 records. The maximum value for limit is 10,000. If no filters
are used, only the first 1,000 records will be returned, limit must be explicitly set to limit=10000,
to get the first 10,000 records in this case.
lit_count() is a convenience wrapper, which will return the number of literature references for a
certain lit_search() query. This is the same as running lit_search()$meta$count.

Value

A named list with two values: $data and $meta. $data is a data.frame of literature references.
map_fetch 43

Examples
## Not run:
lit_search(q="bats")$data
lit_search(datasetKey="50c9509d-22c7-4a22-a47d-8c48425ef4a7")
lit_search(year=2020)
lit_search(year="2011,2020") # year ranges
lit_search(relevance=c("GBIF_CITED","GBIF_USED")) # multiple values
lit_search(relevance=c("GBIF_USED","GBIF_CITED"),
topics=c("EVOLUTION","PHYLOGENETICS"))
lit_count() # total number of literature referencing GBIF
lit_count(peerReview=TRUE)
# number of citations of iNaturalist
lit_count(datasetKey="50c9509d-22c7-4a22-a47d-8c48425ef4a7")
# number of peer-reviewed articles used GBIF mediated data
lit_count(peerReview=TRUE,literatureType="JOURNAL",relevance="GBIF_USED")

# Typically what is meant by "literature that uses GBIF"

lit_search(peerReview=TRUE,literatureType="JOURNAL",relevance="GBIF_USED")
lit_count(peerReview=TRUE,literatureType="JOURNAL",relevance="GBIF_USED")

## End(Not run)

map_fetch Fetch maps of GBIF occurrences

Description
This function is a wrapper for the GBIF mapping api version 2.0. The mapping API is a web map
tile service making it straightforward to visualize GBIF content on interactive maps, and overlay
content from other sources. It returns tile maps with number of GBIF records per area unit that can
be used in a variety of ways, for example in interactive leaflet web maps. Map details are specified
by a number of query parameters, some of them optional. Full documentation of the GBIF mapping
api can be found at https://www.gbif.org/developer/maps

Usage
map_fetch(
source = "density",
x = 0:1,
y = 0,
z = 0,
format = "@1x.png",
srs = "EPSG:4326",
bin = NULL,
hexPerTile = NULL,
squareSize = NULL,
style = NULL,
taxonKey = NULL,
44 map_fetch

datasetKey = NULL,
country = NULL,
publishingOrg = NULL,
publishingCountry = NULL,
year = NULL,
basisOfRecord = NULL,
return = "png",
base_style = NULL,
plot_terra = TRUE,
curlopts = list(http_version = 2),
...
)

Arguments
source (character) Either density for fast, precalculated tiles, or adhoc for any search.
Default: density
x (integer sequence) the column. Default: 0:1
y (integer sequence) the row. Default: 0
z (integer) the zoom. Default: 0
format (character) The data format, one of:
• @Hx.png for a 256px raster tile
• @1x.png for a 512px raster tile (the default)
• @2x.png for a 1024px raster tile
• @3x.png for a 2048px raster tile
• @4x.png for a 4096px raster tile
srs (character) Spatial reference system. One of:
• EPSG:3857 (Web Mercator)
• EPSG:4326 (WGS84 plate care?)
• EPSG:3575 (Arctic LAEA on 10 degrees E)
• EPSG:3031 (Antarctic stereographic)
bin (character) square or hex to aggregate occurrence counts into squares or hexagons.
Points by default.
hexPerTile (integer) sets the size of the hexagons (the number horizontally across a tile).
squareSize (integer) sets the size of the squares. Choose a factor of 4096 so they tessalate
correctly: probably from 8, 16, 32, 64, 128, 256, 512.
style (character) for raster tiles, choose from the available styles. Defaults to clas-
sic.point for source="density" and "scaled.circle" for source="adhoc".
taxonKey (integer/numeric/character) search by taxon key, can only supply 1.
datasetKey (character) search by taxon key, can only supply 1.
country (character) search by taxon key, can only supply 1.
publishingOrg (character) search by taxon key, can only supply 1.
map_fetch 45

publishingCountry
(character) search by taxon key, can only supply 1.
year (integer) integer that limits the search to a certain year or, if passing a vec-
tor of integers, multiple years, for example 1984 or c(2016, 2017, 2018) or
2010:2015 (years 2010 to 2015). optional
basisOfRecord (character) one or more basis of record states to include records with that ba-
sis of record. The full list is: c("OBSERVATION", "HUMAN_OBSERVATION",
"MACHINE_OBSERVATION", "MATERIAL_SAMPLE", "PRESERVED_SPECIMEN", "FOSSIL_SPECIMEN",
"LIVING_SPECIMEN", "LITERATURE", "UNKNOWN").
return (character) Either "png" or "terra".
base_style (character) The style of the base map.
plot_terra (logical) Set whether the terra map be default plotted.
curlopts options passed on to crul::HttpClient
... additional arguments passed to the adhoc interface.

Details
The default settings, return='png', will return a magick-image png. This image will be a com-
posite image of the the occurrence tiles fetched and a base map. This map is primarily useful as a
high quality image of occurrence records.
The args x and y can both be integer sequences. For example, x=0:3 or y=0:1. Note that the tile
index starts at 0. Higher values of z, will will produce more tiles that can be fetched and stitched
together. Selecting a too high value for x or y will produce a blank image.
Setting return='terra' will return a terra::SpatRaster object. This is primarily useful if you
were interested in the underlying aggregated occurrence density data.
See the article

Value
a magick-image or terra::SpatRaster object.

Author(s)
John Waller and Laurens Geffert <[email protected]>

References
https://www.gbif.org/developer/maps
https://api.gbif.org/v2/map/demo.html
https://api.gbif.org/v2/map/demo13.html

See Also
mvt_fetch()
46 mvt_fetch

Examples
## Not run:

# all occurrences
map_fetch()
# get artic map
map_fetch(srs='EPSG:3031')
# only preserved specimens
map_fetch(basisOfRecord="PRESERVED_SPECIMEN")

# Map of occ in Great Britain

map_fetch(z=3,y=1,x=7:8,country="GB")
# Peguins with artic projection
map_fetch(srs='EPSG:3031',taxonKey=2481660,style='glacier.point',
base_style="gbif-dark")

# occ from a long time ago

map_fetch(year=1600)
# polygon style
map_fetch(style="iNaturalist.poly",bin="hex")
# iNaturalist dataset plotted
map_fetch(datasetKey="50c9509d-22c7-4a22-a47d-8c48425ef4a7",
style="iNaturalist.poly")

# use source="adhoc" for more filters

map_fetch(z=1,
source="adhoc",
iucn_red_list_category="CR",
style="scaled.circles",
base_style='gbif-light')

# cropped map of Hawaii

map_fetch(z=5,x=3:4,y=12,source="adhoc",gadmGid="USA.12_1")

## End(Not run)

mvt_fetch Fetch Map Vector Tiles (MVT)

Description
This function is a wrapper for the GBIF mapping api version 2.0. The mapping API is a web map
tile service making it straightforward to visualize GBIF content on interactive maps, and overlay
content from other sources. It returns maps vector tiles with number of GBIF records per area unit
that can be used in a variety of ways, for example in interactive leaflet web maps. Map details are
specified by a number of query parameters, some of them optional. Full documentation of the GBIF
mapping api can be found at https://www.gbif.org/developer/maps
mvt_fetch 47

Usage
mvt_fetch(
source = "density",
x = 0,
y = 0,
z = 0,
srs = "EPSG:4326",
bin = NULL,
hexPerTile = NULL,
squareSize = NULL,
style = "classic.point",
taxonKey = NULL,
datasetKey = NULL,
country = NULL,
publishingOrg = NULL,
publishingCountry = NULL,
year = NULL,
basisOfRecord = NULL,
...
)

Arguments
source (character) Either density for fast, precalculated tiles, or adhoc for any search.
Default: density
x (integer) the column. Default: 0
y (integer) the row. Default: 0
z (integer) the zoom. Default: 0
srs (character) Spatial reference system for the output (input srs for mvt from GBIF
is always EPSG:3857). One of:
• EPSG:3857 (Web Mercator)
• EPSG:4326 (WGS84 plate care?)
• EPSG:3575 (Arctic LAEA on 10 degrees E)
• EPSG:3031 (Antarctic stereographic)
bin (character) square or hex to aggregate occurrence counts into squares or hexagons.
Points by default. optional
hexPerTile (integer) sets the size of the hexagons (the number horizontally across a tile).
optional
squareSize (integer) sets the size of the squares. Choose a factor of 4096 so they tessalate
correctly: probably from 8, 16, 32, 64, 128, 256, 512. optional
style (character) for raster tiles, choose from the available styles. Defaults to clas-
sic.point. optional. THESE DON’T WORK YET.
taxonKey (integer/numeric/character) search by taxon key, can only supply 1. optional
datasetKey (character) search by taxon key, can only supply 1. optional
48 mvt_fetch

country (character) search by taxon key, can only supply 1. optional

publishingOrg (character) search by taxon key, can only supply 1. optional
publishingCountry
(character) search by taxon key, can only supply 1. optional
year (integer) integer that limits the search to a certain year or, if passing a vec-
tor of integers, multiple years, for example 1984 or c(2016, 2017, 2018) or
2010:2015 (years 2010 to 2015). optional
basisOfRecord (character) one or more basis of record states to include records with that ba-
sis of record. The full list is: c("OBSERVATION", "HUMAN_OBSERVATION",
"MACHINE_OBSERVATION", "MATERIAL_SAMPLE", "PRESERVED_SPECIMEN", "FOSSIL_SPECIMEN",
"LIVING_SPECIMEN", "LITERATURE", "UNKNOWN"). optional
... curl options passed on to crul::HttpClient

Details
This function uses the arguments passed on to generate a query to the GBIF web map API. The API
returns a web tile object as png that is read and converted into an R raster object. The break values
or nbreaks generate a custom colour palette for the web tile, with each bin corresponding to one
grey value. After retrieval, the raster is reclassified to the actual break values. This is a somewhat
hacky but nonetheless functional solution in the absence of a GBIF raster API implementation.
We add extent and set the projection for the output. You can reproject after retrieving the output.

Value
an sf object

References
https://www.gbif.org/developer/maps

See Also
map_fetch()

Examples
## Not run:
if (
requireNamespace("sf", quietly = TRUE) &&
requireNamespace("protolite", quietly = TRUE)
) {
x <- mvt_fetch(taxonKey = 2480498, year = 2007:2011)
x

# gives an sf object
class(x)

# different srs
## 3857
name_backbone 49

y <- mvt_fetch(taxonKey = 2480498, year = 2010, srs = "EPSG:3857")

y
## 3031
z <- mvt_fetch(taxonKey = 2480498, year = 2010, srs = "EPSG:3031", verbose = TRUE)
z
# 3575
z <- mvt_fetch(taxonKey = 2480498, year = 2010, srs = "EPSG:3575")
z

# bin
x <- mvt_fetch(taxonKey = 212, year = 1998, bin = "hex",
hexPerTile = 30, style = "classic-noborder.poly")
x

# query with basisOfRecord

mvt_fetch(taxonKey = 2480498, year = 2010,
basisOfRecord = "HUMAN_OBSERVATION")
mvt_fetch(taxonKey = 2480498, year = 2010,
basisOfRecord = c("HUMAN_OBSERVATION", "LIVING_SPECIMEN"))
}

## End(Not run)

name_backbone Lookup names in the GBIF backbone taxonomy.

Description
Lookup names in the GBIF backbone taxonomy.

Usage
name_backbone(
name,
rank = NULL,
kingdom = NULL,
phylum = NULL,
class = NULL,
order = NULL,
family = NULL,
genus = NULL,
strict = FALSE,
verbose = FALSE,
start = NULL,
limit = 100,
curlopts = list()
)

name_backbone_verbose(
50 name_backbone

name,
rank = NULL,
kingdom = NULL,
phylum = NULL,
class = NULL,
order = NULL,
family = NULL,
genus = NULL,
strict = FALSE,
start = NULL,
limit = 100,
curlopts = list()
)

Arguments
name (character) Full scientific name potentially with authorship (required)
rank (character) The rank given as our rank enum. (optional)
kingdom (character) If provided default matching will also try to match against this if no
direct match is found for the name alone. (optional)
phylum (character) If provided default matching will also try to match against this if no
direct match is found for the name alone. (optional)
class (character) If provided default matching will also try to match against this if no
direct match is found for the name alone. (optional)
order (character) If provided default matching will also try to match against this if no
direct match is found for the name alone. (optional)
family (character) If provided default matching will also try to match against this if no
direct match is found for the name alone. (optional)
genus (character) If provided default matching will also try to match against this if no
direct match is found for the name alone. (optional)
strict (logical) If TRUE it (fuzzy) matches only the given name, but never a taxon in the
upper classification (optional)
verbose (logical) should the function give back more (less reliable) results. See function
name_backbone_verbose()
start Record number to start at. Default: 0. Use in combination with limit to page
through results.
limit Number of records to return. Default: 100. Maximum: 1000.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Details
If you don’t get a match, GBIF gives back a data.frame with columns synonym, confidence, and
matchType='NONE'.
name_backbone_checklist 51

Value
For name_backbone, a data.frame for a single taxon with many columns. For name_backbone_verbose,
a larger number of results in a data.frame the results of resulting from fuzzy matching. You will
also get back your input name, rank, kingdom, phylum ect. as columns input_name, input_rank,
input_kingdom ect. so you can check the results.

References
https://www.gbif.org/developer/species#searching

Examples
## Not run:
name_backbone(name='Helianthus annuus', kingdom='plants')
name_backbone(name='Helianthus', rank='genus', kingdom='plants')
name_backbone(name='Poa', rank='genus', family='Poaceae')

# Verbose - gives back alternatives

## Strictness
name_backbone_verbose(name='Poa', kingdom='plants',
strict=FALSE)
name_backbone_verbose(name='Helianthus annuus', kingdom='plants',
strict=TRUE)

# Non-existent name - returns list of lenght 3 stating no match

name_backbone(name='Aso')
name_backbone(name='Oenante')

# Pass on curl options

name_backbone(name='Oenante', curlopts = list(verbose=TRUE))

## End(Not run)

name_backbone_checklist
Lookup names in the GBIF backbone taxonomy in a checklist.

Description
Lookup names in the GBIF backbone taxonomy in a checklist.

Usage
name_backbone_checklist(
name_data = NULL,
rank = NULL,
kingdom = NULL,
phylum = NULL,
52 name_backbone_checklist

class = NULL,
order = NULL,
family = NULL,
genus = NULL,
strict = FALSE,
verbose = FALSE,
curlopts = list()
)

Arguments
name_data (data.frame or vector) see details.
rank (character) default value (optional).
kingdom (character) default value (optional).
phylum (character) default value (optional).
class (character) default value (optional).
order (character) default value (optional).
family (character) default value (optional).
genus (character) default value (optional).
strict (logical) strict=TRUE will not attempt to fuzzy match or return higherrankmatches.
verbose (logical) If true it shows alternative matches which were considered but then
rejected.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Details
This function is an alternative for name_backbone(), which will work with a list of names (a vector
or a data.frame). The data.frame should have the following column names, but only the ’name’
column is required. If only one column is present, then that column is assumed to be the ’name’
column.
• name : (required)
• rank : (optional)
• kingdom : (optional)
• phylum : (optional)
• class : (optional)
• order : (optional)
• family : (optional)
• genus : (optional)
The input columns will be returned as "verbatim_name","verbatim_rank", "verbatim_phylum" ect.
A column of "verbatim_index" will also be returned giving the index of the input.
The following aliases for the ’name’ column will work (any case or with ’_’ will work) :
name_backbone_checklist 53

• "scientificName", "ScientificName", "scientific_name" ...

• "sci_name", "sciname", "SCI_NAME" ...
• "names", "NAMES" ...
• "species", "SPECIES" ...
• "species_name", "speciesname" ...
• "sp_name", "SP_NAME", "spname" ...
• "taxon_name", "taxonname", "TAXON NAME" ...
If more than one aliases is present and no column is named ’name’, then the left-most column with
an acceptable aliased name above is used.
If verbose=TRUE, a column called is_alternative will be returned, which species if a name was
originally a first choice or not. is_alternative=TRUE means the name was not is not considered
to be the best match by GBIF.
Default values for rank, kingdom, phylum, class, order, family, and genus can can be supplied. If a
default value is supplied, the values for these fields are ignored in name_data, and the default value
is used instead. This is most useful if you have a list of names and you know they are all plants,
insects, birds, ect. You can also input multiple values, if they are the same length as list of names
you are trying to match.
This function can also be used with a character vector of names. In that case no column names are
needed of course.
This function is very similar to the GBIF species-lookup tool. https://www.gbif.org/tools/species-
lookup.
If you have 1000s of names to match, it can take some minutes to get back all of the matches. I
have tested it with 60K names. Scientific names with author details usually get better matches.
See also article Working With Taxonomic Names.

Value
A data.frame of matched names.

Examples
## Not run:

library(rgbif)

name_data <- data.frame(

scientificName = c(
"Cirsium arvense (L.) Scop.", # a plant
"Calopteryx splendens (Harris, 1780)", # an insect
"Puma concolor (Linnaeus, 1771)", # a big cat
"Ceylonosticta alwisi (Priyadarshana & Wijewardhane, 2016)", # newly discovered insect
"Puma concuolor (Linnaeus, 1771)", # a mis-spelled big cat
"Fake species (John Waller 2021)", # a fake species
"Calopteryx" # Just a Genus
), description = c(
"a plant",
54 name_issues

"an insect",
"a big cat",
"newly discovered insect",
"a mis-spelled big cat",
"a fake species",
"just a GENUS"
),
kingdom = c(
"Plantae",
"Animalia",
"Animalia",
"Animalia",
"Animalia",
"Johnlia",
"Animalia"
))

name_backbone_checklist(name_data)

# return more than 1 result per name

name_backbone_checklist(name_data,verbose=TRUE)

# works with just vectors too

name_list <- c(
"Cirsium arvense (L.) Scop.",
"Calopteryx splendens (Harris, 1780)",
"Puma concolor (Linnaeus, 1771)",
"Ceylonosticta alwisi (Priyadarshana & Wijewardhane, 2016)",
"Puma concuolor",
"Fake species (John Waller 2021)",
"Calopteryx")

name_backbone_checklist(name_list)
name_backbone_checklist(name_list,verbose=TRUE)
name_backbone_checklist(name_list,strict=TRUE)

# default values
name_backbone_checklist(c("Aloe arborecens Mill.",
"Cirsium arvense (L.) Scop."),kingdom="Plantae")
name_backbone_checklist(c("Aloe arborecens Mill.",
"Calopteryx splendens (Harris, 1780)"),kingdom=c("Plantae","Animalia"))

## End(Not run)

name_issues Parse and examine further GBIF name issues on a dataset.

