rgbif: Interface to the Global 'Biodiversity' Information Facility 'API'

A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility ('GBIF'; <http://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, and getting counts of occurrence records.

AuthorScott Chamberlain [aut, cre], Vijay Barve [ctb], Dan Mcglinn [ctb]
Date of publication2017-01-21 01:27:16
MaintainerScott Chamberlain <myrmecocystus@gmail.com>
LicenseMIT + file LICENSE
Version0.9.7
https://github.com/ropensci/rgbif

View on CRAN

Man pages

blanktheme: Custom ggplot2 theme

check_wkt: Check input WKT

count_facet: Facetted count occurrence search.

create_gist: Function that takes a list of files and creates payload for...

dataset_metrics: Get details on a GBIF dataset.

datasets: Search for datasets and dataset metadata.

dataset_search: Search datasets in GBIF.

dataset_suggest: Suggest datasets in GBIF.

densitylist: The density web service provides access to records showing...

density_spplist: The density web service provides access to records showing...

downloads: Downloads interface

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

enumeration: Enumerations.

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

gbif_citation: Get citation for datasets used

gbifdata: Get data.frame from occurrencelist, occurrencelist_many, or...

gbif_issues: Table of GBIF issues, with codes used in data output, full...

gbifmap: Make a map to visualize GBIF occurrence data.

gbifmap_dens: Make a simple map to visualize GBIF data density data

gbifmap_list: Make a simple map to visualize GBIF point data.

gbif_names: View highlighted terms in name results from GBIF.

gbif_oai: GBIF registry data via OAI-PMH

gbif_photos: View photos from GBIF.

get_credentials: Get Github credentials from use in console

gist: Post a file as a Github gist

installations: Installations metadata.

isocodes: Table of country two character ISO codes, and GBIF names

name_backbone: Lookup names in the GBIF backbone taxonomy.

name_lookup: Lookup names in all taxonomies in GBIF.

name_suggest: A quick and simple autocomplete service that returns up to 20...

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

networks: Networks metadata.

nodes: Nodes metadata.

occ_count: Get number of occurrence records.

occ_data: Search for GBIF occurrences - simplified for speed

occ_download: Spin up a download request for GBIF occurrence data.

occ_download_cancel: Cancel a download cretion process.

occ_download_get: Get a download from GBIF.

occ_download_import: Import a downloaded file from GBIF.

occ_download_list: Lists the downloads created by a user.

occ_download_meta: Retrieves the occurrence download metadata by its unique key.

occ_facet: Facet GBIF occurrences

occ_fields: Vector of fields in the output for the function 'occ_search'

occ_get: Get data for specific GBIF occurrences.

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

occ_issues_lookup: Lookup occurrence issue definitions and short codes

occ_metadata: Search for catalog numbers, collection codes, collector...

occ_search: Search for GBIF occurrences

occ_spellcheck: Spell check search term for occurrence searches

occurrencecount: Counts taxon concept records matching a range of filters.

occurrencedensity: Returns summary counts of occurrence records by one-degree...

occurrenceget: Get individual records for a given occurrence record.

occurrencelist: Occurrencelist searches for taxon concept records matching a...

occurrencelist_all: Occurrencelist_all carries out an occurrencelist query for a...

occurrencelist_many: occurrencelist_many is the same as occurrencelist, but takes...

organizations: Organizations metadata.

parsenames: Parse taxon names using the GBIF name parser.

pipe: Pipe operator

providers: Get data providers and their unique keys.

read_wkt: Check input WKT

resources: Get data resources and their unique keys.

rgb_country_codes: Look up 2 character ISO country codes

rgbif-defunct: Defunct functions in rgbif

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

stylegeojson: Style a data.frame prior to converting to geojson.

suggestfields: Fields available in gbif_suggest function

taxoncount: Search by taxon to retrieve number of records in GBIF.

taxonget: Get taxonomic information on a specific taxon or taxa in GBIF...

taxonsearch: Search for taxa in GBIF.

taxrank: Get the possible values to be used for (taxonomic) rank...

togeojson: Convert spatial data files to GeoJSON from various formats.

