rgbif v3.3.0
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 
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:
- rgbif vignette (https://docs.ropensci.org/rgbif/articles/rgbif.html): an introduction to the package's main functionalities.
- Function reference (https://docs.ropensci.org/rgbif/reference/index.html): an overview of all
rgbiffunctions. - Articles (https://docs.ropensci.org/rgbif/articles/index.html): vignettes/tutorials on how to download data, clean data, and work with taxonomic names.
- Occurrence manual (https://books.ropensci.org/occurrences/): a book covering a suite of R packages used for working with biological occurrence data.
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
rgbifin R doingcitation(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.
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. | |
| No Results! | ||
Vignettes of rgbif
| Name | ||
| downloads.Rmd | ||
| issues.Rmd | ||
| rgbif.Rmd | ||
| taxonomic_names.Rmd | ||
| No Results! | ||
Last month downloads
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 |
| imports | conditionz , crul (>= 0.7.4) , data.table , geoaxe , ggplot2 , jsonlite (>= 1.6) , lazyeval , magrittr , oai (>= 0.2.2) , R6 , tibble , whisker , wicket (>= 0.4.0) , xml2 |
| suggests | knitr , png , protolite (>= 2.0) , randgeo , raster , rgeos , rmarkdown , sf , sp , testthat , vcr (>= 0.5.0) |
| Contributors | Dan Mcglinn, Karthik Ram, Vijay Barve, rOpenSci , Damiano Oldoni, Laurens Geffert, Peter Desmet |
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