Description
Parse and examine further GBIF name issues on a dataset.
name_issues 55

Usage
name_issues(.data, ..., mutate = NULL)

Arguments
.data Output from a call to name_usage()
... Named parameters to only get back (e.g. bbmn), or to remove (e.g. -bbmn).
mutate (character) One of:
• split Split issues into new columns.
• expand Expand issue abbreviated codes into descriptive names. for down-
loads datasets, this is not super useful since the issues come to you as ex-
panded already.
• split_expand Split into new columns, and expand issue names.
For split and split_expand, values in cells become y ("yes") or n ("no")

References
https://gbif.github.io/gbif-api/apidocs/org/gbif/api/vocabulary/NameUsageIssue.
html

Examples
## Not run:
# what do issues mean, can print whole table
head(gbif_issues())
# or just name related issues
gbif_issues()[which(gbif_issues()$type %in% c("name")),]
# or search for matches
gbif_issues()[gbif_issues()$code %in% c('bbmn','clasna','scina'),]
# compare out data to after name_issues use
(aa <- name_usage(name = "Lupus"))
aa %>% name_issues("clasna")

## or parse issues in various ways

### remove data rows with certain issue classes
aa %>% name_issues(-clasna, -scina)

### expand issues to more descriptive names

aa %>% name_issues(mutate = "expand")

### split and expand

aa %>% name_issues(mutate = "split_expand")

### split, expand, and remove an issue class

aa %>% name_issues(-bbmn, mutate = "split_expand")

## Or you can use name_issues without %>%

name_issues(aa, -bbmn, mutate = "split_expand")

## End(Not run)
56 name_lookup

name_lookup Lookup names in all taxonomies in GBIF.

Description
This service uses fuzzy lookup so that you can put in partial names and you should get back those
things that match. See examples below.
Faceting: If facet=FALSE or left to the default (NULL), no faceting is done. And therefore, all
parameters with facet in their name are ignored (facetOnly, facetMincount, facetMultiselect).

Usage
name_lookup(
query = NULL,
rank = NULL,
higherTaxonKey = NULL,
status = NULL,
isExtinct = NULL,
habitat = NULL,
nameType = NULL,
datasetKey = NULL,
origin = NULL,
nomenclaturalStatus = NULL,
limit = 100,
start = 0,
facet = NULL,
facetMincount = NULL,
facetMultiselect = NULL,
type = NULL,
hl = NULL,
issue = NULL,
constituentKey = NULL,
verbose = FALSE,
return = NULL,
curlopts = list()
)

Arguments
query Query term(s) for full text search.
rank CLASS, CULTIVAR, CULTIVAR_GROUP, DOMAIN, FAMILY, FORM, GENUS,
INFORMAL, INFRAGENERIC_NAME, INFRAORDER, INFRASPECIFIC_NAME,
INFRASUBSPECIFIC_NAME, KINGDOM, ORDER, PHYLUM, SECTION,
SERIES, SPECIES, STRAIN, SUBCLASS, SUBFAMILY, SUBFORM, SUB-
GENUS, SUBKINGDOM, SUBORDER, SUBPHYLUM, SUBSECTION, SUB-
SERIES, SUBSPECIES, SUBTRIBE, SUBVARIETY, SUPERCLASS, SUPER-
name_lookup 57

FAMILY, SUPERORDER, SUPERPHYLUM, SUPRAGENERIC_NAME, TRIBE,

UNRANKED, VARIETY
higherTaxonKey Filters by any of the higher Linnean rank keys. Note this is within the respec-
tive checklist and not searching nub keys across all checklists. This parameter
accepts many inputs in a vector ( passed in the same request).
status Filters by the taxonomic status as one of:
• ACCEPTED
• DETERMINATION_SYNONYM Used for unknown child taxa referred to
via spec, ssp, ...
• DOUBTFUL Treated as accepted, but doubtful whether this is correct.
• HETEROTYPIC_SYNONYM More specific subclass of SYNONYM.
• HOMOTYPIC_SYNONYM More specific subclass of SYNONYM.
• INTERMEDIATE_RANK_SYNONYM Used in nub only.
• MISAPPLIED More specific subclass of SYNONYM.
• PROPARTE_SYNONYM More specific subclass of SYNONYM.
• SYNONYM A general synonym, the exact type is unknown.
isExtinct (logical) Filters by extinction status (e.g. isExtinct=TRUE)
habitat (character) Filters by habitat. One of: marine, freshwater, or terrestrial
nameType Filters by the name type as one of:
• BLACKLISTED surely not a scientific name.
• CANDIDATUS Candidatus is a component of the taxonomic name for a
bacterium that cannot be maintained in a Bacteriology Culture Collection.
• CULTIVAR a cultivated plant name.
• DOUBTFUL doubtful whether this is a scientific name at all.
• HYBRID a hybrid formula (not a hybrid name).
• INFORMAL a scientific name with some informal addition like "cf." or
indetermined like Abies spec.
• SCINAME a scientific name which is not well formed.
• VIRUS a virus name.
• WELLFORMED a well formed scientific name according to present nomen-
clatural rules.
datasetKey Filters by the dataset’s key (a uuid)
origin (character) Filters by origin. One of:
• SOURCE
• DENORMED_CLASSIFICATION
• VERBATIM_ACCEPTED
• EX_AUTHOR_SYNONYM
• AUTONYM
• BASIONYM_PLACEHOLDER
• MISSING_ACCEPTED
• IMPLICIT_NAME
• PROPARTE
58 name_lookup

• VERBATIM_BASIONYM
nomenclaturalStatus
Not yet implemented, but will eventually allow for filtering by a nomenclatural
status enum.
limit Number of records to return. Hard maximum limit set by GBIF API: 99999.
start Record number to start at. Default: 0.
facet A vector/list of facet names used to retrieve the 100 most frequent values for a
field. Allowed facets are: datasetKey, higherTaxonKey, rank, status, isExtinct,
habitat, and nameType. Additionally threat and nomenclaturalStatus are legal
values but not yet implemented, so data will not yet be returned for them.
facetMincount Used in combination with the facet parameter. Set facetMincount to exclude
facets with a count less than x, e.g. http://bit.ly/2osAUQB only shows the
type values ’CHECKLIST’ and ’OCCURRENCE’ because the other types have
counts less than 10000
facetMultiselect
(logical) Used in combination with the facet parameter. Set facetMultiselect=TRUE
to still return counts for values that are not currently filtered, e.g. http://bit.ly/2JAymaC
still shows all type values even though type is being filtered by type=CHECKLIST.
type Type of name. One of occurrence, checklist, or metadata.
hl (logical) Set hl=TRUE to highlight terms matching the query when in fulltext
search fields. The highlight will be an emphasis tag of class gbifH1 e.g. query='plant',
hl=TRUE. Fulltext search fields include: title, keyword, country, publishing coun-
try, publishing organization title, hosting organization title, and description. One
additional full text field is searched which includes information from metadata
documents, but the text of this field is not returned in the response.
issue Filters by issue. Issue has to be related to names. Type gbif_issues() to get
complete list of issues.
constituentKey Filters by the dataset’s constituent key (a uuid).
verbose (logical) If TRUE, all data is returned as a list for each element. If FALSE (de-
fault) a subset of the data that is thought to be most essential is organized into a
data.frame.
return Defunct. All components are returned; index to the one(s) you want
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Value
An object of class gbif, which is a S3 class list, with slots for metadata (meta), the data itself
(data), the taxonomic hierarchy data (hierarchies), and vernacular names (names). In addition,
the object has attributes listing the user supplied arguments and type of search, which is, differently
from occurrence data, always equals to ’single’ even if multiple values for some parameters are
given. meta is a list of length four with offset, limit, endOfRecords and count fields. data is a
tibble (aka data.frame) containing all information about the found taxa. hierarchies is a list of
data.frame’s, one per GBIF key (taxon), containing its taxonomic classification. Each data.frame
contains two columns: rankkey and name. names returns a list of data.frame’s, one per GBIF key
name_lookup 59

(taxon), containing all vernacular names. Each data.frame contains two columns: vernacularName
and language.
A list of length five:

• metadata
• data: either a data.frame (verbose=FALSE, default) or a list (verbose=TRUE).
• facets
• hierarchies
• names

Repeat parameter inputs

Some parameters can take many inputs, and treated as ’OR’ (e.g., a or b or c). The following take
many inputs:

• rank
• higherTaxonKey
• status
• habitat
• nameType
• datasetKey
• origin

References
https://www.gbif.org/developer/species#searching

Examples
## Not run:
# Look up names like mammalia
name_lookup(query='mammalia', limit = 20)

# Start with an offset

name_lookup(query='mammalia', limit=1)
name_lookup(query='mammalia', limit=1, start=2)

# large requests (paging is internally implemented).

# hard maximum limit set by GBIF API: 99999
# name_lookup(query = "Carnivora", limit = 10000)

# Get all data and parse it, removing descriptions which can be quite long
out <- name_lookup('Helianthus annuus', rank="species", verbose=TRUE)
lapply(out$data, function(x) {
x[!names(x) %in% c("descriptions","descriptionsSerialized")]
})

# Search for a genus

60 name_lookup

name_lookup(query="Cnaemidophorus", rank="genus")
# Limit records to certain number
name_lookup('Helianthus annuus', rank="species", limit=2)

# Query by habitat
name_lookup(habitat = "terrestrial", limit=2)
name_lookup(habitat = "marine", limit=2)
name_lookup(habitat = "freshwater", limit=2)

# Using faceting
name_lookup(facet='status', limit=0, facetMincount='70000')
name_lookup(facet=c('status','higherTaxonKey'), limit=0,
facetMincount='700000')

name_lookup(facet='nameType', limit=0)
name_lookup(facet='habitat', limit=0)
name_lookup(facet='datasetKey', limit=0)
name_lookup(facet='rank', limit=0)
name_lookup(facet='isExtinct', limit=0)

name_lookup(isExtinct=TRUE, limit=0)

# text highlighting
## turn on highlighting
res <- name_lookup(query='canada', hl=TRUE, limit=5)
res$data
name_lookup(query='canada', hl=TRUE, limit=45)
## and you can pass the output to gbif_names() function
res <- name_lookup(query='canada', hl=TRUE, limit=5)
gbif_names(res)

# Lookup by datasetKey (set up sufficient high limit, API maximum: 99999)

# name_lookup(datasetKey='3f8a1297-3259-4700-91fc-acc4170b27ce',
# limit = 50000)

# Some parameters accept many inputs, treated as OR

name_lookup(rank = c("family", "genus"))
name_lookup(higherTaxonKey = c("119", "120", "121", "204"))
name_lookup(status = c("misapplied", "synonym"))$data
name_lookup(habitat = c("marine", "terrestrial"))
name_lookup(nameType = c("cultivar", "doubtful"))
name_lookup(datasetKey = c("73605f3a-af85-4ade-bbc5-522bfb90d847",
"d7c60346-44b6-400d-ba27-8d3fbeffc8a5"))
name_lookup(datasetKey = "289244ee-e1c1-49aa-b2d7-d379391ce265",
origin = c("SOURCE", "DENORMED_CLASSIFICATION"))

# Pass on curl options

name_lookup(query='Cnaemidophorus', rank="genus",
curlopts = list(verbose = TRUE))

## End(Not run)
name_parse 61

name_parse Parse taxon names using the GBIF name parser.

Description
Parse taxon names using the GBIF name parser.

Usage
name_parse(scientificname, curlopts = list())

Arguments
scientificname A character vector of scientific names.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Value
A data.frame containing fields extracted from parsed taxon names. Fields returned are the union
of fields extracted from all species names in scientificname.

Author(s)
John Baumgartner ([email protected])

References
https://www.gbif.org/developer/species#parser

Examples
## Not run:
name_parse(scientificname='x Agropogon littoralis')
name_parse(c('Arrhenatherum elatius var. elatius',
'Secale cereale subsp. cereale', 'Secale cereale ssp. cereale',
'Vanessa atalanta (Linnaeus, 1758)'))
name_parse("Ajuga pyramidata")
name_parse("Ajuga pyramidata x reptans")

# Pass on curl options

# res <- name_parse(c('Arrhenatherum elatius var. elatius',
# 'Secale cereale subsp. cereale', 'Secale cereale ssp. cereale',
# 'Vanessa atalanta (Linnaeus, 1758)'), curlopts=list(verbose=TRUE))

## End(Not run)
62 name_suggest

name_suggest Suggest up to 20 name usages.

Description
A quick and simple autocomplete service that returns up to 20 name usages by doing prefix match-
ing against the scientific name. Results are ordered by relevance.

Usage
name_suggest(
q = NULL,
datasetKey = NULL,
rank = NULL,
fields = NULL,
start = NULL,
limit = 100,
curlopts = list()
)

Arguments
q (character, required) Simple search parameter. The value for this parameter can
be a simple word or a phrase. Wildcards can be added to the simple word pa-
rameters only, e.g. q=puma
datasetKey (character) Filters by the checklist dataset key (a uuid, see examples)
rank (character) A taxonomic rank. One of class, cultivar, cultivar_group, domain,
family, form, genus, informal, infrageneric_name, infraorder, infraspecific_name,
infrasubspecific_name, kingdom, order, phylum, section, series, species, strain,
subclass, subfamily, subform, subgenus, subkingdom, suborder, subphylum,
subsection, subseries, subspecies, subtribe, subvariety, superclass, superfamily,
superorder, superphylum, suprageneric_name, tribe, unranked, or variety.
fields (character) Fields to return in output data.frame (simply prunes columns off)
start Record number to start at. Default: 0. Use in combination with limit to page
through results.
limit Number of records to return. Default: 100. Maximum: 1000.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Value
A list, with two elements data (tibble) and hierarchy (list of data.frame’s). If ’higherClassifica-
tionMap’ is one of the fields requested, then hierarchy is a list of data.frame’s; if not included,
hierarchy is an empty list.
name_usage 63

Repeat parmeter inputs

Some parameters can take many inputs, and treated as ’OR’ (e.g., a or b or c). The following take
many inputs:

• rank
• datasetKey

References

https://www.gbif.org/developer/species#searching

Examples
## Not run:
name_suggest(q='Puma concolor')
name_suggest(q='Puma')
name_suggest(q='Puma', rank="genus")
name_suggest(q='Puma', rank="subspecies")
name_suggest(q='Puma', rank="species")
name_suggest(q='Puma', rank="infraspecific_name")

name_suggest(q='Puma', limit=2)
name_suggest(q='Puma', fields=c('key','canonicalName'))
name_suggest(q='Puma', fields=c('key','canonicalName',
'higherClassificationMap'))

# Some parameters accept many inputs, treated as OR

name_suggest(rank = c("family", "genus"))
name_suggest(datasetKey = c("73605f3a-af85-4ade-bbc5-522bfb90d847",
"d7c60346-44b6-400d-ba27-8d3fbeffc8a5"))

# If 'higherClassificationMap' in fields, a list is returned

name_suggest(q='Puma', fields=c('key','higherClassificationMap'))

# Pass on curl options

name_suggest(q='Puma', limit=200, curlopts = list(verbose=TRUE))

## End(Not run)

name_usage Lookup details for specific names in all taxonomies in GBIF.

Description

Lookup details for specific names in all taxonomies in GBIF.

64 name_usage

Usage
name_usage(
key = NULL,
name = NULL,
data = "all",
language = NULL,
datasetKey = NULL,
uuid = NULL,
rank = NULL,
shortname = NULL,
start = 0,
limit = 100,
return = NULL,
curlopts = list()
)

Arguments
key (numeric or character) A GBIF key for a taxon
name (character) Filters by a case insensitive, canonical namestring, e.g. ’Puma con-
color’
data (character) Specify an option to select what data is returned. See Description
below.
language (character) Language, default is english
datasetKey (character) Filters by the dataset’s key (a uuid). Must be length=1
uuid (character) A dataset key
rank (character) Taxonomic rank. Filters by taxonomic rank as one of: CLASS, CUL-
TIVAR, CULTIVAR_GROUP, DOMAIN, FAMILY, FORM, GENUS, INFOR-
MAL, INFRAGENERIC_NAME, INFRAORDER, INFRASPECIFIC_NAME,
INFRASUBSPECIFIC_NAME, KINGDOM, ORDER, PHYLUM, SECTION,
SERIES, SPECIES, STRAIN, SUBCLASS, SUBFAMILY, SUBFORM, SUB-
GENUS, SUBKINGDOM, SUBORDER, SUBPHYLUM, SUBSECTION, SUB-
SERIES, SUBSPECIES, SUBTRIBE, SUBVARIETY, SUPERCLASS, SUPER-
FAMILY, SUPERORDER, SUPERPHYLUM, SUPRAGENERIC_NAME, TRIBE,
UNRANKED, VARIETY
shortname (character) A short name for a dataset - it may not do anything
start Record number to start at. Default: 0.
limit Number of records to return. Default: 100.
return Defunct. All components are returned; index to the one(s) you want
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Details
This service uses fuzzy lookup so that you can put in partial names and you should get back those
things that match. See examples below.
name_usage 65

This function is different from name_lookup() in that that function searches for names. This func-
tion encompasses a bunch of API endpoints, most of which require that you already have a taxon
key, but there is one endpoint that allows name searches (see examples below).
Note that data="verbatim" hasn’t been working.
Options for the data parameter are: ’all’, ’verbatim’, ’name’, ’parents’, ’children’, ’related’, ’syn-
onyms’, ’descriptions’,’distributions’, ’media’, ’references’, ’speciesProfiles’, ’vernacularNames’,
’typeSpecimens’, ’root’, ’iucnRedListCategory’
This function used to be vectorized with respect to the data parameter, where you could pass in
multiple values and the function internally loops over each option making separate requests. This
has been removed. You can still loop over many options for the data parameter, just use an lapply
family function, or a for loop, etc.
See name_issues() for more information about issues in issues column.

Value
An object of class gbif, which is a S3 class list, with slots for metadata (meta) and the data itself
(data). In addition, the object has attributes listing the user supplied arguments and type of search,
which is, differently from occurrence data, always equals to ’single’ even if multiple values for
some parameters are given. meta is a list of length four with offset, limit, endOfRecords and count
fields. data is a tibble (aka data.frame) containing all information about the found taxa.

Repeat parameter inputs

These parameters used to accept many inputs, but no longer do:

• rank
• name
• langugae
• datasetKey

References
https://www.gbif.org/developer/species#nameUsages

Examples
## Not run:
# A single name usage
name_usage(key=1)

# Name usage for a taxonomic name

name_usage(name='Puma', rank="GENUS")

# Name usage for all taxa in a dataset

# (set sufficient high limit, but less than 100000)
# name_usage(datasetKey = "9ff7d317-609b-4c08-bd86-3bc404b77c42",
# limit = 10000)
# All name usages
66 network

name_usage()

# References for a name usage

name_usage(key=2435099, data='references')

# Species profiles, descriptions

name_usage(key=3119195, data='speciesProfiles')
name_usage(key=3119195, data='descriptions')
name_usage(key=2435099, data='children')

# Vernacular names for a name usage

name_usage(key=3119195, data='vernacularNames')

# Limit number of results returned

name_usage(key=3119195, data='vernacularNames', limit=3)

# Search for names by dataset with datasetKey parameter

name_usage(datasetKey="d7dddbf4-2cf0-4f39-9b2a-bb099caae36c")

# Search for a particular language

name_usage(key=3119195, language="FRENCH", data='vernacularNames')

# get root usage with a uuid

name_usage(data = "root", uuid = "73605f3a-af85-4ade-bbc5-522bfb90d847")

# search by language
name_usage(language = "spanish")

# Pass on curl options

name_usage(name='Puma concolor', limit=300, curlopts = list(verbose=TRUE))

# look up iucn red list category

name_usage(key = 7707728, data = 'iucnRedListCategory')

## End(Not run)

network Get data about GBIF networks

Description
Get data about GBIF networks

Usage
network(
data = "all",
uuid = NULL,
query = NULL,
identifier = NULL,
network 67

identifierType = NULL,
limit = 100,
start = NULL,
curlopts = list()
)

network_constituents(uuid = NULL, limit = 100, start = 0)

Arguments
data The type of data to get. One or more of: ’contact’, ’endpoint’, ’identifier’, ’tag’,
’machineTag’, ’comment’, ’constituents’, or the special ’all’. Default: 'all'
uuid UUID of the data network provider. This must be specified if data is anything
other than ’all’. Only 1 can be passed in
query Query nodes. Only used when data='all'. Ignored otherwise.
identifier The value for this parameter can be a simple string or integer, e.g. identifier=120.
This parameter doesn’t seem to work right now.
identifierType Used in combination with the identifier parameter to filter identifiers by identi-
fier type. See details. This parameter doesn’t seem to work right now.
limit Number of records to return. Default: 100. Maximum: 1000.
start Record number to start at. Default: 0. Use in combination with limit to page
through results.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Details
identifierType options:

• DOI No description.
• FTP No description.
• GBIF_NODE Identifies the node (e.g: DK for Denmark, sp2000 for Species 2000).
• GBIF_PARTICIPANT Participant identifier from the GBIF IMS Filemaker system.
• GBIF_PORTAL Indicates the identifier originated from an auto_increment column in the por-
tal.data_provider or portal.data_resource table respectively.
• HANDLER No description.
• LSID Reference controlled by a separate system, used for example by DOI.
• SOURCE_ID No description.
• UNKNOWN No description.
• URI No description.
• URL No description.
• UUID No description.