typestatus: Type status options for GBIF searching

wkt_parse: parse wkt into smaller bits

Functions

\%>\% Man page
as.download Man page
as.download.character Man page
as.download.download Man page
blanktheme Man page
check_wkt Man page
count_facet Man page
create_gist Man page
dataset_metrics Man page
datasets Man page
dataset_search Man page
dataset_suggest Man page
densitylist Man page
density_spplist Man page
downloads Man page
elevation Man page
enumeration Man page
enumeration_country Man page
gbif_bbox2wkt Man page
gbif_citation Man page
gbifdata Man page
gbif_issues Man page
gbifmap Man page
gbifmap_dens Man page
gbifmap_list Man page
gbif_names Man page
gbif_oai Man page
gbif_oai_get_records Man page
gbif_oai_identify Man page
gbif_oai_list_identifiers Man page
gbif_oai_list_metadataformats Man page
gbif_oai_list_records Man page
gbif_oai_list_sets Man page
gbif_photos Man page
gbif_wkt2bbox Man page
get_credentials Man page
gist Man page
installations Man page
isocodes Man page
name_backbone Man page
name_lookup Man page
name_suggest Man page
name_usage Man page
networks Man page
nodes Man page
occ_count Man page
occ_data Man page
occ_download Man page
occ_download_cancel Man page
occ_download_cancel_staged Man page
occ_download_get Man page
occ_download_import Man page
occ_download_list Man page
occ_download_meta Man page
occ_facet Man page
occ_fields Man page
occ_get Man page
occ_issues Man page
occ_issues_lookup Man page
occ_metadata Man page
occ_search Man page
occ_spellcheck Man page
occurrencecount Man page
occurrencedensity Man page
occurrenceget Man page
occurrencelist Man page
occurrencelist_all Man page
occurrencelist_many Man page
organizations Man page
parsenames Man page
providers Man page
read_wkt Man page
resources Man page
rgb_country_codes Man page
rgbif Man page
rgbif-defunct Man page
rgbif-package Man page
stylegeojson Man page
suggestfields Man page
taxoncount Man page
taxonget Man page
taxonsearch Man page
taxrank Man page
togeojson Man page
typestatus Man page
wkt_parse Man page

