knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" ) options(verbose = FALSE)
The eurobis
R package allows you to download data from EurOBIS.
You can query on:
Or create your own selection using the EMODnet Biology toolbox. Just copy the webservice URL and paste in R.
You can install the development version from GitHub with devtools
:
devtools::install_github("lifewatch/eurobis")
Use the eurobis_occurrences()
family of functions to query data.
A basic example is:
library(eurobis) # Get one single dataset eurobis_occurrences_basic(dasid = 8045)
For detailed information run:
help(eurobis_occurrences)
Use the functional_group
argument:
# Get one single dataset eurobis_occurrences_basic(dasid = 8045, functional_groups = "angiosperms")
See the full list of queriable traits in the exported dataset species_traits
:
species_traits
You can also filter by location, either using the Marine Regions Gazetteer Identifier (MRGID) or passing any polygon as Well Known Text.
eurobis_occurrences_basic(mrgid = 5688, geometry = "POLYGON ((-9.099426 40.33016, -9.099426 40.9788, -8.366089 40.9788, -8.366089 40.33016, -9.099426 40.33016))")
To help drawing the area of your interest, you can use eurobis_map_draw()
. You can draw here a polygon interactively:
selected_area <- eurobis_map_draw() #> POLYGON ((-9.099426 40.33016, -9.099426 40.9788, -8.366089 40.9788, -8.366089 40.33016, -9.099426 40.33016)) eurobis_occurrences_full(geometry = selected_area)
To help choosing the MRGID from Marine Regions, see the list of queriable regions and their MRGIDs with the family of functions eurobis_map_regions_*
: these will open a leaflet map including the layers, read via Web Map Services (WMS).
# MEOW Ecoregions eurobis_map_regions_ecoregions() # Exclusive Economic Zones (EEZ) eurobis_map_regions_eez() # International Hydrographic Office areas (IHO) eurobis_map_regions_iho() # Marine Regions intersection of EEZ and IHO. Named as Marine Region in eurobis_list_regions() eurobis_map_regions_eez_iho() # EMODnet-Biology Reporting Areas eurobis_map_regions_reportingareas()
See the manual with:
help(eurobis_map_regions)
Note that passing both an MRGID and a geometry does not restrict to the selected area within the MRGID record, but adds both data fetched from the selected data and the MRGID record.
Yes, you could also use the OBIS R package robis
. The main advantage of the eurobis
R package is the functionality to query on species traits.
If data are extracted from the EMODnet Biology for secondary analysis resulting in a publication, the appropriate source should be cited.
The downloaded data should be cited as: EMODnet Biology (yyyy) Fulll Occurrence Data and parameters downloaded from the EMODnet Biology Project (www.emodnet-biology.eu). Available online at www.emodnet-biology.eu/toolbox, consulted on yyyy-mm-dd.
Regarding the citation of the individual datasets, the following guidelines should be taken into account:
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