Get various information about GBIF networks. network_constituents() is a convenience func-

tion that allows you to get all the datasets in a network.
68 networks

Value
• network() returns a list
• network_constituents() returns a data.frame of datasets in the network

References
https://www.gbif.org/developer/registry#networks

Examples
## Not run:
network()
network(uuid='2b7c7b4f-4d4f-40d3-94de-c28b6fa054a6')

network_constituents('2b7c7b4f-4d4f-40d3-94de-c28b6fa054a6')

# curl options
network(curlopts = list(verbose=TRUE))

## End(Not run)

networks Networks metadata.

Description
Networks metadata.

Usage
networks(
data = "all",
uuid = NULL,
query = NULL,
identifier = NULL,
identifierType = NULL,
limit = 100,
start = NULL,
curlopts = list()
)

Arguments
data The type of data to get. One or more of: ’contact’, ’endpoint’, ’identifier’, ’tag’,
’machineTag’, ’comment’, ’constituents’, or the special ’all’. Default: 'all'
uuid UUID of the data network provider. This must be specified if data is anything
other than ’all’. Only 1 can be passed in
networks 69

query Query nodes. Only used when data='all'. Ignored otherwise.

identifier The value for this parameter can be a simple string or integer, e.g. identifier=120.
This parameter doesn’t seem to work right now.
identifierType Used in combination with the identifier parameter to filter identifiers by identi-
fier type. See details. This parameter doesn’t seem to work right now.
limit Number of records to return. Default: 100. Maximum: 1000.
start Record number to start at. Default: 0. Use in combination with limit to page
through results.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Details
identifierType options:

• DOI No description.
• FTP No description.
• GBIF_NODE Identifies the node (e.g: DK for Denmark, sp2000 for Species 2000).
• GBIF_PARTICIPANT Participant identifier from the GBIF IMS Filemaker system.
• GBIF_PORTAL Indicates the identifier originated from an auto_increment column in the por-
tal.data_provider or portal.data_resource table respectively.
• HANDLER No description.
• LSID Reference controlled by a separate system, used for example by DOI.
• SOURCE_ID No description.
• UNKNOWN No description.
• URI No description.
• URL No description.
• UUID No description.

References
https://www.gbif.org/developer/registry#networks

Examples
## Not run:
networks()
networks(uuid='2b7c7b4f-4d4f-40d3-94de-c28b6fa054a6')

# curl options
networks(curlopts = list(verbose=TRUE))

## End(Not run)
70 nodes

nodes Nodes metadata.

Description
Nodes metadata.

Usage
nodes(
data = "all",
uuid = NULL,
query = NULL,
identifier = NULL,
identifierType = NULL,
limit = 100,
start = NULL,
isocode = NULL,
curlopts = list()
)

Arguments
data The type of data to get. One or more of: ’organization’, ’endpoint’, ’identifier’,
’tag’, ’machineTag’, ’comment’, ’pendingEndorsement’, ’country’, ’dataset’,
’installation’, or the special ’all’. Default: 'all'
uuid UUID of the data node provider. This must be specified if data is anything other
than ’all’.
query Query nodes. Only used when data='all'
identifier The value for this parameter can be a simple string or integer, e.g. identifier=120.
This parameter doesn’t seem to work right now.
identifierType Used in combination with the identifier parameter to filter identifiers by identi-
fier type. See details. This parameter doesn’t seem to work right now.
limit Number of records to return. Default: 100. Maximum: 1000.
start Record number to start at. Default: 0. Use in combination with limit to page
through results.
isocode A 2 letter country code. Only used if data=’country’.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Details
identifierType options:

• DOI No description.
nodes 71

• FTP No description.
• GBIF_NODE Identifies the node (e.g: DK for Denmark, sp2000 for Species 2000).
• GBIF_PARTICIPANT Participant identifier from the GBIF IMS Filemaker system.
• GBIF_PORTAL Indicates the identifier originated from an auto_increment column in the por-
tal.data_provider or portal.data_resource table respectively.
• HANDLER No description.
• LSID Reference controlled by a separate system, used for example by DOI.
• SOURCE_ID No description.
• UNKNOWN No description.
• URI No description.
• URL No description.
• UUID No description.

References
https://www.gbif.org/developer/registry#nodes

Examples
## Not run:
nodes(limit=5)
nodes(uuid="1193638d-32d1-43f0-a855-8727c94299d8")
nodes(data='identifier', uuid="03e816b3-8f58-49ae-bc12-4e18b358d6d9")
nodes(data=c('identifier','organization','comment'),
uuid="03e816b3-8f58-49ae-bc12-4e18b358d6d9")

uuids = c("8cb55387-7802-40e8-86d6-d357a583c596",
"02c40d2a-1cba-4633-90b7-e36e5e97aba8",
"7a17efec-0a6a-424c-b743-f715852c3c1f",
"b797ce0f-47e6-4231-b048-6b62ca3b0f55",
"1193638d-32d1-43f0-a855-8727c94299d8",
"d3499f89-5bc0-4454-8cdb-60bead228a6d",
"cdc9736d-5ff7-4ece-9959-3c744360cdb3",
"a8b16421-d80b-4ef3-8f22-098b01a89255",
"8df8d012-8e64-4c8a-886e-521a3bdfa623",
"b35cf8f1-748d-467a-adca-4f9170f20a4e",
"03e816b3-8f58-49ae-bc12-4e18b358d6d9",
"073d1223-70b1-4433-bb21-dd70afe3053b",
"07dfe2f9-5116-4922-9a8a-3e0912276a72",
"086f5148-c0a8-469b-84cc-cce5342f9242",
"0909d601-bda2-42df-9e63-a6d51847ebce",
"0e0181bf-9c78-4676-bdc3-54765e661bb8",
"109aea14-c252-4a85-96e2-f5f4d5d088f4",
"169eb292-376b-4cc6-8e31-9c2c432de0ad",
"1e789bc9-79fc-4e60-a49e-89dfc45a7188",
"1f94b3ca-9345-4d65-afe2-4bace93aa0fe")

res <- lapply(uuids, function(x) nodes(x, data='identifier')$data)

72 occ_count

res <- res[!sapply(res, NROW)==0]

res[1]

# Pass on curl options

nodes(limit=20, curlopts=list(verbose=TRUE))

## End(Not run)

occ_count Get number of occurrence records.

Description

Get number of occurrence records.

Usage

occ_count(..., occurrenceStatus = "PRESENT", curlopts = list())

Arguments

... parameters passed to occ_search().

occurrenceStatus
(character) Default is "PRESENT". Specify whether search should return "PRESENT"
or "ABSENT" data.
curlopts (list) curl options.

Details

occ_count() is a short convenience wrapper for occ_search(limit=0)$meta$count.

The current version (since rgbif 3.7.6) of occ_count() uses a different GBIF API endpoint from
previous versions. This change greatly improves the usability of occ_count(). Legacy parame-
ters georeferenced, type, date, to, from are no longer supported and not guaranteed to work
correctly.
Multiple values of the type c("a","b") will give an error, but "a;b" will work.

Value

The occurrence count of the occ_search() query.

See Also

occ_count_year(), occ_count_country(), occ_count_pub_country(), occ_count_basis_of_record()

occ_count 73

Examples

## Not run:
# total occurrences mediated by GBIF
occ_count() # should be > 2 billion!

# number of plant occurrences

occ_count(kingdomKey=name_backbone("Plantea")$usageKey)
occ_count(scientificName = 'Ursus americanus')

occ_count(country="DK") # found in Denmark

occ_count(country="DK;US") # found in Denmark and United States
occ_count(publishingCountry="US") # published by the United States
# number of repatriated eBird records in India
occ_count(repatriated = TRUE,country="IN")

occ_count(taxonKey=212) # number of bird occurrences

# between years 1800-1900
occ_count(basisOfRecord="PRESERVED_SPECIMEN", year="1800,1900")
occ_count(recordedBy="John Waller") # recorded by John Waller
occ_count(decimalLatitude=0, decimalLongitude=0) # exactly on 0,0

# close to a known iso2 centroid

occ_count(distanceFromCentroidInMeters="0,2000")
# close to a known iso2 centroid in Sweden
occ_count(distanceFromCentroidInMeters="0,2000",country="SE")

occ_count(hasCoordinate=TRUE) # with coordinates

occ_count(protocol = "DIGIR") # published using DIGIR format
occ_count(mediaType = 'StillImage') # with images

# number of occurrences iucn status "critically endangered"

occ_count(iucnRedListCategory="CR")
occ_count(verbatimScientificName="Calopteryx splendens;Calopteryx virgo")
occ_count(
geometry="POLYGON((24.70938 48.9221,24.71056 48.92175,24.71107
48.92296,24.71002 48.92318,24.70938 48.9221))")

# getting a table of counts using the facets interface

# occurrence counts by year
occ_count(facet="year")
occ_count(facet="year",facetLimit=400)

# top scientificNames from Japan

occ_count(facet="scientificName",country="JP")
# top countries publishing specimen bird records between 1850 and 1880
occ_count(facet="scientificName",taxonKey=212,basisOfRecord="PRESERVED_SPECIMEN"
,year="1850,1880")

# Number of present or absence records of Elephants

occ_count(facet="occurrenceStatus",scientificName="Elephantidae")

# top 100 datasets publshing occurrences to GBIF

74 occ_count_

occ_count(facet="datasetKey",facetLimit=100)
# top datasets publishing country centroids on GBIF
occ_count(facet="datasetKey",distanceFromCentroidInMeters="0")

# common values for coordinateUncertaintyInMeters for museum specimens

occ_count(facet="coordinateUncertaintyInMeters",basisOfRecord="PRESERVED_SPECIMEN")

# number of iucn listed bird and insect occurrences in Mexico

occ_count(facet="iucnRedListCategory",taxonKey="212;216",country="MX")

# most common latitude values mediated by GBIF

occ_count(facet="decimalLatitude")

# top iNaturalist users publishing research-grade obs to GBIF

occ_count(facet="recordedBy",datasetKey="50c9509d-22c7-4a22-a47d-8c48425ef4a7")
# top 100 iNaturalist users from Ukraine
occ_count(facet="recordedBy",datasetKey="50c9509d-22c7-4a22-a47d-8c48425ef4a7"
,country="UA",facetLimit=100)

# top institutions publishing specimen occurrences to GBIF

occ_count(facet="institutionCode",basisOfRecord="PRESERVED_SPECIMEN")

## End(Not run)

occ_count_ Get quick pre-computed occurrence counts of a limited number of di-

mensions.

Description
Get quick pre-computed occurrence counts of a limited number of dimensions.

Usage
occ_count_country(publishingCountry = NULL)

occ_count_pub_country(country = NULL)

occ_count_year(year = NULL)

occ_count_basis_of_record(curlopts = list())

Arguments
publishingCountry
The 2-letter country code (as per ISO-3166-1) the country from which the oc-
currence was published.
occ_count_ 75

country (character) The 2-letter country code (ISO-3166-1) in which the occurrence was
recorded.
year The 4 digit year. Supports range queries, ’smaller,larger’ (e.g., ’1990,1991’,
whereas 1991, 1990’ wouldn’t work).
curlopts (list) curl options.

Details
Get quick pre-computed counts of a limited number of dimensions.
occ_count_country() will return a data.frame with occurrence counts by country. By using
occ_count_country(publishingCountry="DK") will return the occurrence contributions Den-
mark has made to each country.
occ_count_pub_country() will return a data.frame with occurrence counts by publishing country.
Using occ_count_pub_country(country="DK"), will return the occurrence contributions each
country has made to that focal country=DK.
occ_count_year() will return a data.frame with the total occurrences mediated by GBIF for each
year. By using occ_counts_year(year="1800,1900") will only return counts for that range.
occ_count_basis_of_record() will return a data.frame with total occurrences mediated by GBIF
for each basis of record.

Value
A data.frame of counts.

See Also
occ_count()

Examples
## Not run:
# total occurrence counts for all countries and iso2 places
occ_count_country()
# the occurrences Mexico has published in other countries
occ_count_country("MX")
# the occurrences Denmark has published in other countries
occ_count_country("DK")

# the occurrences other countries have published in Denmark

occ_count_pub_country("DK")
# the occurrences other countries have published in Mexico
occ_count_pub_country("MX")

# total occurrence counts for each year that an occurrence was

# recorded or collected.
occ_count_year()
# supports ranges
occ_count_year("1800,1900")
76 occ_data

# table of occurrence counts by basis of record

occ_count_basis_of_record()

## End(Not run)

occ_data Legacy alternative to occ_search

Description
Legacy alternative to occ_search

Usage
occ_data(
taxonKey = NULL,
scientificName = NULL,
country = NULL,
publishingCountry = NULL,
hasCoordinate = NULL,
typeStatus = NULL,
recordNumber = NULL,
lastInterpreted = NULL,
continent = NULL,
geometry = NULL,
geom_big = "asis",
geom_size = 40,
geom_n = 10,
recordedBy = NULL,
recordedByID = NULL,
identifiedByID = NULL,
basisOfRecord = NULL,
datasetKey = NULL,
eventDate = NULL,
catalogNumber = NULL,
year = NULL,
month = NULL,
decimalLatitude = NULL,
decimalLongitude = NULL,
elevation = NULL,
depth = NULL,
institutionCode = NULL,
collectionCode = NULL,
hasGeospatialIssue = NULL,
issue = NULL,
search = NULL,
occ_data 77

mediaType = NULL,
subgenusKey = NULL,
repatriated = NULL,
phylumKey = NULL,
kingdomKey = NULL,
classKey = NULL,
orderKey = NULL,
familyKey = NULL,
genusKey = NULL,
speciesKey = NULL,
establishmentMeans = NULL,
degreeOfEstablishment = NULL,
protocol = NULL,
license = NULL,
organismId = NULL,
publishingOrg = NULL,
stateProvince = NULL,
waterBody = NULL,
locality = NULL,
occurrenceStatus = "PRESENT",
gadmGid = NULL,
coordinateUncertaintyInMeters = NULL,
verbatimScientificName = NULL,
eventId = NULL,
identifiedBy = NULL,
networkKey = NULL,
verbatimTaxonId = NULL,
occurrenceId = NULL,
organismQuantity = NULL,
organismQuantityType = NULL,
relativeOrganismQuantity = NULL,
iucnRedListCategory = NULL,
lifeStage = NULL,
isInCluster = NULL,
distanceFromCentroidInMeters = NULL,
skip_validate = TRUE,
limit = 500,
start = 0,
curlopts = list(http_version = 2)
)

Arguments

taxonKey (numeric) A taxon key from the GBIF backbone. All included and synonym
taxa are included in the search, so a search for aves with taxononKey=212
will match all birds, no matter which species. You can pass many keys to
occ_search(taxonKey=c(1,212)).
scientificName A scientific name from the GBIF backbone. All included and synonym taxa are
78 occ_data

included in the search.

country (character) The 2-letter country code (ISO-3166-1) in which the occurrence was
recorded. enumeration_country().
publishingCountry
The 2-letter country code (as per ISO-3166-1) of the country in which the oc-
currence was recorded. See enumeration_country().
hasCoordinate (logical) Return only occurrence records with lat/long data (TRUE) or all records
(FALSE, default).
typeStatus Type status of the specimen. One of many options.
recordNumber Number recorded by collector of the data, different from GBIF record number.
lastInterpreted
Date the record was last modified in GBIF, in ISO 8601 format: yyyy, yyyy-
MM, yyyy-MM-dd, or MM-dd. Supports range queries, ’smaller,larger’ (e.g.,
’1990,1991’, whereas ’1991,1990’ wouldn’t work).
continent The source supplied continent.
• "africa"
• "antarctica"
• "asia"
• "europe"
• "north_america"
• "oceania"
• "south_america"
Continent is not inferred but only populated if provided by the dataset publisher.
Applying this filter may exclude many relevant records.
geometry (character) Searches for occurrences inside a polygon in Well Known Text (WKT)
format. A WKT shape written as either
• "POINT"
• "LINESTRING"
• "LINEARRING"
• "POLYGON"
• "MULTIPOLYGON"
For Example, "POLYGON((37.08 46.86,38.06 46.86,38.06 47.28,37.08 47.28,
37.0 46.8))". See also the section WKT below.
geom_big (character) One"bbox" or "asis" (default).
geom_size (integer) An integer indicating size of the cell. Default: 40.
geom_n (integer) An integer indicating number of cells in each dimension. Default: 10.
recordedBy (character) The person who recorded the occurrence.
recordedByID (character) Identifier (e.g. ORCID) for the person who recorded the occurrence
identifiedByID (character) Identifier (e.g. ORCID) for the person who provided the taxonomic
identification of the occurrence.
basisOfRecord (character) The specific nature of the data record. See here.
occ_data 79

