rgbif v3.3.0

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Interface to the Global 'Biodiversity' Information Facility API

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.

Readme

rgbif

Project Status: Active – The project has reached a stable, usable state and is being actively developed. cran checks R-CMD-check codecov.io rstudio mirror downloads cran version DOI

rgbif gives you access to data from GBIF via their REST API. GBIF versions their API - we are currently using v1 of their API. You can no longer use their old API in this package - see ?rgbif-defunct.

Please cite rgbif. Run the following to get the appropriate citation for the version you're using:

citation(package = "rgbif")

To get started, see:

Check out the rgbif paper for more information on this package and the sister Python and Ruby clients.

Note: Maximum number of records you can get with occ_search() and occ_data() is 100,000. See https://www.gbif.org/developer/occurrence

Installation

install.packages("rgbif")

Or, install development version

install.packages("remotes")
remotes::install_github("ropensci/rgbif")
# OR
install.packages("rgbif", repos="https://dev.ropensci.org")
library("rgbif")

Note: Windows users have to first install Rtools (https://cran.r-project.org/bin/windows/Rtools/) to use devtools

Mac Users: (in case of errors)

Terminal:

Install gdal : https://github.com/edzer/sfr/blob/master/README.md#macos

brew install openssl

in R:

install.packages('openssl')
install.packages('rgeos')
install.packages('rgbif')

Screencast

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for rgbif in R doing citation(package = 'rgbif')
  • Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

This package is part of spocc, along with several other packages, that provide access to occurrence records from multiple data sources.


rofooter

Functions in rgbif

Name Description
check_wkt Check input WKT
dataset_suggest Suggest datasets in GBIF.
count_facet Facetted count occurrence search.
DownReq DownReq
dataset_search Search datasets in GBIF.
dataset_metrics Get details on a GBIF dataset.
datasets Search for datasets and dataset metadata.
blanktheme Custom ggplot2 theme
create_gist Function that takes a list of files and creates payload for API
GbifQueue GbifQueue
gbif_bbox2wkt Convert a bounding box to a Well Known Text polygon, and a WKT to a bounding box
gbif_issues_lookup Lookup issue definitions and short codes
gbif_issues List all GBIF issues and their codes.
gbif_oai GBIF registry data via OAI-PMH
gbif_names View highlighted terms in name results from GBIF.
elevation Get elevation for lat/long points from a data.frame or list of points.
densitylist The density web service provides access to records showing the density of occurrence records from the GBIF Network by one-degree cell.
density_spplist The density web service provides access to records showing the density of occurrence records from the GBIF Network by one-degree cell.
gbifdata Get data.frame from occurrencelist, occurrencelist_many, or densitylist.
name_lookup Lookup names in all taxonomies in GBIF.
gbif_photos View photos from GBIF.
download_predicate_dsl Download predicate DSL (domain specific language)
downloads Downloads interface
name_suggest Suggest up to 20 name usages.
gist Post a file as a Github gist
gbif_citation Get citation for datasets used
installations Installations metadata.
enumeration Enumerations.
gbifmap_list Make a simple map to visualize GBIF point data.
occ_count Get number of occurrence records.
nodes Nodes metadata.
isocodes Table of country two character ISO codes, and GBIF names
parsenames Parse taxon names using the GBIF name parser.
gbifmap_dens Make a simple map to visualize GBIF data density data
gbifmap Get Github credentials from use in console
many-values Many value inputs to some parameters
get_credentials Get Github credentials from use in console
occ_download_dataset_activity Lists the downloads activity of a dataset
occ_download_cancel Cancel a download creation process.
occ_download_cached Check for downloads already in your GBIF account
occ_download_datasets List datasets for a download
%>% Pipe operator
taxonget Get taxonomic information on a specific taxon or taxa in GBIF by their taxon concept keys.
occ_download_queue Download requests in a queue
occ_metadata Search for catalog numbers, collection codes, collector names, and institution codes.
name_backbone Lookup names in the GBIF backbone taxonomy.
occ_search Search for GBIF occurrences
taxonsearch Search for taxa in GBIF.
taxrank Get the possible values to be used for (taxonomic) rank arguments in GBIF API methods.
mvt_fetch Fetch Map Vector Tiles (MVT)
map_fetch Fetch aggregated density maps of GBIF occurrences
organizations Organizations metadata.
name_issues Parse and examine further GBIF name issues on a dataset.
occ_data Search for GBIF occurrences - simplified for speed
occurrencelist_many occurrencelist_many is the same as occurrencelist, but takes in a vector of species names.
networks Networks metadata.
name_usage Lookup details for specific names in all taxonomies in GBIF.
togeojson Convert spatial data files to GeoJSON from various formats.
occ_download Spin up a download request for GBIF occurrence data.
occ_get Get data for GBIF occurrences by occurrence key
occ_issues Parse and examine further GBIF occurrence issues on a dataset.
occurrencecount Counts taxon concept records matching a range of filters.
rgbif-package Interface to the Global Biodiversity Information Facility API.
occ_download_get Get a download from GBIF.
occ_spellcheck Spell check search term for occurrence searches
occ_download_import Import a downloaded file from GBIF.
occ_facet Facet GBIF occurrences
stylegeojson Style a data.frame prior to converting to geojson.
occ_fields Vector of fields in the output for the function occ_search()
occ_download_list Lists the downloads created by a user.
occ_download_wait Wait for an occurrence download to be done
occurrencedensity Returns summary counts of occurrence records by one-degree cell for a single taxon, country, dataset, data publisher or data network.
occurrencelist Occurrencelist searches for taxon concept records matching a range of filters.
rgb_country_codes Look up 2 character ISO country codes
typestatus Type status options for GBIF searching
rgbif-defunct Defunct functions in rgbif
occ_download_meta Retrieves the occurrence download metadata by its unique key.
occurrencelist_all Occurrencelist_all carries out an occurrencelist query for a single name and all its name variants according to GBIF's name matching.
resources Get data resources and their unique keys.
providers Get data providers and their unique keys.
wkt_parse parse wkt into smaller bits
suggestfields Fields available in gbif_suggest function
occurrenceget Get individual records for a given occurrence record.
taxoncount Search by taxon to retrieve number of records in GBIF.
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Vignettes of rgbif

Name
downloads.Rmd
issues.Rmd
rgbif.Rmd
taxonomic_names.Rmd
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Details

License MIT + file LICENSE
URL https://github.com/ropensci/rgbif (devel), https://docs.ropensci.org/rgbif/ (documentation), https://books.ropensci.org/occurrences/ (user manual)
BugReports https://github.com/ropensci/rgbif/issues
LazyData true
LazyLoad true
VignetteBuilder knitr
Encoding UTF-8
Language en-US
RoxygenNote 7.1.1
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
Packaged 2020-09-08 15:44:04 UTC; sckott
Repository CRAN
Date/Publication 2020-09-08 16:10:03 UTC

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