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'). '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.

Author
Scott Chamberlain [aut, cre], Vijay Barve [ctb], Dan Mcglinn [ctb]
Date of publication
2016-10-06 13:06:10
Maintainer
Scott Chamberlain <myrmecocystus@gmail.com>
License
MIT + file LICENSE
Version
0.9.5
URLs

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
type_sum
Type summary
wkt_parse
parse wkt into smaller bits

Files in this package

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/tbl_df_utils.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/type_sum.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