• "FOSSIL_SPECIMEN"
• "HUMAN_OBSERVATION"
• "MATERIAL_CITATION"
• "MATERIAL_SAMPLE"
• "LIVING_SPECIMEN"
• "MACHINE_OBSERVATION"
• "OBSERVATION"
• "PRESERVED_SPECIMEN"
• "OCCURRENCE"
datasetKey (character) The occurrence dataset uuid key. That can be found in the dataset
page url. For example, "7e380070-f762-11e1-a439-00145 eb45e9a" is the key
for Natural History Museum (London) Collection Specimens.
eventDate (character) Occurrence date in ISO 8601 format: yyyy, yyyy-MM, yyyy-MM-
dd, or MM-dd. Supports range queries, ’smaller,larger’ (’1990,1991’, whereas
’1991,1990’ wouldn’t work).
catalogNumber (character) An identifier of any form assigned by the source within a physical
collection or digital dataset for the record which may not unique, but should be
fairly unique in combination with the institution and collection code.
year The 4 digit year. A year of 98 will be interpreted as AD 98. Supports range
queries, ’smaller,larger’ (e.g., ’1990,1991’, whereas 1991, 1990’ wouldn’t work).
month The month of the year, starting with 1 for January. Supports range queries,
’smaller,larger’ (e.g., ’1,2’, whereas ’2,1’ wouldn’t work).
decimalLatitude
Latitude in decimals between -90 and 90 based on WGS84. Supports range
queries, ’smaller,larger’ (e.g., ’25,30’, whereas ’30,25’ wouldn’t work).
decimalLongitude
Longitude in decimals between -180 and 180 based on WGS84. Supports range
queries (e.g., ’-0.4,-0.2’, whereas ’-0.2,-0.4’ wouldn’t work).
elevation Elevation in meters above sea level. Supports range queries, ’smaller,larger’
(e.g., ’5,30’, whereas ’30,5’ wouldn’t work).
depth Depth in meters relative to elevation. For example 10 meters below a lake sur-
face with given elevation. Supports range queries, ’smaller,larger’ (e.g., ’5,30’,
whereas ’30,5’ wouldn’t work).
institutionCode
An identifier of any form assigned by the source to identify the institution the
record belongs to.
collectionCode (character) An identifier of any form assigned by the source to identify the phys-
ical collection or digital dataset uniquely within the text of an institution.
hasGeospatialIssue
(logical) Includes/excludes occurrence records which contain spatial issues (as
determined in our record interpretation), i.e. hasGeospatialIssue=TRUE re-
turns only those records with spatial issues while hasGeospatialIssue=FALSE
includes only records without spatial issues. The absence of this parameter re-
turns any record with or without spatial issues.
80 occ_data

issue (character) One or more of many possible issues with each occurrence record.
Issues passed to this parameter filter results by the issue. One of many options.
See here for definitions.
search (character) Query terms. The value for this parameter can be a simple word or a
phrase. For example, search="puma"
mediaType (character) Media type of "MovingImage", "Sound", or "StillImage".
subgenusKey (numeric) Subgenus classification key.
repatriated (character) Searches for records whose publishing country is different to the
country where the record was recorded in.
phylumKey (numeric) Phylum classification key.
kingdomKey (numeric) Kingdom classification key.
classKey (numeric) Class classification key.
orderKey (numeric) Order classification key.
familyKey (numeric) Family classification key.
genusKey (numeric) Genus classification key.
speciesKey (numeric) Species classification key.
establishmentMeans
(character) provides information about whether an organism or organisms have
been introduced to a given place and time through the direct or indirect activity
of modern humans.
• "Introduced"
• "Native"
• "NativeReintroduced"
• "Vagrant"
• "Uncertain"
• "IntroducedAssistedColonisation"
degreeOfEstablishment
(character) Provides information about degree to which an Organism survives,
reproduces, and expands its range at the given place and time. One of many
options.
protocol (character) Protocol or mechanism used to provide the occurrence record. One
of many options.
license (character) The type license applied to the dataset or record.
• "CC0_1_0"
• "CC_BY_4_0"
• "CC_BY_NC_4_0"
organismId (numeric) An identifier for the Organism instance (as opposed to a particular
digital record of the Organism). May be a globally unique identifier or an iden-
tifier specific to the data set.
publishingOrg (character) The publishing organization key (a UUID).
stateProvince (character) The name of the next smaller administrative region than country
(state, province, canton, department, region, etc.) in which the Location occurs.
occ_data 81

waterBody (character) The name of the water body in which the locations occur
locality (character) The specific description of the place.
occurrenceStatus
(character) Default is "PRESENT". Specify whether search should return "PRESENT"
or "ABSENT" data.
gadmGid (character) The gadm id of the area occurrences are desired from. https://gadm.org/.
coordinateUncertaintyInMeters
A number or range between 0-1,000,000 which specifies the desired coordi-
nate uncertainty. A coordinateUncertainty InMeters=1000 will be interpreted
all records with exactly 1000m. Supports range queries, ’smaller,larger’ (e.g.,
’1000,10000’, whereas ’10000,1000’ wouldn’t work).
verbatimScientificName
(character) Scientific name as provided by the source.
eventId (character) identifier(s) for a sampling event.
identifiedBy (character) names of people, groups, or organizations.
networkKey (character) The occurrence network key (a uuid) who assigned the Taxon to the
subject.
verbatimTaxonId
(character) The taxon identifier provided to GBIF by the data publisher.
occurrenceId (character) occurrence id from source.
organismQuantity
A number or range which specifies the desired organism quantity. An organ-
ismQuantity=5 will be interpreted all records with exactly 5. Supports range
queries, smaller,larger (e.g., ’5,20’, whereas ’20,5’ wouldn’t work).
organismQuantityType
(character) The type of quantification system used for the quantity of organisms.
For example, "individuals" or "biomass".
relativeOrganismQuantity
(numeric) A relativeOrganismQuantity=0.1 will be interpreted all records with
exactly 0.1 The relative measurement of the quantity of the organism (a number
between 0-1). Supports range queries, "smaller,larger" (e.g., ’0.1,0.5’, whereas
’0.5,0.1’ wouldn’t work).
iucnRedListCategory
(character) The IUCN threat status category.
• "NE" (Not Evaluated)
• "DD" (Data Deficient)
• "LC" (Least Concern)
• "NT" (Near Threatened)
• "VU" (Vulnerable)
• "EN" (Endangered)
• "CR" (Critically Endangered)
• "EX" (Extinct)
• "EW" (Extinct in the Wild)
82 occ_download

lifeStage (character) the life stage of the occurrence. One of many options.
isInCluster (logical) identify potentially related records on GBIF.
distanceFromCentroidInMeters
A number or range. A value of "2000,*" means at least 2km from known cen-
troids. A value of "0" would mean occurrences exactly on known centroids. A
value of "0,2000" would mean within 2km of centroids. Max value is 5000.
skip_validate (logical) whether to skip wellknown::validate_wkt call or not. passed down to
check_wkt(). Default: TRUE
limit Number of records to return. Default: 500. Note that the per request maximum
is 300, but since we set it at 500 for the function, we do two requests to get
you the 500 records (if there are that many). Note that there is a hard maxi-
mum of 100,000, which is calculated as the limit+start, so start=99,000
and limit=2000 won’t work
start Record number to start at. Use in combination with limit to page through results.
Note that we do the paging internally for you, but you can manually set the
start parameter
curlopts (list)

Details
This function is a legacy alternative to occ_search(). It is not recommended to use occ_data()
as it is not as flexible as occ_search(). New search terms will not be added to this function and it
is only supported for legacy reasons.

Value
An object of class gbif_data, which is a S3 class list, with slots for metadata (meta) and the
occurrence data itself (data), and with attributes listing the user supplied arguments and whether it
was a "single" or "many" search; that is, if you supply two values of the datasetKey parameter to
searches are done, and it’s a "many". meta is a list of length four with offset, limit, endOfRecords
and count fields. data is a tibble (aka data.frame)

occ_download Spin up a download request for GBIF occurrence data.

Description
Spin up a download request for GBIF occurrence data.

Usage
occ_download(
...,
body = NULL,
type = "and",
format = "DWCA",
occ_download 83

user = NULL,
pwd = NULL,
email = NULL,
curlopts = list()
)

occ_download_prep(
...,
body = NULL,
type = "and",
format = "DWCA",
user = NULL,
pwd = NULL,
email = NULL,
curlopts = list()
)

Arguments
... For occ_download() and occ_download_prep(), one or more objects of class
occ_predicate or occ_predicate_list, created by pred* functions (see down-
load_predicate_dsl). If you use this, don’t use body parameter.
body if you prefer to pass in the payload yourself, use this parameter. If you use this,
don’t pass anything to the dots. Accepts either an R list, or JSON. JSON is
likely easier, since the JSON library jsonlite requires that you unbox strings that
shouldn’t be auto-converted to arrays, which is a bit tedious for large queries.
optional
type (character) One of equals (=), and (&), or (|), lessThan (<), lessThanOrEquals
(<=), greaterThan (>), greaterThanOrEquals (>=), in, within, not (!), like, isNot-
Null
format (character) The download format. One of ’DWCA’ (default), ’SIMPLE_CSV’,
or ’SPECIES_LIST’
user (character) User name within GBIF’s website. Required. See "Authentication"
below
pwd (character) User password within GBIF’s website. Required. See "Authentica-
tion" below
email (character) Email address to receive download notice done email. Required. See
"Authentication" below
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

geometry
When using the geometry parameter, make sure that your well known text (WKT) is formatted as
GBIF expects it. They expect WKT to have a counter-clockwise winding order. For example, the
following is clockwise POLYGON((-19.5 34.1, -25.3 68.1, 35.9 68.1, 27.8 34.1, -19.5 34.1)),
whereas they expect the other order: POLYGON((-19.5 34.1, 27.8 34.1, 35.9 68.1, -25.3 68.1, -19.5 34.1))
84 occ_download

note that coordinate pairs are longitude latitude, longitude first, then latitude
you should not get any results if you supply WKT that has clockwise winding order.
also note that occ_search()/occ_data() behave differently with respect to WKT in that you can
supply clockwise WKT to those functions but they treat it as an exclusion, so get all data not inside
the WKT area.

Methods

• occ_download_prep: prepares a download request, but DOES NOT execute it. meant for use
with occ_download_queue()
• occ_download: prepares a download request and DOES execute it

Authentication

For user, pwd, and email parameters, you can set them in one of three ways:

• Set them in your .Rprofile file with the names gbif_user, gbif_pwd, and gbif_email
• Set them in your .Renviron/.bash_profile (or similar) file with the names GBIF_USER,
GBIF_PWD, and GBIF_EMAIL
• Simply pass strings to each of the parameters in the function call

We strongly recommend the second option - storing your details as environment variables as it’s the
most widely used way to store secrets.
See ?Startup for help.

Query length

GBIF has a limit of 12,000 characters for a download query. This means that you can have a pretty
long query, but at some point it may lead to an error on GBIF’s side and you’ll have to split your
query into a few.

Note

see downloads for an overview of GBIF downloads methods

References

See the API docs https://www.gbif.org/developer/occurrence#download for more info, and

the predicates docs https://www.gbif.org/developer/occurrence#predicates

See Also

Other downloads: download_predicate_dsl, occ_download_cached(), occ_download_cancel(),

occ_download_dataset_activity(), occ_download_datasets(), occ_download_get(), occ_download_import(),
occ_download_list(), occ_download_meta(), occ_download_queue(), occ_download_wait()
occ_download 85

Examples

## Not run:
# occ_download(pred("basisOfRecord", "LITERATURE"))
# occ_download(pred("taxonKey", 3119195), pred_gt("elevation", 5000))
# occ_download(pred_gt("decimalLatitude", 50))
# occ_download(pred_gte("elevation", 9000))
# occ_download(pred_gte('decimalLatitude", 65))
# occ_download(pred("country", "US"))
# occ_download(pred("institutionCode", "TLMF"))
# occ_download(pred("catalogNumber", 217880))
# occ_download(pred("gbifId", 142317604))

# download format
# z <- occ_download(pred_gte("decimalLatitude", 75),
# format = "SPECIES_LIST")

# res <- occ_download(pred("taxonKey", 7264332), pred("hasCoordinate", TRUE))

# pass output directly, or later, to occ_download_meta for more information

# occ_download(pred_gt('decimalLatitude', 75)) %>% occ_download_meta

# Multiple queries
# occ_download(pred_gte("decimalLatitude", 65),
# pred_lte("decimalLatitude", -65), type="or")
# gg <- occ_download(pred("depth", 80), pred("taxonKey", 2343454),
# type="or")
# x <- occ_download(pred_and(pred_within("POLYGON((-14 42, 9 38, -7 26, -14 42))"),
# pred_gte("elevation", 5000)))

# complex example with many predicates

# shows example of how to do date ranges for both year and month
# res <- occ_download(
# pred_gt("elevation", 5000),
# pred_in("basisOfRecord", c('HUMAN_OBSERVATION','OBSERVATION','MACHINE_OBSERVATION')),
# pred("country", "US"),
# pred("hasCoordinate", TRUE),
# pred("hasGeospatialIssue", FALSE),
# pred_gte("year", 1999),
# pred_lte("year", 2011),
# pred_gte("month", 3),
# pred_lte("month", 8)
# )

# Using body parameter - pass in your own complete query

## as JSON
query1 <- '{"creator":"sckott",
"notification_address":["[email protected]"],
"predicate":{"type":"and","predicates":[
{"type":"equals","key":"TAXON_KEY","value":"7264332"},
{"type":"equals","key":"HAS_COORDINATE","value":"TRUE"}]}
}'
# res <- occ_download(body = query1, curlopts=list(verbose=TRUE))
86 occ_download

## as a list
library(jsonlite)
query <- list(
creator = unbox("sckott"),
notification_address = "[email protected]",
predicate = list(
type = unbox("and"),
predicates = list(
list(type = unbox("equals"), key = unbox("TAXON_KEY"),
value = unbox("7264332")),
list(type = unbox("equals"), key = unbox("HAS_COORDINATE"),
value = unbox("TRUE"))
)
)
)
# res <- occ_download(body = query, curlopts = list(verbose = TRUE))

# Prepared query
occ_download_prep(pred("basisOfRecord", "LITERATURE"))
occ_download_prep(pred("basisOfRecord", "LITERATURE"), format = "SIMPLE_CSV")
occ_download_prep(pred("basisOfRecord", "LITERATURE"), format = "SPECIES_LIST")
occ_download_prep(pred_in("taxonKey", c(2977832, 2977901, 2977966, 2977835)))
occ_download_prep(pred_within("POLYGON((-14 42, 9 38, -7 26, -14 42))"))

## a complicated example
occ_download_prep(
pred_in("basisOfRecord", c("MACHINE_OBSERVATION", "HUMAN_OBSERVATION")),
pred_in("taxonKey", c(2498343, 2481776, 2481890)),
pred_in("country", c("GB", "IE")),
pred_or(pred_lte("year", 1989), pred("year", 2000))
)

# x = occ_download(
# pred_in("basisOfRecord", c("MACHINE_OBSERVATION", "HUMAN_OBSERVATION")),
# pred_in("taxonKey", c(9206251, 3112648)),
# pred_in("country", c("US", "MX")),
# pred_and(pred_gte("year", 1989), pred_lte("year", 1991))
# )
# occ_download_meta(x)
# z <- occ_download_get(x)
# df <- occ_download_import(z)
# str(df)
# library(dplyr)
# unique(df$basisOfRecord)
# unique(df$taxonKey)
# unique(df$countryCode)
# sort(unique(df$year))

## End(Not run)
occ_download_cached 87

occ_download_cached Check for downloads already in your GBIF account

Description
Check for downloads already in your GBIF account

Usage
occ_download_cached(
...,
body = NULL,
type = "and",
format = "DWCA",
user = NULL,
pwd = NULL,
email = NULL,
refresh = FALSE,
age = 30,
curlopts = list()
)

Arguments
... For occ_download() and occ_download_prep(), one or more objects of class
occ_predicate or occ_predicate_list, created by pred* functions (see down-
load_predicate_dsl). If you use this, don’t use body parameter.
body if you prefer to pass in the payload yourself, use this parameter. If you use this,
don’t pass anything to the dots. Accepts either an R list, or JSON. JSON is
likely easier, since the JSON library jsonlite requires that you unbox strings that
shouldn’t be auto-converted to arrays, which is a bit tedious for large queries.
optional
type (character) One of equals (=), and (&), or (|), lessThan (<), lessThanOrEquals
(<=), greaterThan (>), greaterThanOrEquals (>=), in, within, not (!), like, isNot-
Null
format (character) The download format. One of ’DWCA’ (default), ’SIMPLE_CSV’,
or ’SPECIES_LIST’
user (character) User name within GBIF’s website. Required. See "Authentication"
below
pwd (character) User password within GBIF’s website. Required. See "Authentica-
tion" below
email (character) Email address to receive download notice done email. Required. See
"Authentication" below
88 occ_download_cancel

refresh (logical) refresh your list of downloads. on the first request of each R session
we’ll cache your stored GBIF occurrence downloads locally. you can refresh
this list by setting refresh=TRUE; if you’re in the same R session, and you’ve
done many download requests, then refreshing may be a good idea if you’re
using this function
age (integer) number of days after which you want a new download. default: 30
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Note
see downloads for an overview of GBIF downloads methods

See Also
Other downloads: download_predicate_dsl, occ_download_cancel(), occ_download_dataset_activity(),
occ_download_datasets(), occ_download_get(), occ_download_import(), occ_download_list(),
occ_download_meta(), occ_download_queue(), occ_download_wait(), occ_download()

Examples
## Not run:
# these are examples from the package maintainer's account;
# outcomes will vary by user
occ_download_cached(pred_gte("elevation", 12000L))
occ_download_cached(pred("catalogNumber", 217880))
occ_download_cached(pred_gte("decimalLatitude", 65),
pred_lte("decimalLatitude", -65), type="or")
occ_download_cached(pred_gte("elevation", 12000L))
occ_download_cached(pred_gte("elevation", 12000L), refresh = TRUE)

## End(Not run)

occ_download_cancel Cancel a download creation process.

Description
Cancel a download creation process.

Usage
occ_download_cancel(key, user = NULL, pwd = NULL, curlopts = list())

occ_download_cancel_staged(
user = NULL,
pwd = NULL,
limit = 20,
occ_download_cancel 89

start = 0,
curlopts = list()
)

Arguments

key (character) A key generated from a request, like that from occ_download. Re-
quired.
user (character) User name within GBIF’s website. Required. See Details.
pwd (character) User password within GBIF’s website. Required. See Details.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options
limit Number of records to return. Default: 20
start Record number to start at. Default: 0

Details

Note, these functions only cancel a job in progress. If your download is already prepared for you,
this won’t do anything to change that.
occ_download_cancel cancels a specific job by download key - returns success message
occ_download_cancel_staged cancels all jobs with status RUNNING or PREPARING - if none are
found, returns a message saying so - if some found, they are cancelled, returning message saying so

Note

see downloads for an overview of GBIF downloads methods

See Also

Other downloads: download_predicate_dsl, occ_download_cached(), occ_download_dataset_activity(),

occ_download_datasets(), occ_download_get(), occ_download_import(), occ_download_list(),
occ_download_meta(), occ_download_queue(), occ_download_wait(), occ_download()

Examples

## Not run:
# occ_download_cancel(key="0003984-140910143529206")
# occ_download_cancel_staged()

## End(Not run)
90 occ_download_datasets

occ_download_datasets List datasets for a download

Description
List datasets for a download

Usage
occ_download_datasets(key, limit = 20, start = 0, curlopts = list())

Arguments
key A key generated from a request, like that from occ_download()
limit (integer/numeric) Number of records to return. Default: 20, Max: 1000
start (integer/numeric) Record number to start at. Default: 0
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Value
a list with two slots:

• meta: a single row data.frame with columns: offset, limit, endofrecords, count
• results: a tibble with the results, of three columns: downloadKey, datasetKey, numberRecords

Note
see downloads for an overview of GBIF downloads methods

See Also
Other downloads: download_predicate_dsl, occ_download_cached(), occ_download_cancel(),
occ_download_dataset_activity(), occ_download_get(), occ_download_import(), occ_download_list(),
occ_download_meta(), occ_download_queue(), occ_download_wait(), occ_download()

Examples
## Not run:
occ_download_datasets(key="0003983-140910143529206")
occ_download_datasets(key="0003983-140910143529206", limit = 3)
occ_download_datasets(key="0003983-140910143529206", limit = 3, start = 10)

## End(Not run)
occ_download_dataset_activity 91

occ_download_dataset_activity
Lists the downloads activity of a dataset

Description

Lists the downloads activity of a dataset

Usage

occ_download_dataset_activity(
dataset,
limit = 20,
start = 0,
curlopts = list()
)

Arguments

dataset (character) A dataset key

limit (integer/numeric) Number of records to return. Default: 20, Max: 1000
start (integer/numeric) Record number to start at. Default: 0
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Value

a list with two slots:

• meta: a single row data.frame with columns: offset, limit, endofrecords, count
• results: a tibble with the nested data flattened, with many columns with the same download.
or download.request. prefixes

Note

see downloads for an overview of GBIF downloads methods

See Also

Other downloads: download_predicate_dsl, occ_download_cached(), occ_download_cancel(),

occ_download_datasets(), occ_download_get(), occ_download_import(), occ_download_list(),
occ_download_meta(), occ_download_queue(), occ_download_wait(), occ_download()
92 occ_download_describe

Examples
## Not run:
res <- occ_download_dataset_activity("7f2edc10-f762-11e1-a439-00145eb45e9a")
res
res$meta
res$meta$count

# pagination
occ_download_dataset_activity("7f2edc10-f762-11e1-a439-00145eb45e9a",
limit = 3000)
occ_download_dataset_activity("7f2edc10-f762-11e1-a439-00145eb45e9a",
limit = 3, start = 10)

## End(Not run)

occ_download_describe Describes the fields available in GBIF downloads

Description
Describes the fields available in GBIF downloads

Usage
occ_download_describe(x = "dwca")

Arguments
x a character string (default: "dwca"). Accepted values: "simpleCsv", "sim-
pleAvro", "simpleParquet","speciesList".