Files

rgbif
rgbif/inst
rgbif/inst/singlemaplayout.html
rgbif/inst/assets
rgbif/inst/assets/class_checking_occ_search.r
rgbif/inst/assets/img
rgbif/inst/assets/img/occurrencelist_many.png
rgbif/inst/assets/img/occurrencelist.png
rgbif/inst/assets/img/unnamed-chunk-8-1.png
rgbif/inst/assets/img/gbifmap.png
rgbif/inst/assets/typestatus.csv
rgbif/inst/doc
rgbif/inst/doc/rgbif_vignette.Rmd
rgbif/inst/doc/issues_vignette.Rmd
rgbif/inst/doc/rgbif_vignette.html
rgbif/inst/doc/issues_vignette.html
rgbif/inst/doc/taxonomic_names.Rmd
rgbif/inst/doc/taxonomic_names.html
rgbif/inst/js
rgbif/inst/js/terraformer-wkt-parser.js
rgbif/inst/js/README.md
rgbif/inst/js/LICENSE
rgbif/inst/vign
rgbif/inst/vign/rgbif_vignette.Rmd
rgbif/inst/vign/issues_vignette.Rmd
rgbif/inst/vign/taxonomic_names.md
rgbif/inst/vign/figure
rgbif/inst/vign/figure/gbifmap1-1.png
rgbif/inst/vign/rgbif_vignette.md
rgbif/inst/vign/taxonomic_names.Rmd
rgbif/inst/vign/issues_vignette.md
rgbif/tests
rgbif/tests/testthat
rgbif/tests/testthat/test-read_wkt.R
rgbif/tests/testthat/test-wkt_large.R
rgbif/tests/testthat/test-occ_facet.R
rgbif/tests/testthat/test-dataset_search.r
rgbif/tests/testthat/test-dataset_suggest.r
rgbif/tests/testthat/test-installations.r
rgbif/tests/testthat/test-gbif_photos.R
rgbif/tests/testthat/test-gbifmap.r
rgbif/tests/testthat/test-name_usage.r
rgbif/tests/testthat/test-datasets.r
rgbif/tests/testthat/test-count_facet.r
rgbif/tests/testthat/test-gbif_names.R
rgbif/tests/testthat/test-occ_spellcheck.R
rgbif/tests/testthat/test-organizations.r
rgbif/tests/testthat/test-occ_data.R
rgbif/tests/testthat/test-occ_search.r
rgbif/tests/testthat/test-networks.r
rgbif/tests/testthat/test-occ_count.r
rgbif/tests/testthat/test-nodes.r
rgbif/tests/testthat/test-occ_metadata.r
rgbif/tests/testthat/test-occ_get.r
rgbif/tests/testthat/test-download_parsing.R
rgbif/tests/testthat/test-country_codes.r
rgbif/tests/testthat/test-elevation.R
rgbif/tests/testthat/test-name_backbone.r
rgbif/tests/testthat/test-dataset_metrics.r
rgbif/tests/testthat/test-name_lookup.r
rgbif/tests/testthat/test-enumeration.r
rgbif/tests/testthat/test-occ_issues_lookup.R
rgbif/tests/testthat/test-name_suggest.r
rgbif/tests/testthat/test-oai.R
rgbif/tests/testthat/test-parsenames.r
rgbif/tests/testthat/test-occ_issues.R
rgbif/tests/test-all.R
rgbif/NAMESPACE
rgbif/NEWS.md
rgbif/data
rgbif/data/typestatus.rda
rgbif/data/occ_fields.rda
rgbif/data/isocodes.rda
rgbif/R
rgbif/R/gbif_issues.R
rgbif/R/occ_search.r
rgbif/R/organizations.r
rgbif/R/globals.r
rgbif/R/geometry_utils.R rgbif/R/read_wkt.R rgbif/R/on_load.R rgbif/R/occ_facet.R rgbif/R/occ_download_import.R rgbif/R/parsenames.R rgbif/R/print_gbif.R
rgbif/R/occ_metadata.r
rgbif/R/plyr_fxns.R
rgbif/R/dataset_search.r
rgbif/R/nodes.r
rgbif/R/check_wkt.r
rgbif/R/pipe.R
rgbif/R/occ_get.r
rgbif/R/name_suggest.r
rgbif/R/downloads.R rgbif/R/occ_download_cancel.R
rgbif/R/rgbif-package.r
rgbif/R/elevation.r
rgbif/R/rgb_country_codes.r
rgbif/R/datasets.r
rgbif/R/installations.r
rgbif/R/dataset_metrics.r
rgbif/R/occ_download_get.r
rgbif/R/overload_classes.R rgbif/R/enumeration.R
rgbif/R/occ_issues.r
rgbif/R/oai-pmh.R rgbif/R/taxrank.R rgbif/R/occ_download.R
rgbif/R/gbif_photos.r
rgbif/R/name_usage.r
rgbif/R/gbif_citation.R
rgbif/R/count_facet.r
rgbif/R/zzz.r
rgbif/R/wkt_parse.R rgbif/R/defunct.R
rgbif/R/occ_issues_lookup.r
rgbif/R/name_backbone.r
rgbif/R/name_lookup.r
rgbif/R/occ_download_meta.R rgbif/R/bbox.R rgbif/R/occ_data.R rgbif/R/gbif_names.R
rgbif/R/networks.r
rgbif/R/occ_download_list.R rgbif/R/occ_spellcheck.R
rgbif/R/dataset_suggest.r
rgbif/R/occ_count.r
rgbif/R/gbifmap.r
rgbif/vignettes
rgbif/vignettes/rgbif_vignette.Rmd
rgbif/vignettes/issues_vignette.Rmd
rgbif/vignettes/taxonomic_names.Rmd
rgbif/README.md
rgbif/MD5
rgbif/build
rgbif/build/vignette.rds
rgbif/DESCRIPTION
rgbif/man
rgbif/man/rgb_country_codes.Rd rgbif/man/organizations.Rd rgbif/man/create_gist.Rd rgbif/man/rgbif-package.Rd rgbif/man/pipe.Rd rgbif/man/occurrenceget.Rd rgbif/man/occ_fields.Rd rgbif/man/name_lookup.Rd rgbif/man/check_wkt.Rd rgbif/man/density_spplist.Rd rgbif/man/occ_search.Rd rgbif/man/occ_data.Rd rgbif/man/gbif_oai.Rd rgbif/man/enumeration.Rd rgbif/man/occurrencelist.Rd rgbif/man/occurrencelist_many.Rd rgbif/man/resources.Rd rgbif/man/gbifdata.Rd rgbif/man/datasets.Rd rgbif/man/gbifmap.Rd rgbif/man/occ_download.Rd rgbif/man/count_facet.Rd rgbif/man/occ_download_list.Rd rgbif/man/dataset_metrics.Rd rgbif/man/dataset_search.Rd rgbif/man/gbifmap_dens.Rd rgbif/man/suggestfields.Rd rgbif/man/providers.Rd rgbif/man/gbif_photos.Rd rgbif/man/stylegeojson.Rd rgbif/man/dataset_suggest.Rd rgbif/man/occurrencecount.Rd rgbif/man/occ_issues.Rd rgbif/man/occ_spellcheck.Rd rgbif/man/elevation.Rd rgbif/man/densitylist.Rd rgbif/man/taxrank.Rd rgbif/man/blanktheme.Rd rgbif/man/parsenames.Rd rgbif/man/occ_issues_lookup.Rd rgbif/man/isocodes.Rd rgbif/man/downloads.Rd rgbif/man/gbif_citation.Rd rgbif/man/occ_get.Rd rgbif/man/wkt_parse.Rd rgbif/man/taxoncount.Rd rgbif/man/gbif_bbox2wkt.Rd rgbif/man/name_usage.Rd rgbif/man/typestatus.Rd rgbif/man/networks.Rd rgbif/man/get_credentials.Rd rgbif/man/occ_download_meta.Rd rgbif/man/occ_download_cancel.Rd rgbif/man/nodes.Rd rgbif/man/occ_metadata.Rd rgbif/man/gist.Rd rgbif/man/rgbif-defunct.Rd rgbif/man/name_backbone.Rd rgbif/man/gbif_names.Rd rgbif/man/taxonsearch.Rd rgbif/man/occurrencelist_all.Rd rgbif/man/togeojson.Rd rgbif/man/occurrencedensity.Rd rgbif/man/read_wkt.Rd rgbif/man/occ_download_get.Rd rgbif/man/taxonget.Rd rgbif/man/installations.Rd rgbif/man/occ_count.Rd rgbif/man/gbifmap_list.Rd rgbif/man/occ_facet.Rd rgbif/man/name_suggest.Rd rgbif/man/occ_download_import.Rd rgbif/man/gbif_issues.Rd
rgbif/LICENSE

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