rgeobon

The goal of rgeobon is to provide an interface between R and the GEOBON open data portal RESTfull API (please note that the portal is currently in beta). It allows to consult the datasets available on the portal and download them.

Installation

You can install rgeobon from GitHub:

devtools::install_github("vlucet/rgeobon")

Example

This demonstrates the basic abilities of rgeobon. You can first get the list of all the available datasets:

library(rgeobon)
# Get the list of GEOBON datasets
dataset_list <- geobon_list()
dataset_list
#> # A tibble: 6 x 33
#>   id    title publication_date environmental_d… provenance_desc… license doi  
#>   <chr> <chr> <chr>            <chr>            <chr>            <chr>   <lis>
#> 1 1     Chan… 2018             Terrestrial      To be added soon CC BY … <chr…
#> 2 2     Fore… 2019             Terrestrial      To be added soon CC BY … <chr…
#> 3 3     Pred… 2016             Terrestrial      To be added soon CC BY … <chr…
#> 4 4     Rela… 2020             Terrestrial      To be added soon CC BY … <chr…
#> 5 5     Mamm… 2020             Terrestrial      To be added soon CC BY … <chr…
#> 6 10    Glob… 2020             Terrestrial, Ma… To develop the … CC BY … <chr…
#> # … with 26 more variables: external_link <list>, description <chr>,
#> #   keywords <list>, additional_info <chr>, path_name_dataset <chr>,
#> #   path_name_metadata <chr>, creator_creator_name <chr>,
#> #   creator_creator_organisation <chr>, creator_creator_email <chr>,
#> #   contact_contact_name <chr>, contact_contact_organisation <chr>,
#> #   contact_contact_email <chr>, ebv_ebv_class <chr>, ebv_ebv_name <chr>,
#> #   spatial_domain_spatial_extent <chr>,
#> #   spatial_domain_spatial_description <chr>,
#> #   spatial_domain_spatial_resolution <chr>,
#> #   spatial_domain_spatial_accuracy <chr>,
#> #   temporal_domain_temporal_resolution <chr>,
#> #   temporal_domain_temporal_extent_start <chr>,
#> #   temporal_domain_temporal_extent_end <chr>,
#> #   biological_entity_entity_type <chr>,
#> #   biological_entity_taxonomic_coverage <chr>,
#> #   biological_entity_classification_classification_system_name <chr>,
#> #   biological_entity_classification_classification_system_type <chr>,
#> #   biological_entity_classification_classification_system_reference <chr>

From here, you can request information on a single record, and download the data associated with this record, if any is available.

# List possible ids
dataset_list$id
#> [1] "1"  "2"  "3"  "4"  "5"  "10"

# Get a specific record
geobon_get(id = 1)
#> # A tibble: 1 x 33
#>   id    title publication_date environmental_d… provenance_desc… license doi  
#>   <chr> <chr> <chr>            <chr>            <chr>            <chr>   <lis>
#> 1 1     Chan… 2018             Terrestrial      To be added soon CC BY … <chr…
#> # … with 26 more variables: external_link <list>, description <chr>,
#> #   keywords <list>, additional_info <chr>, path_name_dataset <chr>,
#> #   path_name_metadata <chr>, creator_creator_name <chr>,
#> #   creator_creator_organisation <chr>, creator_creator_email <chr>,
#> #   contact_contact_name <chr>, contact_contact_organisation <chr>,
#> #   contact_contact_email <chr>, ebv_ebv_class <chr>, ebv_ebv_name <chr>,
#> #   spatial_domain_spatial_extent <chr>,
#> #   spatial_domain_spatial_description <chr>,
#> #   spatial_domain_spatial_resolution <chr>,
#> #   spatial_domain_spatial_accuracy <chr>,
#> #   temporal_domain_temporal_resolution <chr>,
#> #   temporal_domain_temporal_extent_start <chr>,
#> #   temporal_domain_temporal_extent_end <chr>,
#> #   biological_entity_entity_type <chr>,
#> #   biological_entity_taxonomic_coverage <chr>,
#> #   biological_entity_classification_classification_system_name <chr>,
#> #   biological_entity_classification_classification_system_type <chr>,
#> #   biological_entity_classification_classification_system_reference <chr>

# Download the data from that record into a temp directory
geobon_download(id = 1, path = tempdir())