Details
The function returns a list with the fields available in GBIF downloads. It is considered experimental
by GBIF, so the output might change in the future.

Value
a list.

Examples
## Not run:
occ_download_describe("dwca")$verbatimFields
occ_download_describe("dwca")$verbatimExtensions
occ_download_describe("simpleCsv")$fields

## End(Not run)
occ_download_get 93

occ_download_get Get a download from GBIF.

Description
Get a download from GBIF.

Usage
occ_download_get(key, path = ".", overwrite = FALSE, ...)

Arguments
key A key generated from a request, like that from occ_download
path Path to write zip file to. Default: ".", with a .zip appended to the end.
overwrite Will only overwrite existing path if TRUE.
... named curl options passed on to crul::verb-GET. see curl::curl_options()
for curl options

Details
Downloads the zip file to a directory you specify on your machine. crul::HttpClient() is used
internally to write the zip file to disk. See crul::writing-options. This function only downloads the
file. See occ_download_import to open a downloaded file in your R session. The speed of this
function is of course proportional to the size of the file to download. For example, a 58 MB file on
my machine took about 26 seconds.

Note
see downloads for an overview of GBIF downloads methods
This function used to check for HTTP response content type, but it has changed enough that we no
longer check it. If you run into issues with this function, open an issue in the GitHub repository.

See Also
Other downloads: download_predicate_dsl, occ_download_cached(), occ_download_cancel(),
occ_download_dataset_activity(), occ_download_datasets(), occ_download_import(), occ_download_list(),
occ_download_meta(), occ_download_queue(), occ_download_wait(), occ_download()

Examples
## Not run:
occ_download_get("0000066-140928181241064")
occ_download_get("0003983-140910143529206", overwrite = TRUE)

## End(Not run)
94 occ_download_import

occ_download_import Import a downloaded file from GBIF.

Description
Import a downloaded file from GBIF.

Usage
occ_download_import(
x = NULL,
key = NULL,
path = ".",
fill = FALSE,
encoding = "UTF-8",
...
)

as.download(path = ".", key = NULL)

## S3 method for class 'character'

as.download(path = ".", key = NULL)

## S3 method for class 'download'

as.download(path = ".", key = NULL)

Arguments
x The output of a call to occ_download_get
key A key generated from a request, like that from occ_download
path Path to unzip file to. Default: "." Writes to folder matching zip file name
fill (logical) (default: FALSE). If TRUE then in case the rows have unequal length,
blank fields are implicitly filled. passed on to fill parameter in data.table::fread.
encoding (character) encoding to read in data; passed to data.table::fread(). default:
"UTF-8". other allowed options: "Latin-1" and "unknown". see ?data.table::fread
docs
... parameters passed on to data.table::fread(). See fread docs for details.
Some fread parameters that may be particular useful here are: select (select
which columns to read in; others are dropped), nrows (only read in a certain
number of rows)

Details
You can provide either x as input, or both key and path. We use data.table::fread() internally
to read data.
occ_download_import 95

Value
a tibble (data.frame)

Problems reading data

You may run into errors when using occ_download_import(); most often these are due to data.table::fread()
not being able to parse the occurrence.txt file correctly. The fill parameter passes down to
data.table::fread() and the ... allows you to pass on any other parameters that data.table::fread()
accepts. Read the docs for fread for help.

countryCode result column and Namibia

The country code for Namibia is "NA". Unfortunately in R an "NA" string will be read in to R as an
NA/missing. To avoid this, in this function we read in the data, then convert an NA/missing values
to the character string "NA". When a country code is truly missing it will be an empty string.

Note
see downloads for an overview of GBIF downloads methods

See Also
Other downloads: download_predicate_dsl, occ_download_cached(), occ_download_cancel(),
occ_download_dataset_activity(), occ_download_datasets(), occ_download_get(), occ_download_list(),
occ_download_meta(), occ_download_queue(), occ_download_wait(), occ_download()

Examples
## Not run:
# First, kick off at least 1 download, then wait for the job to be complete
# Then use your download keys
res <- occ_download_get(key="0000066-140928181241064", overwrite=TRUE)
occ_download_import(res)

occ_download_get(key="0000066-140928181241064", overwrite = TRUE) %>%

occ_download_import

# coerce a file path to the right class to feed to occ_download_import

# as.download("0000066-140928181241064.zip")
# as.download(key = "0000066-140928181241064")
# occ_download_import(as.download("0000066-140928181241064.zip"))

# download a dump that has a CSV file

# res <- occ_download_get(key = "0001369-160509122628363", overwrite=TRUE)
# occ_download_import(res)
# occ_download_import(key = "0001369-160509122628363")

# download and import a species list (in csv format)

# x <- occ_download_get("0000172-190415153152247")
# occ_download_import(x)
96 occ_download_list

## End(Not run)

occ_download_list Lists the downloads created by a user.

Description
Lists the downloads created by a user.

Usage
occ_download_list(
user = NULL,
pwd = NULL,
limit = 20,
start = 0,
curlopts = list()
)

Arguments
user (character) User name within GBIF’s website. Required. See Details.
pwd (character) User password within GBIF’s website. Required. See Details.
limit (integer/numeric) Number of records to return. Default: 20, Max: 1000
start (integer/numeric) Record number to start at. Default: 0
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Value
a list with two slots:

• meta: a single row data.frame with columns: offset, limit, endofrecords, count
• results: a tibble with the nested data flattened, with many columns with the same request.
prefix

Note
see downloads for an overview of GBIF downloads methods

See Also
Other downloads: download_predicate_dsl, occ_download_cached(), occ_download_cancel(),
occ_download_dataset_activity(), occ_download_datasets(), occ_download_get(), occ_download_import(),
occ_download_meta(), occ_download_queue(), occ_download_wait(), occ_download()
occ_download_meta 97

Examples
## Not run:
occ_download_list(user="sckott")
occ_download_list(user="sckott", limit = 5)
occ_download_list(user="sckott", start = 21)

## End(Not run)

occ_download_meta Retrieves the occurrence download metadata by its unique key.

Description
Retrieves the occurrence download metadata by its unique key.

Usage
occ_download_meta(key, curlopts = list())

Arguments
key A key generated from a request, like that from occ_download
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Value
an object of class occ_download_meta, a list with slots for the download key, the DOI assigned
to the download, license link, the request details you sent in the occ_download() request, and
metadata about the size and date/time of the request

Note
see downloads for an overview of GBIF downloads methods

See Also
Other downloads: download_predicate_dsl, occ_download_cached(), occ_download_cancel(),
occ_download_dataset_activity(), occ_download_datasets(), occ_download_get(), occ_download_import(),
occ_download_list(), occ_download_queue(), occ_download_wait(), occ_download()

Examples
## Not run:
occ_download_meta(key="0003983-140910143529206")
occ_download_meta("0000066-140928181241064")

## End(Not run)
98 occ_download_queue

occ_download_queue Download requests in a queue

Description
Download requests in a queue

Usage
occ_download_queue(..., .list = list(), status_ping = 10)

Arguments
... any number of occ_download() requests
.list any number of occ_download_prep() requests
status_ping (integer) seconds between pings checking status of the download request. gen-
erally larger numbers for larger requests. default: 10 (i.e., 10 seconds). must be
10 or greater

Details
This function is a convenience wrapper around occ_download(), allowing the user to kick off any
number of requests, while abiding by GBIF rules of 3 concurrent requests per user.

Value
a list of occ_download class objects, see occ_download_get() to fetch data

How it works
It works by using lazy evaluation to collect your requests into a queue (but does not use lazy evalua-
tion if use the .list parameter). Then it kicks of the first 3 requests. Then in a while loop, we check
status of those requests, and when any request finishes (see When is a job done? below), we kick
off the next, and so on. So in theory, there may not always strictly be 3 running concurrently, but
the function will usually provide for 3 running concurrently.

When is a job done?

We mark a job as done by checking the /occurrence/download/ API route with our occ_download_meta()
function. If the status of the job is any of "succeeded", "killed", or "cancelled", then we mark the
job as done and move on to other jobs in the queue.

Beware
This function is still in development. There’s a lot of complexity to this problem. We’ll be rolling
out fixes and improvements in future versions of the package, so expect to have to adjust your code
with new versions.
occ_download_queue 99

Note
see downloads for an overview of GBIF downloads methods

See Also
Other downloads: download_predicate_dsl, occ_download_cached(), occ_download_cancel(),
occ_download_dataset_activity(), occ_download_datasets(), occ_download_get(), occ_download_import(),
occ_download_list(), occ_download_meta(), occ_download_wait(), occ_download()

Examples
## Not run:
if (interactive()) { # dont run in automated example runs, too costly
# passing occ_download() requests via ...
out <- occ_download_queue(
occ_download(pred('taxonKey', 3119195), pred("year", 1976)),
occ_download(pred('taxonKey', 3119195), pred("year", 2001)),
occ_download(pred('taxonKey', 3119195), pred("year", 2001),
pred_lte("month", 8)),
occ_download(pred('taxonKey', 5229208), pred("year", 2011)),
occ_download(pred('taxonKey', 2480946), pred("year", 2015)),
occ_download(pred("country", "NZ"), pred("year", 1999),
pred("month", 3)),
occ_download(pred("catalogNumber", "Bird.27847588"),
pred("year", 1998), pred("month", 2))
)

# supports <= 3 requests too

out <- occ_download_queue(
occ_download(pred("country", "NZ"), pred("year", 1999), pred("month", 3)),
occ_download(pred("catalogNumber", "Bird.27847588"), pred("year", 1998),
pred("month", 2))
)

# using pre-prepared requests via .list

keys <- c(7905507, 5384395, 8911082)
queries <- list()
for (i in seq_along(keys)) {
queries[[i]] <- occ_download_prep(
pred("taxonKey", keys[i]),
pred_in("basisOfRecord", c("HUMAN_OBSERVATION","OBSERVATION")),
pred("hasCoordinate", TRUE),
pred("hasGeospatialIssue", FALSE),
pred("year", 1993)
)
}
out <- occ_download_queue(.list = queries)
out

# another pre-prepared example

yrs <- 1930:1934
queries <- list()
100 occ_download_wait

for (i in seq_along(yrs)) {
queries[[i]] <- occ_download_prep(
pred("taxonKey", 2877951),
pred_in("basisOfRecord", c("HUMAN_OBSERVATION","OBSERVATION")),
pred("hasCoordinate", TRUE),
pred("hasGeospatialIssue", FALSE),
pred("year", yrs[i])
)
}
out <- occ_download_queue(.list = queries)
out
}
## End(Not run)

occ_download_wait Wait for an occurrence download to be done

Description
Wait for an occurrence download to be done

Usage
occ_download_wait(
x,
status_ping = 5,
curlopts = list(http_version = 2),
quiet = FALSE
)

Arguments
x and object of class occ_download or downloadkey
status_ping (integer) seconds between each occ_download_meta() request. default is 5,
and cannot be < 3
curlopts (list) curl options, as named list, passed on to occ_download_meta()
quiet (logical) suppress messages. default: FALSE

Value
an object of class occ_download_meta, see occ_download_meta() for details

Note
occ_download_queue() is similar, but handles many requests at once; occ_download_wait han-
dles one request at a time
occ_facet 101

See Also
Other downloads: download_predicate_dsl, occ_download_cached(), occ_download_cancel(),
occ_download_dataset_activity(), occ_download_datasets(), occ_download_get(), occ_download_import(),
occ_download_list(), occ_download_meta(), occ_download_queue(), occ_download()

Examples
## Not run:
x <- occ_download(
pred("taxonKey", 9206251),
pred_in("country", c("US", "MX")),
pred_gte("year", 1971)
)
res <- occ_download_wait(x)
occ_download_meta(x)

# works also with a downloadkey

occ_download_wait("0000066-140928181241064")

## End(Not run)

occ_facet Facet GBIF occurrences

Description
Facet GBIF occurrences

Usage
occ_facet(facet, facetMincount = NULL, curlopts = list(), ...)

Arguments
facet (character) a character vector of length 1 or greater. Required.
facetMincount (numeric) minimum number of records to be included in the faceting results
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options
... Facet parameters, such as for paging based on each facet variable, e.g., country.facetLimit

Details
All fields can be faceted on except for last "lastInterpreted", "eventDate", and "geometry"
If a faceted variable is not found, it is silently dropped, returning nothing for that query
102 occ_get

Value
A list of tibbles (data.frame’s) for each facet (each element of the facet parameter).

See Also
occ_search() also has faceting ability, but can include occurrence data in addition to facets.

Examples
## Not run:
occ_facet(facet = "country")

# facetMincount - minimum number of records to be included

# in the faceting results
occ_facet(facet = "country", facetMincount = 30000000L)
occ_facet(facet = c("country", "basisOfRecord"))

# paging with many facets

occ_facet(
facet = c("country", "basisOfRecord", "hasCoordinate"),
country.facetLimit = 3,
basisOfRecord.facetLimit = 6
)

# paging
## limit
occ_facet(facet = "country", country.facetLimit = 3)
## offset
occ_facet(facet = "country", country.facetLimit = 3,
country.facetOffset = 3)

# Pass on curl options

occ_facet(facet = "country", country.facetLimit = 3,
curlopts = list(verbose = TRUE))

## End(Not run)

occ_get Get data for GBIF occurrences by occurrence key

Description
Get data for GBIF occurrences by occurrence key

Usage
occ_get(
key,
fields = "minimal",
occ_get 103

curlopts = list(),
return = NULL,
verbatim = NULL
)

occ_get_verbatim(key, fields = "minimal", curlopts = list())

Arguments
key (numeric/integer) one or more occurrence keys. required
fields (character) Default ("minimal") will return just taxon name, key, latitude, and
longitude. ’all’ returns all fields. Or specify each field you want returned by
name, e.g. fields = c(’name’, ’decimalLatitude’,’altitude’).
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options
return Defunct. All components are returned now; index to the one(s) you want
verbatim Defunct. verbatim records can now be retrieved using occ_get_verbatim()

Value
For occ_get a list of lists. For occ_get_verbatim a data.frame

References
https://www.gbif.org/developer/occurrence#occurrence

Examples
## Not run:
occ_get(key=855998194)

# many occurrences
occ_get(key=c(101010, 240713150, 855998194))

# Verbatim data
occ_get_verbatim(key=855998194)
occ_get_verbatim(key=855998194, fields='all')
occ_get_verbatim(key=855998194,
fields=c('scientificName', 'lastCrawled', 'county'))
occ_get_verbatim(key=c(855998194, 620594291))
occ_get_verbatim(key=c(855998194, 620594291), fields='all')
occ_get_verbatim(key=c(855998194, 620594291),
fields=c('scientificName', 'decimalLatitude', 'basisOfRecord'))

# curl options, pass in a named list

occ_get(key=855998194, curlopts = list(verbose=TRUE))

## End(Not run)
104 occ_issues

occ_issues Parse and examine further GBIF occurrence issues on a dataset.

Description
Parse and examine further GBIF occurrence issues on a dataset.

Usage
occ_issues(.data, ..., mutate = NULL)

Arguments
.data Output from a call to occ_search(), occ_data(), or occ_download_import().
The data from occ_download_import is just a regular data.frame so you can
pass in a data.frame to this function, but if it doesn’t have certain columns it will
fail.
... Named parameters to only get back (e.g. cdround), or to remove (e.g. -cdround).
mutate (character) One of:
• split Split issues into new columns.
• expand Expand issue abbreviated codes into descriptive names. for down-
loads datasets, this is not super useful since the issues come to you as ex-
panded already.
• split_expand Split into new columns, and expand issue names.
For split and split_expand, values in cells become y ("yes") or n ("no")

Details
See also the vignette Cleaning data using GBIF issues
Note that you can also query based on issues, e.g., occ_search(taxonKey=1, issue='DEPTH_UNLIKELY').
However, I imagine it’s more likely that you want to search for occurrences based on a taxonomic
name, or geographic area, not based on issues, so it makes sense to pull data down, then clean as
needed using this function.
This function only affects the data element in the gbif class that is returned from a call to occ_search().
Maybe in a future version we will remove the associated records from the hierarchy and media
elements as they are removed from the data element.
You’ll notice that we sort columns to make it easier to glimpse the important parts of your data,
namely taxonomic name, taxon key, latitude and longitude, and the issues. The columns are un-
changed otherwise.

References
https://gbif.github.io/gbif-api/apidocs/org/gbif/api/vocabulary/OccurrenceIssue.html
occ_issues 105

Examples

## Not run:
# what do issues mean, can print whole table
head(gbif_issues())
# or just occurrence related issues
gbif_issues()[which(gbif_issues()$type %in% c("occurrence")),]
# or search for matches
iss <- c('cdround','cudc','gass84','txmathi')
gbif_issues()[ gbif_issues()$code %in% iss, ]

# compare out data to after occ_issues use

(out <- occ_search(limit=100))
out %>% occ_issues(cdround)

# occ_data
(out <- occ_data(limit=100))
out %>% occ_issues(cdround)

# Parsing output by issue

(res <- occ_data(
geometry='POLYGON((30.1 10.1,40 40,20 40,10 20,30.1 10.1))',
limit = 600))

## or parse issues in various ways

### include only rows with cdround issue
gg <- res %>% occ_issues(cdround)
NROW(res$data)
NROW(gg$data)
head(res$data)[,c(1:5)]
head(gg$data)[,c(1:5)]

### remove data rows with certain issue classes

res %>% occ_issues(-cdround, -cudc)

### split issues into separate columns

res %>% occ_issues(mutate = "split")
res %>% occ_issues(-cudc, -mdatunl, mutate = "split")
res %>% occ_issues(gass84, mutate = "split")

### expand issues to more descriptive names

res %>% occ_issues(mutate = "expand")

### split and expand

res %>% occ_issues(mutate = "split_expand")

### split, expand, and remove an issue class

res %>% occ_issues(-cdround, mutate = "split_expand")

## Or you can use occ_issues without %>%

occ_issues(res, -cdround, mutate = "split_expand")

# from GBIF downloaded data via occ_download_* functions

106 occ_metadata

res <- occ_download_get(key="0000066-140928181241064", overwrite=TRUE)

x <- occ_download_import(res)
occ_issues(x, -txmathi)
occ_issues(x, txmathi)
occ_issues(x, gass84)
occ_issues(x, zerocd)
occ_issues(x, gass84, txmathi)
occ_issues(x, mutate = "split")
occ_issues(x, -gass84, mutate = "split")
occ_issues(x, mutate = "expand")
occ_issues(x, mutate = "split_expand")

# occ_search/occ_data with many inputs - give slightly different output

# format than normal 2482598, 2498387
xyz <- occ_data(taxonKey = c(9362842, 2492483, 2435099), limit = 300)
xyz
length(xyz) # length 3
names(xyz) # matches taxonKey values passed in
occ_issues(xyz, -gass84)
occ_issues(xyz, -cdround)
occ_issues(xyz, -cdround, -gass84)

## End(Not run)

occ_metadata Search for catalog numbers, collection codes, collector names, and
institution codes.

