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Download data from EurOBIS using the LifeWatch/EMODnet-Biology Web Feature Services

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Funding Lifecycle:
experimental R-CMD-check

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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.

Installation

You can install the development version from GitHub with devtools:

devtools::install_github("lifewatch/eurobis")

Get occurrences

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)
#> Loading ISO 19139 XML schemas...
#> Loading ISO 19115 codelists...
#> Loading IANA mime types...
#> No encoding supplied: defaulting to UTF-8.
#> ✔ Downloading layer: EMODnet EurOBIS Basic Occurrence Data
#> ℹ The Basic Occurrence Data download provides you data for the following 8 essential terms: datasetid, datecollected, decimallongitude, decimallatitude, coordinateuncertaintyinmeters, scientificname, aphiaid, scientificnameaccepted. For more information, please consult: https://www.emodnet-biology.eu/emodnet-data-format.
#> Simple feature collection with 52 features and 10 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: -8.73964 ymin: 40.61773 xmax: -8.73902 ymax: 40.61899
#> CRS:           EPSG:4326
#> # A tibble: 52 × 11
#>    gml_id         id datas…¹ datecollected       decim…² decim…³ coord…⁴ scien…⁵
#>  * <fct>       <int> <chr>   <dttm>                <dbl>   <dbl>   <dbl> <chr>  
#>  1 eurobis-o… 3.68e7 https:… 2020-05-05 00:00:00   -8.74    40.6       5 Zoster…
#>  2 eurobis-o… 3.68e7 https:… 2019-12-13 00:00:00   -8.74    40.6       5 Zoster…
#>  3 eurobis-o… 3.68e7 https:… 2020-03-03 00:00:00   -8.74    40.6       5 Zoster…
#>  4 eurobis-o… 3.68e7 https:… 2019-12-13 00:00:00   -8.74    40.6       5 Zoster…
#>  5 eurobis-o… 3.68e7 https:… 2020-08-10 00:00:00   -8.74    40.6       5 Zoster…
#>  6 eurobis-o… 3.68e7 https:… 2020-08-10 00:00:00   -8.74    40.6       5 Zoster…
#>  7 eurobis-o… 3.68e7 https:… 2020-05-05 00:00:00   -8.74    40.6       5 Zoster…
#>  8 eurobis-o… 3.68e7 https:… 2020-05-05 00:00:00   -8.74    40.6       5 Zoster…
#>  9 eurobis-o… 3.68e7 https:… 2020-03-03 00:00:00   -8.74    40.6       5 Zoster…
#> 10 eurobis-o… 3.68e7 https:… 2020-05-05 00:00:00   -8.74    40.6       5 Zoster…
#> # … with 42 more rows, 3 more variables: aphiaid <chr>,
#> #   scientificnameaccepted <chr>, geometry <POINT [°]>, and abbreviated
#> #   variable names ¹​datasetid, ²​decimallongitude, ³​decimallatitude,
#> #   ⁴​coordinateuncertaintyinmeters, ⁵​scientificname

For detailed information run:

help(eurobis_occurrences)

Query by traits

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
#>                         category                    group
#> 1                  Species group         Functional group
#> 2                  Species group         Functional group
#> 3                  Species group         Functional group
#> 4                  Species group         Functional group
#> 5                  Species group         Functional group
#> 6                  Species group         Functional group
#> 7                  Species group         Functional group
#> 8                  Species group         Functional group
#> 9                  Species group         Functional group
#> 10 Species importance to society              CITES Annex
#> 11 Species importance to society              CITES Annex
#> 12 Species importance to society              CITES Annex
#> 13 Species importance to society Habitats Directive Annex
#> 14 Species importance to society Habitats Directive Annex
#> 15 Species importance to society   IUCN Red List Category
#> 16 Species importance to society   IUCN Red List Category
#> 17 Species importance to society   IUCN Red List Category
#> 18 Species importance to society          MSFD indicators
#> 19 Species importance to society          MSFD indicators
#> 20 Species importance to society          MSFD indicators
#> 21 Species importance to society          MSFD indicators
#> 22 Species importance to society          MSFD indicators
#> 23 Species importance to society          MSFD indicators
#> 24 Species importance to society          MSFD indicators
#> 25 Species importance to society          MSFD indicators
#> 26 Species importance to society          MSFD indicators
#> 27 Species importance to society          MSFD indicators
#> 28 Species importance to society          MSFD indicators
#> 29 Species importance to society          MSFD indicators
#> 30 Species importance to society          MSFD indicators
#> 31 Species importance to society          MSFD indicators
#> 32 Species importance to society          MSFD indicators
#>                                                             selection
#> 1                                                               algae
#> 2                                                         angiosperms
#> 3                                                             benthos
#> 4                                                               birds
#> 5                                                             mammals
#> 6                                                       phytoplankton
#> 7                                                              pisces
#> 8                                                            reptiles
#> 9                                                         zooplankton
#> 10                                                                  I
#> 11                                                                 II
#> 12                                                                III
#> 13                                                                 II
#> 14                                                                 IV
#> 15                                                     data deficient
#> 16                                                      least concern
#> 17                                                    near threatened
#> 18                                      Black Sea proposed indicators
#> 19                                HELCOM core biodiversity indicators
#> 20                   Mediterranean proposed indicators - Adriatic Sea
#> 21           Mediterranean proposed indicators - Aegean-Levantine Sea
#> 22                     Mediterranean proposed indicators - Ionian Sea
#> 23              Mediterranean proposed indicators - Mediterranean Sea
#> 24          Mediterranean proposed indicators - Western Mediterranean
#> 25    OSPAR candidate indicators: Bay of Biscay and the Iberian Coast
#> 26                            OSPAR candidate indicators: Celtic Seas
#> 27 OSPAR candidate indicators: Greater North Sea including outside EU
#> 28                              OSPAR candidate indicators: North Sea
#> 29           OSPAR common indicators: Bay of Biscay and Iberian Coast
#> 30                               OSPAR common indicators: Celtic Seas
#> 31                         OSPAR common indicators: Greater North Sea
#> 32    OSPAR common indicators: Greater North Sea including outside EU
#>         selectid
#> 1          Algae
#> 2    Angiosperms
#> 3        Benthos
#> 4          Birds
#> 5        Mammals
#> 6  phytoplankton
#> 7         pisces
#> 8       Reptiles
#> 9    zooplankton
#> 10      28_280_0
#> 11      28_281_0
#> 12      28_282_0
#> 13      26_269_0
#> 14      26_271_0
#> 15         1_8_3
#> 16         1_7_3
#> 17         1_6_3
#> 18     23_285_41
#> 19     23_285_29
#> 20     23_285_31
#> 21     23_285_32
#> 22     23_285_33
#> 23     23_285_34
#> 24     23_285_30
#> 25     23_285_35
#> 26     23_285_36
#> 27     23_285_37
#> 28     23_285_38
#> 29     23_285_44
#> 30     23_285_45
#> 31     23_285_46
#> 32     23_285_40

Query by location

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.

Why an EurOBIS R package? Didn’t exist an OBIS package already?

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.

Disclaimer

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:

LifeWatch.be