Description
Search for catalog numbers, collection codes, collector names, and institution codes.

Usage
occ_metadata(
type = "catalogNumber",
q = NULL,
limit = 5,
pretty = TRUE,
curlopts = list()
)

Arguments
type Type of data, one of catalogNumber, collectionCode, recordedBy, or institution-
Code. Unique partial strings work too, like ’cat’ for catalogNumber
q Search term
limit Number of results, default=5
occ_search 107

pretty Pretty as true (Default) uses cat to print data, FALSE gives character strings.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

References
https://www.gbif.org/developer/occurrence#search

Examples
## Not run:
# catalog number
occ_metadata(type = "catalogNumber", q=122)

# collection code
occ_metadata(type = "collectionCode", q=12)

# institution code
occ_metadata(type = "institutionCode", q='GB')

# recorded by
occ_metadata(type = "recordedBy", q='scott')

# data as character strings

occ_metadata(type = "catalogNumber", q=122, pretty=FALSE)

# Change number of results returned

occ_metadata(type = "catalogNumber", q=122, limit=10)

# Partial unique type strings work too

occ_metadata(type = "cat", q=122)

# Pass on curl options

occ_metadata(type = "cat", q=122, curlopts = list(verbose = TRUE))

## End(Not run)

occ_search Search for GBIF occurrences

Description
Search for GBIF occurrences

Usage
occ_search(
taxonKey = NULL,
scientificName = NULL,
108 occ_search

country = NULL,
publishingCountry = NULL,
hasCoordinate = NULL,
typeStatus = NULL,
recordNumber = NULL,
lastInterpreted = NULL,
continent = NULL,
geometry = NULL,
geom_big = "asis",
geom_size = 40,
geom_n = 10,
recordedBy = NULL,
recordedByID = NULL,
identifiedByID = NULL,
basisOfRecord = NULL,
datasetKey = NULL,
eventDate = NULL,
catalogNumber = NULL,
year = NULL,
month = NULL,
decimalLatitude = NULL,
decimalLongitude = NULL,
elevation = NULL,
depth = NULL,
institutionCode = NULL,
collectionCode = NULL,
hasGeospatialIssue = NULL,
issue = NULL,
search = NULL,
mediaType = NULL,
subgenusKey = NULL,
repatriated = NULL,
phylumKey = NULL,
kingdomKey = NULL,
classKey = NULL,
orderKey = NULL,
familyKey = NULL,
genusKey = NULL,
speciesKey = NULL,
establishmentMeans = NULL,
degreeOfEstablishment = NULL,
protocol = NULL,
license = NULL,
organismId = NULL,
publishingOrg = NULL,
stateProvince = NULL,
waterBody = NULL,
locality = NULL,
occ_search 109

occurrenceStatus = "PRESENT",
gadmGid = NULL,
coordinateUncertaintyInMeters = NULL,
verbatimScientificName = NULL,
eventId = NULL,
identifiedBy = NULL,
networkKey = NULL,
verbatimTaxonId = NULL,
occurrenceId = NULL,
organismQuantity = NULL,
organismQuantityType = NULL,
relativeOrganismQuantity = NULL,
iucnRedListCategory = NULL,
lifeStage = NULL,
isInCluster = NULL,
distanceFromCentroidInMeters = NULL,
geoDistance = NULL,
sex = NULL,
dwcaExtension = NULL,
gbifId = NULL,
gbifRegion = NULL,
projectId = NULL,
programme = NULL,
preparations = NULL,
datasetId = NULL,
datasetName = NULL,
publishedByGbifRegion = NULL,
island = NULL,
islandGroup = NULL,
taxonId = NULL,
taxonConceptId = NULL,
taxonomicStatus = NULL,
acceptedTaxonKey = NULL,
collectionKey = NULL,
institutionKey = NULL,
otherCatalogNumbers = NULL,
georeferencedBy = NULL,
installationKey = NULL,
hostingOrganizationKey = NULL,
crawlId = NULL,
modified = NULL,
higherGeography = NULL,
fieldNumber = NULL,
parentEventId = NULL,
samplingProtocol = NULL,
sampleSizeUnit = NULL,
pathway = NULL,
gadmLevel0Gid = NULL,
110 occ_search

gadmLevel1Gid = NULL,
gadmLevel2Gid = NULL,
gadmLevel3Gid = NULL,
earliestEonOrLowestEonothem = NULL,
latestEonOrHighestEonothem = NULL,
earliestEraOrLowestErathem = NULL,
latestEraOrHighestErathem = NULL,
earliestPeriodOrLowestSystem = NULL,
latestPeriodOrHighestSystem = NULL,
earliestEpochOrLowestSeries = NULL,
latestEpochOrHighestSeries = NULL,
earliestAgeOrLowestStage = NULL,
latestAgeOrHighestStage = NULL,
lowestBiostratigraphicZone = NULL,
highestBiostratigraphicZone = NULL,
group = NULL,
formation = NULL,
member = NULL,
bed = NULL,
associatedSequences = NULL,
isSequenced = NULL,
startDayOfYear = NULL,
endDayOfYear = NULL,
limit = 500,
start = 0,
fields = "all",
return = NULL,
facet = NULL,
facetMincount = NULL,
facetMultiselect = NULL,
skip_validate = TRUE,
curlopts = list(http_version = 2),
...
)

Arguments
taxonKey (numeric) A taxon key from the GBIF backbone. All included and synonym
taxa are included in the search, so a search for aves with taxononKey=212
will match all birds, no matter which species. You can pass many keys to
occ_search(taxonKey=c(1,212)).
scientificName A scientific name from the GBIF backbone. All included and synonym taxa are
included in the search.
country (character) The 2-letter country code (ISO-3166-1) in which the occurrence was
recorded. enumeration_country().
publishingCountry
The 2-letter country code (as per ISO-3166-1) of the country in which the oc-
currence was recorded. See enumeration_country().
occ_search 111

hasCoordinate (logical) Return only occurrence records with lat/long data (TRUE) or all records
(FALSE, default).
typeStatus Type status of the specimen. One of many options.
recordNumber Number recorded by collector of the data, different from GBIF record number.
lastInterpreted
Date the record was last modified in GBIF, in ISO 8601 format: yyyy, yyyy-
MM, yyyy-MM-dd, or MM-dd. Supports range queries, ’smaller,larger’ (e.g.,
’1990,1991’, whereas ’1991,1990’ wouldn’t work).
continent The source supplied continent.
• "africa"
• "antarctica"
• "asia"
• "europe"
• "north_america"
• "oceania"
• "south_america"
Continent is not inferred but only populated if provided by the dataset publisher.
Applying this filter may exclude many relevant records.
geometry (character) Searches for occurrences inside a polygon in Well Known Text (WKT)
format. A WKT shape written as either
• "POINT"
• "LINESTRING"
• "LINEARRING"
• "POLYGON"
• "MULTIPOLYGON"
For Example, "POLYGON((37.08 46.86,38.06 46.86,38.06 47.28,37.08 47.28,
37.0 46.8))". See also the section WKT below.
geom_big (character) One"bbox" or "asis" (default).
geom_size (integer) An integer indicating size of the cell. Default: 40.
geom_n (integer) An integer indicating number of cells in each dimension. Default: 10.
recordedBy (character) The person who recorded the occurrence.
recordedByID (character) Identifier (e.g. ORCID) for the person who recorded the occurrence
identifiedByID (character) Identifier (e.g. ORCID) for the person who provided the taxonomic
identification of the occurrence.
basisOfRecord (character) The specific nature of the data record. See here.
• "FOSSIL_SPECIMEN"
• "HUMAN_OBSERVATION"
• "MATERIAL_CITATION"
• "MATERIAL_SAMPLE"
• "LIVING_SPECIMEN"
• "MACHINE_OBSERVATION"
112 occ_search

• "OBSERVATION"
• "PRESERVED_SPECIMEN"
• "OCCURRENCE"
datasetKey (character) The occurrence dataset uuid key. That can be found in the dataset
page url. For example, "7e380070-f762-11e1-a439-00145 eb45e9a" is the key
for Natural History Museum (London) Collection Specimens.
eventDate (character) Occurrence date in ISO 8601 format: yyyy, yyyy-MM, yyyy-MM-
dd, or MM-dd. Supports range queries, ’smaller,larger’ (’1990,1991’, whereas
’1991,1990’ wouldn’t work).
catalogNumber (character) An identifier of any form assigned by the source within a physical
collection or digital dataset for the record which may not unique, but should be
fairly unique in combination with the institution and collection code.
year The 4 digit year. A year of 98 will be interpreted as AD 98. Supports range
queries, ’smaller,larger’ (e.g., ’1990,1991’, whereas 1991, 1990’ wouldn’t work).
month The month of the year, starting with 1 for January. Supports range queries,
’smaller,larger’ (e.g., ’1,2’, whereas ’2,1’ wouldn’t work).
decimalLatitude
Latitude in decimals between -90 and 90 based on WGS84. Supports range
queries, ’smaller,larger’ (e.g., ’25,30’, whereas ’30,25’ wouldn’t work).
decimalLongitude
Longitude in decimals between -180 and 180 based on WGS84. Supports range
queries (e.g., ’-0.4,-0.2’, whereas ’-0.2,-0.4’ wouldn’t work).
elevation Elevation in meters above sea level. Supports range queries, ’smaller,larger’
(e.g., ’5,30’, whereas ’30,5’ wouldn’t work).
depth Depth in meters relative to elevation. For example 10 meters below a lake sur-
face with given elevation. Supports range queries, ’smaller,larger’ (e.g., ’5,30’,
whereas ’30,5’ wouldn’t work).
institutionCode
An identifier of any form assigned by the source to identify the institution the
record belongs to.
collectionCode (character) An identifier of any form assigned by the source to identify the phys-
ical collection or digital dataset uniquely within the text of an institution.
hasGeospatialIssue
(logical) Includes/excludes occurrence records which contain spatial issues (as
determined in our record interpretation), i.e. hasGeospatialIssue=TRUE re-
turns only those records with spatial issues while hasGeospatialIssue=FALSE
includes only records without spatial issues. The absence of this parameter re-
turns any record with or without spatial issues.
issue (character) One or more of many possible issues with each occurrence record.
Issues passed to this parameter filter results by the issue. One of many options.
See here for definitions.
search (character) Query terms. The value for this parameter can be a simple word or a
phrase. For example, search="puma"
mediaType (character) Media type of "MovingImage", "Sound", or "StillImage".
occ_search 113

subgenusKey (numeric) Subgenus classification key.

repatriated (character) Searches for records whose publishing country is different to the
country where the record was recorded in.
phylumKey (numeric) Phylum classification key.
kingdomKey (numeric) Kingdom classification key.
classKey (numeric) Class classification key.
orderKey (numeric) Order classification key.
familyKey (numeric) Family classification key.
genusKey (numeric) Genus classification key.
speciesKey (numeric) Species classification key.
establishmentMeans
(character) provides information about whether an organism or organisms have
been introduced to a given place and time through the direct or indirect activity
of modern humans.
• "Introduced"
• "Native"
• "NativeReintroduced"
• "Vagrant"
• "Uncertain"
• "IntroducedAssistedColonisation"
degreeOfEstablishment
(character) Provides information about degree to which an Organism survives,
reproduces, and expands its range at the given place and time. One of many
options.
protocol (character) Protocol or mechanism used to provide the occurrence record. One
of many options.
license (character) The type license applied to the dataset or record.
• "CC0_1_0"
• "CC_BY_4_0"
• "CC_BY_NC_4_0"
organismId (numeric) An identifier for the Organism instance (as opposed to a particular
digital record of the Organism). May be a globally unique identifier or an iden-
tifier specific to the data set.
publishingOrg (character) The publishing organization key (a UUID).
stateProvince (character) The name of the next smaller administrative region than country
(state, province, canton, department, region, etc.) in which the Location occurs.
waterBody (character) The name of the water body in which the locations occur
locality (character) The specific description of the place.
occurrenceStatus
(character) Default is "PRESENT". Specify whether search should return "PRESENT"
or "ABSENT" data.
114 occ_search

gadmGid (character) The gadm id of the area occurrences are desired from. https://gadm.org/.
coordinateUncertaintyInMeters
A number or range between 0-1,000,000 which specifies the desired coordi-
nate uncertainty. A coordinateUncertainty InMeters=1000 will be interpreted
all records with exactly 1000m. Supports range queries, ’smaller,larger’ (e.g.,
’1000,10000’, whereas ’10000,1000’ wouldn’t work).
verbatimScientificName
(character) Scientific name as provided by the source.
eventId (character) identifier(s) for a sampling event.
identifiedBy (character) names of people, groups, or organizations.
networkKey (character) The occurrence network key (a uuid) who assigned the Taxon to the
subject.
verbatimTaxonId
(character) The taxon identifier provided to GBIF by the data publisher.
occurrenceId (character) occurrence id from source.
organismQuantity
A number or range which specifies the desired organism quantity. An organ-
ismQuantity=5 will be interpreted all records with exactly 5. Supports range
queries, smaller,larger (e.g., ’5,20’, whereas ’20,5’ wouldn’t work).
organismQuantityType
(character) The type of quantification system used for the quantity of organisms.
For example, "individuals" or "biomass".
relativeOrganismQuantity
(numeric) A relativeOrganismQuantity=0.1 will be interpreted all records with
exactly 0.1 The relative measurement of the quantity of the organism (a number
between 0-1). Supports range queries, "smaller,larger" (e.g., ’0.1,0.5’, whereas
’0.5,0.1’ wouldn’t work).
iucnRedListCategory
(character) The IUCN threat status category.
• "NE" (Not Evaluated)
• "DD" (Data Deficient)
• "LC" (Least Concern)
• "NT" (Near Threatened)
• "VU" (Vulnerable)
• "EN" (Endangered)
• "CR" (Critically Endangered)
• "EX" (Extinct)
• "EW" (Extinct in the Wild)
lifeStage (character) the life stage of the occurrence. One of many options.
isInCluster (logical) identify potentially related records on GBIF.
distanceFromCentroidInMeters
A number or range. A value of "2000,*" means at least 2km from known cen-
troids. A value of "0" would mean occurrences exactly on known centroids. A
value of "0,2000" would mean within 2km of centroids. Max value is 5000.
occ_search 115

geoDistance (character) Filters to match occurrence records with coordinate values within a
specified distance of a coordinate. Distance may be specified in kilometres (km)
or metres (m). Example : "90,100,5km"
sex (character) The sex of the biological individual(s) represented in the occurrence.
dwcaExtension (character) A known Darwin Core Archive extension RowType. Limits the
search to occurrences which have this extension, although they will not nec-
essarily have any useful data recorded using the extension.
gbifId (numeric) The unique GBIF key for a single occurrence.
gbifRegion (character) Gbif region based on country code.
projectId (character) The identifier for a project, which is often assigned by a funded
programme.
programme (character) A group of activities, often associated with a specific funding stream,
such as the GBIF BID programme.
preparations (character) Preparation or preservation method for a specimen.
datasetId (character) The ID of the dataset. Parameter may be repeated. Example :
https://doi.org/10.1594/PANGAEA.315492
datasetName (character) The exact name of the dataset. Not the same as dataset title.
publishedByGbifRegion
(character) GBIF region based on the owning organization’s country.
island (character) The name of the island on or near which the location occurs.
islandGroup (character) The name of the island group in which the location occurs.
taxonId (character) The taxon identifier provided to GBIF by the data publisher. Exam-
ple : urn:lsid:dyntaxa.se:Taxon:103026
taxonConceptId (character) An identifier for the taxonomic concept to which the record refers
- not for the nomenclatural details of a taxon. Example : 8fa58e08-08de-4ac1-
b69c-1235340b7001
taxonomicStatus
(character) A taxonomic status. Example : SYNONYM
acceptedTaxonKey
(numeric) A taxon key from the GBIF backbone. Only synonym taxa are in-
cluded in the search, so a search for Aves with acceptedTaxonKey=212 will
match occurrences identified as birds, but not any known family, genus or species
of bird.
collectionKey (character) A key (UUID) for a collection registered in the Global Registry of
Scientific Collections. Example : dceb8d52-094c-4c2c-8960-75e0097c6861
institutionKey (character) A key (UUID) for an institution registered in the Global Registry of
Scientific Collections.
otherCatalogNumbers
(character) Previous or alternate fully qualified catalog numbers.
georeferencedBy
(character) Name of a person, group, or organization who determined the geo-
reference (spatial representation) for the location. Example : Brad Millen
116 occ_search

installationKey
(character) The occurrence installation key (a UUID). Example : 17a83780-
3060-4851-9d6f-029d5fcb81c9
hostingOrganizationKey
(character) The key (UUID) of the publishing organization whose installation
(server) hosts the original dataset. Example : fbca90e3-8aed-48b1-84e3-369afbd000ce
crawlId (numeric) Crawl attempt that harvested this record.
modified (character) The most recent date-time on which the occurrence was changed,
according to the publisher. Can be a range. Example : 2023-02-20
higherGeography
(character) Geographic name less specific than the information captured in the
locality term.
fieldNumber (character) An identifier given to the event in the field. Often serves as a link
between field notes and the event.
parentEventId (character) An identifier for the information associated with a sampling event.
samplingProtocol
(character) The name of, reference to, or description of the method or protocol
used during a sampling event. Example : malaise trap
sampleSizeUnit (character) The unit of measurement of the size (time duration, length, area, or
volume) of a sample in a sampling event. Example : hectares
pathway (character) The process by which an organism came to be in a given place at a
given time, as defined in the GBIF Pathway vocabulary. Example : Agriculture
gadmLevel0Gid (character) A GADM geographic identifier at the zero level, for example AGO.
gadmLevel1Gid (character) A GADM geographic identifier at the first level, for example AGO.1_1.
gadmLevel2Gid (character) A GADM geographic identifier at the second level, for example
AFG.1.1_1.
gadmLevel3Gid (character) A GADM geographic identifier at the third level, for example AFG.1.1.1_1.
earliestEonOrLowestEonothem
(character) geochronologic era term.
latestEonOrHighestEonothem
(character) geochronologic era term.
earliestEraOrLowestErathem
(character) geochronologic era term.
latestEraOrHighestErathem
(character) geochronologic era term.
earliestPeriodOrLowestSystem
(character) geochronologic era term.
latestPeriodOrHighestSystem
(character) geochronologic era term.
earliestEpochOrLowestSeries
(character) geochronologic era term.
latestEpochOrHighestSeries
(character) geochronologic era term.
occ_search 117

earliestAgeOrLowestStage
(character) geochronologic era term.
latestAgeOrHighestStage
(character) geochronologic era term.
lowestBiostratigraphicZone
(character) geochronologic era term.
highestBiostratigraphicZone
(character) geochronologic era term.
group (character) The full name of the lithostratigraphic group from which the material
entity was collected.
formation (character) The full name of the lithostratigraphic formation from which the
material entity was collected.
member (character) The full name of the lithostratigraphic member from which the ma-
terial entity was collected.
bed (character) The full name of the lithostratigraphic bed from which the material
entity was collected.
associatedSequences
(character) Identifier (publication, global unique identifier, URI) of genetic se-
quence information associated with the material entity. Example : http://www.ncbi.nlm.nih.gov/nuccore/U
isSequenced (logical) Indicates whether associatedSequences genetic sequence informa-
tion exists.
startDayOfYear (numeric) The earliest integer day of the year on which the event occurred.
endDayOfYear (numeric) The latest integer day of the year on which the event occurred.
limit Number of records to return. Default: 500. Note that the per request maximum
is 300, but since we set it at 500 for the function, we do two requests to get
you the 500 records (if there are that many). Note that there is a hard maxi-
mum of 100,000, which is calculated as the limit+start, so start=99,000
and limit=2000 won’t work
start Record number to start at. Use in combination with limit to page through results.
Note that we do the paging internally for you, but you can manually set the
start parameter
fields (character) Default (’all’) returns all fields. ’minimal’ returns just taxon name,
key, datasetKey, latitude, and longitute. Or specify each field you want returned
by name, e.g. fields = c(’name’,’latitude’,’elevation’).
return Defunct. All components (meta, hierarchy, data, media, facets) are returned
now; index to the one(s) you want. See occ_data() if you just want the data
component
facet (character) a character vector of length 1 or greater. Required.
facetMincount (numeric) minimum number of records to be included in the faceting results
facetMultiselect
(logical) Set to TRUE to still return counts for values that are not currently filtered.
See examples. Default: FALSE
Faceting: All fields can be faceted on except for last "lastInterpreted", "event-
Date", and "geometry"
118 occ_search

You can do facet searches alongside searching occurrence data, and return both,
or only return facets, or only occurrence data, etc.
skip_validate (logical) whether to skip wellknown::validate_wkt call or not. passed down
to check_wkt(). Default: TRUE
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options
... additional facet parameters

Value
An object of class gbif, which is a S3 class list, with slots for metadata (meta), the occurrence
data itself (data), the taxonomic hierarchy data (hier), and media metadata (media). In addition,
the object has attributes listing the user supplied arguments and whether it was a ’single’ or ’many’
search; that is, if you supply two values of the datasetKey parameter to searches are done, and
it’s a ’many’. meta is a list of length four with offset, limit, endOfRecords and count fields. data
is a tibble (aka data.frame). hier is a list of data.frames of the unique set of taxa found, where
each data.frame is its taxonomic classification. media is a list of media objects, where each element
holds a set of metadata about the media object.

Multiple values passed to a parameter

There are some parameters you can pass multiple values to in a vector, each value of which produces
a different request (multiple different requests = c("a","b")). Some parameters allow multiple values
to be passed in the same request (multiple same request = "a;b") in a semicolon separated string
(e.g., ’a;b’); if given we’ll do a single request with that parameter repeated for each value given
(e.g., foo=a&foo=b if the parameter is foo).
See article Multiple Values.

Hierarchies
Hierarchies are returned with each occurrence object. There is no option to return them from the
API. However, within the occ_search function you can select whether to return just hierarchies,
just data, all of data and hierarchies and metadata, or just metadata. If all hierarchies are the same
we just return one for you.

curl debugging
You can pass parameters not defined in this function into the call to the GBIF API to control things
about the call itself using curlopts. See an example below that passes in the verbose function to
get details on the http call.

WKT
Examples of valid WKT objects:

• ’POLYGON((-19.5 34.1, 27.8 34.1, 35.9 68.1, -25.3 68.1, -19.5 34.1))’
• ’MULTIPOLYGON(((-123 38,-116 38,-116 43,-123 43,-123 38)),((-97 41,-93 41,-93 45,-97
45,-97 41)))’
occ_search 119

• ’POINT(-120 40)’
• ’LINESTRING(3 4,10 50,20 25)’

Note that GBIF expects counter-clockwise winding order for WKT. You can supply clockwise
WKT, but GBIF treats it as an exclusion, so you get all data not inside the WKT area. occ_download()
behaves differently in that you should simply get no data back at all with clockwise WKT.

Long WKT
Options for handling long WKT strings: Note that long WKT strings are specially handled when us-
ing occ_search or occ_data. Here are the three options for long WKT strings (> 1500 characters),
set one of these three via the parameter geom_big:

• asis - the default setting. This means we don’t do anything internally. That is, we just pass on
your WKT string just as we’ve done before in this package.
• axe - this option is deprecated since rgbif v3.8.0. Might return error, since the GBIF’s polygon
interpretation has changed.
This method uses sf::st_make_grid and sf::st_intersection, which has two parameters
cellsize and n. You can tweak those parameters here by tweaking geom_size and geom_n.
geom_size seems to be more useful in toggling the number of WKT strings you get back.
See wkt_parse to manually break make WKT bounding box from a larger WKT string, or
break a larger WKT string into many smaller ones.
• bbox - this option checks whether your WKT string is longer than 1500 characters, and if it
is we create a bounding box from the WKT, do the GBIF search with that bounding box, then
prune the resulting data to only those occurrences in your original WKT string. There is a big
caveat however. Because we create a bounding box from the WKT, and the limit parameter
determines some subset of records to get, then when we prune the resulting data to the WKT,
the number of records you get could be less than what you set with your limit parameter.
However, you could set the limit to be high enough so that you get all records back found in
that bounding box, then you’ll get all the records available within the WKT.

Counts
There is a slight difference in the way records are counted here vs. results from occ_count. For
equivalent outcomes, in this function use hasCoordinate=TRUE, and hasGeospatialIssue=FALSE
to have the same outcome using occ_count with isGeoreferenced=TRUE

Note
Maximum number of records you can get with this function is 100,000. See https://www.gbif.org/developer/occurrence

References
https://www.gbif.org/developer/occurrence#search

See Also
downloads(), occ_data()
120 occ_search

Examples

## Not run:
# Search by species name, using \code{\link{name_backbone}} first to get key
(key <- name_suggest(q='Helianthus annuus', rank='species')$data$key[1])
occ_search(taxonKey=key, limit=2)

# Return 20 results, this is the default by the way

occ_search(taxonKey=key, limit=20)

# Get just metadata

occ_search(taxonKey=key, limit=0)$meta

# Instead of getting a taxon key first, you can search for a name directly
## However, note that using this approach (with \code{scientificName="..."})
## you are getting synonyms too. The results for using \code{scientifcName} and
## \code{taxonKey} parameters are the same in this case, but I wouldn't be surprised if for some
## names they return different results
occ_search(scientificName = 'Ursus americanus')
key <- name_backbone(name = 'Ursus americanus', rank='species')$usageKey
occ_search(taxonKey = key)

# Search by dataset key

occ_search(datasetKey='7b5d6a48-f762-11e1-a439-00145eb45e9a', limit=20)$data

# Search by catalog number

occ_search(catalogNumber="49366", limit=20)
## separate requests: use a vector of strings
occ_search(catalogNumber=c("49366","Bird.27847588"), limit=10)
## one request, many instances of same parameter: use semi-colon sep. string
occ_search(catalogNumber="49366;Bird.27847588", limit=10)

# Get all data, not just lat/long and name

occ_search(taxonKey=key, fields='all', limit=20)

# Or get specific fields. Note that this isn't done on GBIF's side of things. This
# is done in R, but before you get the return object, so other fields are garbage
# collected
occ_search(taxonKey=key, fields=c('name','basisOfRecord','protocol'), limit=20)

# Use paging parameters (limit and start) to page. Note the different results
# for the two queries below.
occ_search(datasetKey='7b5d6a48-f762-11e1-a439-00145eb45e9a',start=10,limit=5)$data
occ_search(datasetKey='7b5d6a48-f762-11e1-a439-00145eb45e9a',start=20,limit=5)$data

# Many dataset keys

## separate requests: use a vector of strings
occ_search(datasetKey=c("50c9509d-22c7-4a22-a47d-8c48425ef4a7",
"7b5d6a48-f762-11e1-a439-00145eb45e9a"), limit=20)
## one request, many instances of same parameter: use semi-colon sep. string
v="50c9509d-22c7-4a22-a47d-8c48425ef4a7;7b5d6a48-f762-11e1-a439-00145eb45e9a"
occ_search(datasetKey = v, limit=20)
occ_search 121

# Occurrence data: lat/long data, and associated metadata with occurrences

## The `data` slot has a data.frame of all data together
## for easy manipulation
occ_search(taxonKey=key, limit=20)$data

# Taxonomic hierarchy data

## In the `hier` slot
occ_search(taxonKey=key, limit=10)$hier

# Search by recorder
occ_search(recordedBy="smith", limit=20)

# Many collector names

occ_search(recordedBy=c("smith","BJ Stacey"), limit=20)

# recordedByID
occ_search(recordedByID="https://orcid.org/0000-0003-1691-239X", limit=20)

# identifiedByID
occ_search(identifiedByID="https://orcid.org/0000-0003-4710-2648", limit=20)

# Pass in curl options for extra fun

occ_search(taxonKey=2433407, limit=20, curlopts=list(verbose=TRUE))$hier
occ_search(taxonKey=2433407, limit=20,
curlopts = list(
noprogress = FALSE,
progressfunction = function(down, up) {
cat(sprintf("up: %d | down %d\n", up, down))
return(TRUE)
}
)
)$hier
# occ_search(taxonKey=2433407, limit=20,
# curlopts = list(timeout_ms = 1))

# Search for many species

splist <- c('Cyanocitta stelleri', 'Junco hyemalis', 'Aix sponsa')
keys <- sapply(splist, function(x) name_suggest(x)$data$key[1], USE.NAMES=FALSE)
## separate requests: use a vector of strings
occ_search(taxonKey = keys, limit=5)
## one request, many instances of same parameter: use semi-colon sep. string
occ_search(taxonKey = paste0(keys, collapse = ";"), limit=5)

# Search using a synonym name

# Note that you'll see a message printing out that the accepted name will be used
occ_search(scientificName = 'Pulsatilla patens', fields = c('name','scientificName'), limit=5)

# Search on latitidue and longitude

occ_search(decimalLatitude=48, decimalLongitude=10)

# Search on a bounding box

## in well known text format
### polygon
122 occ_search

occ_search(geometry='POLYGON((30.1 10.1,40 40,20 40,10 20,30.1 10.1))', limit=20)

### multipolygon
wkt <- 'MULTIPOLYGON(((-123 38,-116 38,-116 43,-123 43,-123 38)),
((-97 41,-93 41,-93 45,-97 45,-97 41)))'
occ_search(geometry = gsub("\n\\s+", "", wkt), limit = 20)

## taxonKey + WKT
key <- name_suggest(q='Aesculus hippocastanum')$data$key[1]
occ_search(taxonKey=key, geometry='POLYGON((30.1 10.1,40 40,20 40,10 20,30.1 10.1))',
limit=20)
## or using bounding box, converted to WKT internally
occ_search(geometry=c(-125.0,38.4,-121.8,40.9), limit=20)

# Search on a long WKT string - too long for a GBIF search API request
## We internally convert your WKT string to a bounding box
## then do the query
## then clip the results down to just those in the original polygon
## - Alternatively, you can set the parameter `geom_big="bbox"`
## - An additional alternative is to use the GBIF download API, see ?downloads
wkt <- "POLYGON((-9.178796777343678 53.22769021556159,
-12.167078027343678 51.56540789297837,
-12.958093652343678 49.78333685689162,-11.024499902343678 49.21251756301334,
-12.079187402343678 46.68179685941719,-15.067468652343678 45.83103608186854,
-15.770593652343678 43.58271629699817,-15.067468652343678 41.57676278827219,
-11.815515527343678 40.44938999172728,-12.958093652343678 37.72112962230871,
-11.639734277343678 36.52987439429357,-8.299890527343678 34.96062625095747,
-8.739343652343678 32.62357394385735,-5.223718652343678 30.90497915232165,
1.1044063476563224 31.80562077746643,1.1044063476563224 30.754036557416256,
6.905187597656322 32.02942785462211,5.147375097656322 32.99292810780193,
9.629796972656322 34.164474406524725,10.860265722656322 32.91918014319603,
14.551671972656322 33.72700959356651,13.409093847656322 34.888564192275204,
16.748937597656322 35.104560368110114,19.561437597656322 34.81643887792552,
18.594640722656322 36.38849705969625,22.989171972656322 37.162874858929854,
19.825109472656322 39.50651757842751,13.760656347656322 38.89353140585116,
14.112218847656322 42.36091601976124,10.596593847656322 41.11488736647705,
9.366125097656322 43.70991402658437,5.059484472656322 42.62015372417812,
2.3348750976563224 45.21526500321446,-0.7412967773436776 46.80225692528942,
6.114171972656322 47.102229890207894,8.047765722656322 45.52399303437107,
12.881750097656322 48.22681126957933,9.190343847656322 48.693079457106684,
8.750890722656322 50.68283120621287,5.059484472656322 50.40356146487845,
4.268468847656322 52.377558897655156,1.4559688476563224 53.28027243658647,
0.8407344726563224 51.62000971578333,0.5770625976563224 49.32721423860726,
-2.5869999023436776 49.49875947592088,-2.4991092773436776 51.18135535408638,
-2.0596561523436776 52.53822562473851,-4.696374902343678 51.67454591918756,
-5.311609277343678 50.009802108095776,-6.629968652343678 48.75106196817059,
-7.684656152343678 50.12263634382465,-6.190515527343678 51.83776110910459,
-5.047937402343678 54.267098895684235,-6.893640527343678 53.69860705549198,
-8.915124902343678 54.77719740243195,-12.079187402343678 54.52294465763567,
-13.573328027343678 53.437631551347174,
-11.288171777343678 53.48995552517918,
-9.178796777343678 53.22769021556159))"
wkt <- gsub("\n", " ", wkt)
occ_search 123

#### Default option with large WKT string fails

# res <- occ_search(geometry = wkt)

#### if WKT too long, with 'geom_big=bbox': makes into bounding box
res <- occ_search(geometry = wkt, geom_big = "bbox")$data

# Search on country
occ_search(country='US', fields=c('name','country'), limit=20)
occ_search(country='FR', fields=c('name','country'), limit=20)
occ_search(country='DE', fields=c('name','country'), limit=20)
### separate requests: use a vector of strings
occ_search(country=c('US','DE'), limit=20)
### one request, many instances of same parameter: use semi-colon sep. string
occ_search(country = 'US;DE', limit=20)

# Get only occurrences with lat/long data

occ_search(taxonKey=key, hasCoordinate=TRUE, limit=20)

# Get only occurrences that were recorded as living specimens

occ_search(taxonKey=key, basisOfRecord="LIVING_SPECIMEN", hasCoordinate=TRUE, limit=20)
## multiple values in a vector = a separate request for each value
occ_search(taxonKey=key,
basisOfRecord=c("LIVING_SPECIMEN", "HUMAN_OBSERVATION"), limit=20)
## mutiple values in a single string, ";" separated = one request including all values
occ_search(taxonKey=key,
basisOfRecord="LIVING_SPECIMEN;HUMAN_OBSERVATION", limit=20)

# Get occurrences for a particular eventDate

occ_search(taxonKey=key, eventDate="2013", limit=20)
occ_search(taxonKey=key, year="2013", limit=20)
occ_search(taxonKey=key, month="6", limit=20)

# Get occurrences based on depth

key <- name_backbone(name='Salmo salar', kingdom='animals')$speciesKey
occ_search(taxonKey=key, depth="5", limit=20)

# Get occurrences based on elevation

key <- name_backbone(name='Puma concolor', kingdom='animals')$speciesKey
occ_search(taxonKey=key, elevation=50, hasCoordinate=TRUE, limit=20)

# Get occurrences based on institutionCode

occ_search(institutionCode="TLMF", limit=20)
### separate requests: use a vector of strings
occ_search(institutionCode=c("TLMF","ArtDatabanken"), limit=20)
### one request, many instances of same parameter: use semi-colon sep. string
occ_search(institutionCode = "TLMF;ArtDatabanken", limit=20)

# Get occurrences based on collectionCode

occ_search(collectionCode="Floristic Databases MV - Higher Plants", limit=20)
occ_search(collectionCode=c("Floristic Databases MV - Higher Plants","Artport"))

# Get only those occurrences with spatial issues

occ_search(taxonKey=key, hasGeospatialIssue=TRUE, limit=20)
124 occ_search

# Search using a query string

occ_search(search = "kingfisher", limit=20)

# search on repatriated - doesn't work right now

# occ_search(repatriated = "")

# search on phylumKey
occ_search(phylumKey = 7707728, limit = 5)

# search on kingdomKey
occ_search(kingdomKey = 1, limit = 5)

# search on classKey
occ_search(classKey = 216, limit = 5)

# search on orderKey
occ_search(orderKey = 7192402, limit = 5)

# search on familyKey
occ_search(familyKey = 3925, limit = 5)

# search on genusKey
occ_search(genusKey = 1935496, limit = 5)

# search on establishmentMeans
occ_search(establishmentMeans = "INVASIVE", limit = 5)
occ_search(establishmentMeans = "NATIVE", limit = 5)
occ_search(establishmentMeans = "UNCERTAIN", limit = 5)

# search on protocol
occ_search(protocol = "DIGIR", limit = 5)

# search on license
occ_search(license = "CC_BY_4_0", limit = 5)

# search on organismId
occ_search(organismId = "100", limit = 5)

# search on publishingOrg
occ_search(publishingOrg = "28eb1a3f-1c15-4a95-931a-4af90ecb574d", limit = 5)

# search on stateProvince
occ_search(stateProvince = "California", limit = 5)

# search on waterBody
occ_search(waterBody = "AMAZONAS BASIN, RIO JURUA", limit = 5)

# search on locality
res <- occ_search(locality = c("Trondheim", "Hovekilen"), limit = 5)
res$Trondheim$data
res$Hovekilen$data
occ_search 125

# Range queries
## See Detail for parameters that support range queries
occ_search(depth='50,100') # this is a range depth, with lower/upper limits in character string
occ_search(depth=c(50,100)) # this is not a range search, but does two searches for each depth

## Range search with year

occ_search(year='1999,2000', limit=20)

## Range search with latitude

occ_search(decimalLatitude='29.59,29.6')

## Range search with distanceFromCentroidInMeters

occ_search(distanceFromCentroidInMeters = "2000,*") # at least 2km from centroids
occ_search(distanceFromCentroidInMeters = "0,2000") # close to centroids within 2km
occ_search(distanceFromCentroidInMeters = 0) # exactly on centroids

# Search by specimen type status

## Look for possible values of the typeStatus parameter looking at the typestatus dataset
occ_search(typeStatus = 'allotype', fields = c('name','typeStatus'))

# Search by specimen record number

## This is the record number of the person/group that submitted the data, not GBIF's numbers
## You can see that many different groups have record number 1, so not super helpful
occ_search(recordNumber = 1, fields = c('name','recordNumber','recordedBy'))

# Search by last time interpreted: Date the record was last modified in GBIF
## The lastInterpreted parameter accepts ISO 8601 format dates, including
## yyyy, yyyy-MM, yyyy-MM-dd, or MM-dd. Range queries are accepted for lastInterpreted
occ_search(lastInterpreted = '2014-04-02', fields = c('name','lastInterpreted'))

# Search by continent
## One of africa, antarctica, asia, europe, north_america, oceania, or south_america
occ_search(continent = 'south_america')$meta
occ_search(continent = 'africa')$meta
occ_search(continent = 'oceania')$meta
occ_search(continent = 'antarctica')$meta

# Search for occurrences with images

occ_search(mediaType = 'StillImage')$media
occ_search(mediaType = 'MovingImage')$media
occ_search(mediaType = 'Sound')$media

# Query based on issues - see Details for options

## one issue
occ_search(taxonKey=1, issue='DEPTH_UNLIKELY', fields =
c('name','key','decimalLatitude','decimalLongitude','depth'))
## two issues
occ_search(taxonKey=1, issue=c('DEPTH_UNLIKELY','COORDINATE_ROUNDED'))
# Show all records in the Arizona State Lichen Collection that cant be matched to the GBIF
# backbone properly:
occ_search(datasetKey='84c0e1a0-f762-11e1-a439-00145eb45e9a',
126 occ_search

issue=c('TAXON_MATCH_NONE','TAXON_MATCH_HIGHERRANK'))

# Parsing output by issue

(res <- occ_search(geometry='POLYGON((30.1 10.1,40 40,20 40,10 20,30.1 10.1))', limit = 50))
## what do issues mean, can print whole table, or search for matches
head(gbif_issues())
gbif_issues()[ gbif_issues()$code %in% c('cdround','cudc','gass84','txmathi'), ]
## or parse issues in various ways
### remove data rows with certain issue classes
library('magrittr')
res %>% occ_issues(gass84)
### split issues into separate columns
res %>% occ_issues(mutate = "split")
### expand issues to more descriptive names
res %>% occ_issues(mutate = "expand")
### split and expand
res %>% occ_issues(mutate = "split_expand")
### split, expand, and remove an issue class
res %>% occ_issues(-cudc, mutate = "split_expand")

# If you try multiple values for two different parameters you are wacked on the hand
# occ_search(taxonKey=c(2482598,2492010), recordedBy=c("smith","BJ Stacey"))

# Get a lot of data, here 1500 records for Helianthus annuus

# out <- occ_search(taxonKey=key, limit=1500)
# nrow(out$data)

# If you pass in an invalid polygon you get hopefully informative errors

### the WKT string is fine, but GBIF says bad polygon
wkt <- 'POLYGON((-178.59375 64.83258989321493,-165.9375 59.24622380205539,
-147.3046875 59.065977905449806,-130.78125 51.04484764446178,-125.859375 36.70806354647625,
-112.1484375 23.367471303759686,-105.1171875 16.093320185359257,-86.8359375 9.23767076398516,
-82.96875 2.9485268155066175,-82.6171875 -14.812060061226388,-74.8828125 -18.849111862023985,
-77.34375 -47.661687803329166,-84.375 -49.975955187343295,174.7265625 -50.649460483096114,
179.296875 -42.19189902447192,-176.8359375 -35.634976650677295,176.8359375 -31.835565983656227,
163.4765625 -6.528187613695323,152.578125 1.894796132058301,135.703125 4.702353722559447,
127.96875 15.077427674847987,127.96875 23.689804541429606,139.921875 32.06861069132688,
149.4140625 42.65416193033991,159.2578125 48.3160811030533,168.3984375 57.019804336633165,
178.2421875 59.95776046458139,-179.6484375 61.16708631440347,-178.59375 64.83258989321493))'

# occ_search(geometry = gsub("\n", '', wkt))

### unable to parse due to last number pair needing two numbers, not one
# wkt <- 'POLYGON((-178.5 64.8,-165.9 59.2,-147.3 59.0,-130.7 51.0,-125.8))'
# occ_search(geometry = wkt)

### unable to parse due to unclosed string

# wkt <- 'POLYGON((-178.5 64.8,-165.9 59.2,-147.3 59.0,-130.7 51.0))'
# occ_search(geometry = wkt)
### another of the same
# wkt <- 'POLYGON((-178.5 64.8,-165.9 59.2,-147.3 59.0,-130.7 51.0,-125.8 36.7))'
# occ_search(geometry = wkt)
organizations 127

### returns no results

# wkt <- 'LINESTRING(3 4,10 50,20 25)'
# occ_search(geometry = wkt)

### Apparently a point is allowed, but errors

# wkt <- 'POINT(45 -122)'
# occ_search(geometry = wkt)

## Faceting
x <- occ_search(facet = "country", limit = 0)
x$facets
x <- occ_search(facet = "establishmentMeans", limit = 10)
x$facets
x$data
x <- occ_search(facet = c("country", "basisOfRecord"), limit = 10)
x$data
x$facets
x$facets$country
x$facets$basisOfRecord
x$facets$basisOfRecord$count
x <- occ_search(facet = "country", facetMincount = 30000000L, limit = 10)
x$facets
x$data
# paging per each faceted variable
(x <- occ_search(
facet = c("country", "basisOfRecord", "hasCoordinate"),
country.facetLimit = 3,
basisOfRecord.facetLimit = 6,
limit = 0
))
x$facets

# You can set limit=0 to get number of results found

occ_search(datasetKey = '7b5d6a48-f762-11e1-a439-00145eb45e9a', limit = 0)$meta
occ_search(scientificName = 'Ursus americanus', limit = 0)$meta
occ_search(scientificName = 'Ursus americanus', limit = 0)$meta

## End(Not run)

organizations Organizations metadata.

Description

Organizations metadata.
128 organizations

Usage
organizations(
data = "all",
country = NULL,
uuid = NULL,
query = NULL,
limit = 100,
start = NULL,
curlopts = list()
)

Arguments
data (character) The type of data to get. One or more of: ’organization’, ’con-
tact’, ’endpoint’, ’identifier’, ’tag’, ’machineTag’, ’comment’, ’hostedDataset’,
’ownedDataset’, ’deleted’, ’pending’, ’nonPublishing’, or the special ’all’. De-
fault: 'all'
country (character) Filters by country.
uuid (character) UUID of the data node provider. This must be specified if data is
anything other than ’all’, ’deleted’, ’pending’, or ’nonPublishing’.
query (character) Query nodes. Only used when data='all'
limit Number of records to return. Default: 100. Maximum: 1000.
start Record number to start at. Default: 0. Use in combination with limit to page
through results.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Value
A list of length of two, consisting of a data.frame meta when uuid is NULL, and data which can
either be a list or a data.frame depending on the requested type of data.

References
https://www.gbif.org/developer/registry#organizations

Examples
## Not run:
organizations(limit=5)
organizations(query="france", limit=5)
organizations(country = "SPAIN")
organizations(uuid="4b4b2111-ee51-45f5-bf5e-f535f4a1c9dc")
organizations(data='contact', uuid="4b4b2111-ee51-45f5-bf5e-f535f4a1c9dc")
organizations(data='pending')
organizations(data=c('contact','endpoint'),
uuid="4b4b2111-ee51-45f5-bf5e-f535f4a1c9dc")
parsenames 129

# Pass on curl options

organizations(query="spain", curlopts = list(verbose=TRUE))

## End(Not run)

parsenames Parse taxon names using the GBIF name parser.

Description
Parse taxon names using the GBIF name parser.

Usage
parsenames(scientificname, curlopts = list())

Arguments
scientificname A character vector of scientific names.
curlopts list of named curl options passed on to HttpClient. see curl::curl_options
for curl options

Value
A data.frame containing fields extracted from parsed taxon names. Fields returned are the union
of fields extracted from all species names in scientificname.

Author(s)
John Baumgartner ([email protected])

References
https://www.gbif.org/developer/species#parser

Examples
## Not run:
parsenames(scientificname='x Agropogon littoralis')
parsenames(c('Arrhenatherum elatius var. elatius',
'Secale cereale subsp. cereale', 'Secale cereale ssp. cereale',
'Vanessa atalanta (Linnaeus, 1758)'))
parsenames("Ajuga pyramidata")
parsenames("Ajuga pyramidata x reptans")

# Pass on curl options

# res <- parsenames(c('Arrhenatherum elatius var. elatius',
# 'Secale cereale subsp. cereale', 'Secale cereale ssp. cereale',
# 'Vanessa atalanta (Linnaeus, 1758)'), curlopts=list(verbose=TRUE))
130 rgb_country_codes

## End(Not run)

rgbif-defunct Defunct functions in rgbif

Description
• density_spplist(): service no longer provided
• densitylist(): service no longer provided
• gbifdata(): service no longer provided
• gbifmap_dens(): service no longer provided
• gbifmap_list(): service no longer provided
• occurrencedensity(): service no longer provided
• providers(): service no longer provided
• resources(): service no longer provided
• taxoncount(): service no longer provided
• taxonget(): service no longer provided
• taxonsearch(): service no longer provided
• stylegeojson(): moving this functionality to spocc package, will be removed soon
• togeojson(): moving this functionality to spocc package, will be removed soon
• gist(): moving this functionality to spocc package, will be removed soon
• occ_spellcheck(): GBIF has removed the spellCheck parameter from their API

Details
The above functions have been removed. See https://github.com/ropensci/rgbif and poke
around the code if you want to find the old functions in previous versions of the package

rgb_country_codes Look up 2 character ISO country codes

Description
Look up 2 character ISO country codes

Usage
rgb_country_codes(country_name, fuzzy = FALSE, ...)
taxrank 131

Arguments
country_name Name of country to look up
fuzzy If TRUE, uses agrep to do fuzzy search on names.
... Further arguments passed on to agrep or grep

Examples
## Not run:
rgb_country_codes(country_name="United")

## End(Not run)

taxrank Get the possible values to be used for (taxonomic) rank arguments in
GBIF API methods.

Description
Get the possible values to be used for (taxonomic) rank arguments in GBIF API methods.

Usage
taxrank()

Examples
## Not run:
taxrank()

## End(Not run)

wkt_parse parse wkt into smaller bits

Description
parse wkt into smaller bits

Usage
wkt_parse(wkt, geom_big = "bbox", geom_size = 40, geom_n = 10)
132 wkt_parse

Arguments
wkt (character) A WKT string. Required.
geom_big (character) Only "bbox" works since rgbif 3.8.0.
geom_size (integer) An integer indicating size of the cell. Default: 40.
geom_n (integer) An integer indicating number of cells in each dimension. Default: 10.

Examples
wkt <- "POLYGON((13.26349675655365 52.53991761181831,18.36115300655365 54.11445544219924,
21.87677800655365 53.80418956368524,24.68927800655365 54.217364774722455,28.20490300655365
54.320018299365124,30.49005925655365 52.85948216284084,34.70880925655365 52.753220564427814,
35.93927800655365 50.46131871049754,39.63068425655365 49.55761261299145,40.86115300655365
46.381388009130845,34.00568425655365 45.279102926537,33.30255925655365 48.636868465271846,
30.13849675655365 49.78513301801265,28.38068425655365 47.2236377039631,29.78693425655365
44.6572866068524,27.67755925655365 42.62220075124676,23.10724675655365 43.77542058000212,
24.51349675655365 47.10412345120368,26.79865300655365 49.55761261299145,23.98615300655365
52.00209943876426,23.63459050655365 49.44345313705238,19.41584050655365 47.580567827212114,
19.59162175655365 44.90682206053508,20.11896550655365 42.36297154876359,22.93146550655365
40.651849782081555,25.56818425655365 39.98171166226459,29.61115300655365 40.78507856230178,
32.95099675655365 40.38459278067577,32.95099675655365 37.37491910393631,26.27130925655365
33.65619609886799,22.05255925655365 36.814081996401605,18.71271550655365 36.1072176729021,
18.53693425655365 39.16878677351903,15.37287175655365 38.346355762190846,15.19709050655365
41.578843777436326,12.56037175655365 41.050735748143424,12.56037175655365 44.02872991212046,
15.19709050655365 45.52594200494078,16.42755925655365 48.05271546733352,17.48224675655365
48.86865641518059,10.62677800655365 47.817178329053135,9.57209050655365 44.154980365192,
8.16584050655365 40.51835445724746,6.05646550655365 36.53210972067291,0.9588092565536499
31.583640057148145,-5.54509699344635 35.68001485298146,-6.77556574344635 40.51835445724746,
-9.41228449344635 38.346355762190846,-12.40056574344635 35.10683619158607,-15.74040949344635
38.07010978950028,-14.68572199344635 41.31532459432774,-11.69744074344635 43.64836179231387,
-8.88494074344635 42.88035509418534,-4.31462824344635 43.52103366008421,-8.35759699344635
47.2236377039631,-8.18181574344635 50.12441989397795,-5.01775324344635 49.55761261299145,
-2.73259699344635 46.25998980446569,-1.67790949344635 44.154980365192,-1.32634699344635
39.30493590580802,2.18927800655365 41.44721797271696,4.47443425655365 43.26556960420879,
2.18927800655365 46.7439668697322,1.83771550655365 50.3492841273576,6.93537175655365
49.671505849335254,5.00177800655365 52.32557322466785,7.81427800655365 51.67627099802223,
7.81427800655365 54.5245591562317,10.97834050655365 51.89375191441792,10.97834050655365
55.43241335888528,13.26349675655365 52.53991761181831))"
wkt <- gsub("\n", " ", wkt)

if (requireNamespace("sf", quietly=TRUE)) {
# to a bounding box in wkt format
wkt_parse(wkt, geom_big = "bbox")

}
Index

∗ downloads dataset_list_funs, 11
download_predicate_dsl, 22 dataset_machinetag (dataset_uuid_funs),
occ_download, 82 16
occ_download_cached, 87 dataset_metrics (dataset_uuid_funs), 16
occ_download_cancel, 88 dataset_networks (dataset_uuid_funs), 16
occ_download_dataset_activity, 91 dataset_noendpoint (dataset_list_funs),
occ_download_datasets, 90 11
occ_download_get, 93 dataset_process (dataset_uuid_funs), 16
occ_download_import, 94 dataset_search, 12
occ_download_list, 96 dataset_suggest (dataset_search), 12
occ_download_meta, 97 dataset_tag (dataset_uuid_funs), 16
occ_download_queue, 98 dataset_uuid_funs, 16
occ_download_wait, 100 datasets, 8
density_spplist(), 130
as.download (occ_download_import), 94 densitylist(), 130
derived_dataset, 17
check_wkt, 4 derived_dataset(), 32
check_wkt(), 118 derived_dataset_prep (derived_dataset),
count_facet, 5 17
crul::HttpClient, 7, 9, 11, 14, 16, 45, 48 download_predicate_dsl, 21, 22, 83, 84,
crul::HttpClient(), 93 87–91, 93, 95–97, 99, 101
crul::verb-GET, 28, 93 downloads, 20, 84, 88–91, 93, 95–97, 99
crul::writing-options, 93 downloads(), 119

data.table::fread, 94 elevation, 27
data.table::fread(), 94, 95 enumeration, 30
dataset, 6 enumeration_country (enumeration), 30
dataset_comment (dataset_uuid_funs), 16
dataset_constituents gbif_bbox2wkt, 31
(dataset_uuid_funs), 16 gbif_citation, 32
dataset_contact (dataset_uuid_funs), 16 gbif_geocode, 33
dataset_doi, 9 gbif_issues, 34
dataset_duplicate (dataset_list_funs), gbif_issues_lookup, 34
11 gbif_names, 35
dataset_endpoint (dataset_uuid_funs), 16 gbif_oai, 35
dataset_export (dataset_search), 12 gbif_oai_get_records (gbif_oai), 35
dataset_get (dataset_uuid_funs), 16 gbif_oai_identify (gbif_oai), 35
dataset_gridded, 10 gbif_oai_list_identifiers (gbif_oai), 35
dataset_identifier (dataset_uuid_funs), gbif_oai_list_metadataformats
16 (gbif_oai), 35

133
134 INDEX

gbif_oai_list_records (gbif_oai), 35 occ_count_year (occ_count_), 74

gbif_oai_list_sets (gbif_oai), 35 occ_count_year(), 72
gbif_photos, 37 occ_data, 76, 119
gbif_wkt2bbox (gbif_bbox2wkt), 31 occ_data(), 32, 84, 104, 117, 119
gbifdata(), 130 occ_download, 27, 82, 88–91, 93, 95–97, 99,
gbifmap_dens(), 130 101
gbifmap_list(), 130 occ_download(), 20, 21, 90, 98, 119
gist(), 130 occ_download_cached, 27, 84, 87, 89–91, 93,
95–97, 99, 101
HttpClient, 8, 30, 39, 50, 52, 58, 61, 62, 64, occ_download_cached(), 21
67, 69, 70, 83, 88–91, 96, 97, 101, occ_download_cancel, 27, 84, 88, 88, 90, 91,
103, 107, 118, 128, 129 93, 95–97, 99, 101
installations, 38 occ_download_cancel(), 21
occ_download_cancel_staged
lit_count (lit_search), 40 (occ_download_cancel), 88
lit_search, 40 occ_download_cancel_staged(), 21
occ_download_dataset_activity, 27, 84,
map_fetch, 43 88–90, 91, 93, 95–97, 99, 101
map_fetch(), 48 occ_download_dataset_activity(), 21
mvt_fetch, 46 occ_download_datasets, 27, 84, 88, 89, 90,
mvt_fetch(), 45 91, 93, 95–97, 99, 101
occ_download_datasets(), 21
name_backbone, 49 occ_download_describe, 92
name_backbone_checklist, 51 occ_download_get, 27, 84, 88–91, 93, 95–97,
name_backbone_verbose (name_backbone), 99, 101
49 occ_download_get(), 21, 32, 98
name_issues, 54
occ_download_import, 27, 84, 88–91, 93, 94,
name_issues(), 65
96, 97, 99, 101
name_lookup, 56
occ_download_import(), 21, 104
name_lookup(), 65
occ_download_list, 27, 84, 88–91, 93, 95,
name_parse, 61
96, 97, 99, 101
name_suggest, 62
occ_download_list(), 21
name_usage, 63
occ_download_meta, 27, 84, 88–91, 93, 95,
name_usage(), 55
96, 97, 99, 101
network, 66
occ_download_meta(), 21, 32, 98, 100
network_constituents (network), 66
occ_download_prep (occ_download), 82
networks, 68
nodes, 70 occ_download_prep(), 21, 98
occ_download_queue, 27, 84, 88–91, 93,
occ_count, 72, 119 95–97, 98, 101
occ_count(), 75 occ_download_queue(), 21, 84, 100
occ_count_, 74 occ_download_wait, 27, 84, 88–91, 93,
occ_count_basis_of_record (occ_count_), 95–97, 99, 100
74 occ_download_wait(), 21
occ_count_basis_of_record(), 72 occ_facet, 101
occ_count_country (occ_count_), 74 occ_get, 102
occ_count_country(), 72 occ_get_verbatim (occ_get), 102
occ_count_pub_country (occ_count_), 74 occ_issues, 104
occ_count_pub_country(), 72 occ_metadata, 106
INDEX 135

occ_search, 107, 119

occ_search(), 20, 32, 84, 102, 104
occ_spellcheck(), 130
occurrencedensity(), 130
options(), 20
organizations, 127

parsenames, 129
pred (download_predicate_dsl), 22
pred_and (download_predicate_dsl), 22
pred_default (download_predicate_dsl),
22
pred_gt (download_predicate_dsl), 22
pred_gte (download_predicate_dsl), 22
pred_in (download_predicate_dsl), 22
pred_isnull (download_predicate_dsl), 22
pred_like (download_predicate_dsl), 22
pred_lt (download_predicate_dsl), 22
pred_lte (download_predicate_dsl), 22
pred_not (download_predicate_dsl), 22
pred_notnull (download_predicate_dsl),
22
pred_or (download_predicate_dsl), 22
pred_within (download_predicate_dsl), 22
providers(), 130

resources(), 130
rgb_country_codes, 130
rgbif (rgbif-package), 3
rgbif-defunct, 130
rgbif-package, 3

stylegeojson(), 130
Sys.setenv(), 20

taxoncount(), 130
taxonget(), 130
taxonsearch(), 130
taxrank, 131
togeojson(), 130

wkt_parse, 119, 131