Access EMODnet Web Feature Service data through R • EMODnetWFS

The goal of EMODnetWFS is to allow interrogation of and access to EMODnet geographic vector data in R though the EMODnet Web Feature Services. Web Feature services (WFS) represent a change in the way geographic information is created, modified and exchanged on the Internet and offer direct fine-grained access to geographic information at the feature and feature property level. EMODnetWFS aims at offering an user-friendly interface to this rich data.

Installation

You can install the development version of EMODnetWFS from GitHub with:

# install.packages("remotes")
remotes::install_github("EMODnet/EMODnetWFS")

Available services

All available services are contained in the tibble returned by emodnet_wfs().

service_name	service_url
bathymetry	https://ows.emodnet-bathymetry.eu/wfs
biology	https://geo.vliz.be/geoserver/Emodnetbio/wfs
biology_occurrence_data	https://geo.vliz.be/geoserver/Dataportal/wfs
chemistry_cdi_data_discovery_and_access_service	https://geo-service.maris.nl/emodnet_chemistry/wfs
chemistry_cdi_distribution_observations_per_category_and_region	https://geo-service.maris.nl/emodnet_chemistry_p36/wfs
chemistry_contaminants	https://nodc.ogs.trieste.it/geoserver/Contaminants/wfs
chemistry_marine_litter	https://www.ifremer.fr/services/wfs/emodnet_chemistry2
geology_coastal_behavior	https://drive.emodnet-geology.eu/geoserver/tno/wfs
geology_events_and_probabilities	https://drive.emodnet-geology.eu/geoserver/ispra/wfs
geology_marine_minerals	https://drive.emodnet-geology.eu/geoserver/gsi/wfs
geology_sea_floor_bedrock	https://drive.emodnet-geology.eu/geoserver/bgr/wfs
geology_seabed_substrate_maps	https://drive.emodnet-geology.eu/geoserver/gtk/wfs
geology_submerged_landscapes	https://drive.emodnet-geology.eu/geoserver/bgs/wfs
human_activities	https://ows.emodnet-humanactivities.eu/wfs
physics	https://geoserver.emodnet-physics.eu/geoserver/emodnet/wfs
seabed_habitats_general_datasets_and_products	https://ows.emodnet-seabedhabitats.eu/geoserver/emodnet_open/wfs
seabed_habitats_individual_habitat_map_and_model_datasets	https://ows.emodnet-seabedhabitats.eu/geoserver/emodnet_open_maplibrary/wfs

To explore available services in Rstudio use:

View(emodnet_wfs())

Create Service Client

Create new WFS Client. Specify the service using the service argument.

wfs_bio <- emodnet_init_wfs_client(service = "biology")
#> Loading ISO 19139 XML schemas...
#> Loading ISO 19115 codelists...
#> Loading IANA mime types...
#> No encoding supplied: defaulting to UTF-8.
#> ✔ WFS client created successfully
#> ℹ Service: 'https://geo.vliz.be/geoserver/Emodnetbio/wfs'
#> ℹ Version: '2.0.0'

wfs_bio
#> <WFSClient>
#>   Inherits from: <OWSClient>
#>   Public:
#>     attrs: list
#>     capabilities: WFSCapabilities, OWSCapabilities, OGCAbstractObject, R6
#>     clone: function (deep = FALSE) 
#>     defaults: list
#>     describeFeatureType: function (typeName) 
#>     element: AbstractObject
#>     encode: function (addNS = TRUE, geometa_validate = TRUE, geometa_inspire = FALSE, 
#>     ERROR: function (text) 
#>     getCapabilities: function () 
#>     getCASUrl: function () 
#>     getClass: function () 
#>     getClassName: function () 
#>     getConfig: function () 
#>     getFeatures: function (typeName, ...) 
#>     getFeatureTypes: function (pretty = FALSE) 
#>     getHeaders: function () 
#>     getNamespaceDefinition: function (recursive = FALSE) 
#>     getPwd: function () 
#>     getToken: function () 
#>     getUrl: function () 
#>     getUser: function () 
#>     getVersion: function () 
#>     INFO: function (text) 
#>     initialize: function (url, serviceVersion = NULL, user = NULL, pwd = NULL, 
#>     isFieldInheritedFrom: function (field) 
#>     logger: function (type, text) 
#>     loggerType: NULL
#>     namespace: OWSNamespace, R6
#>     reloadCapabilities: function () 
#>     url: https://geo.vliz.be/geoserver/Emodnetbio/wfs
#>     verbose.debug: FALSE
#>     verbose.info: FALSE
#>     version: 2.0.0
#>     WARN: function (text) 
#>     wrap: FALSE
#>   Private:
#>     cas_url: NULL
#>     config: request
#>     fromComplexTypes: function (value) 
#>     headers: EMODnetWFS R package https://github.com/EMODnet/EMODnetWFS
#>     pwd: NULL
#>     serviceName: WFS
#>     system_fields: verbose.info verbose.debug loggerType wrap element names ...
#>     token: NULL
#>     user: NULL
#>     xmlElement: AbstractObject
#>     xmlExtraNamespaces: NULL
#>     xmlNamespacePrefix: OWS
#>     xmlNodeToCharacter: function (x, ..., indent = "", tagSeparator = "\n")

Get WFS Layer info

You can get metadata about the layers available from a service.

emodnet_get_wfs_info(service = "biology")
#> ✔ WFS client created successfully
#> ℹ Service: 'https://geo.vliz.be/geoserver/Emodnetbio/wfs'
#> ℹ Version: '2.0.0'
#> # A tibble: 33 × 9
#>    data_source service_name service…¹ layer…² layer…³ title abstr…⁴ class format
#>    <chr>       <chr>        <chr>     <chr>   <chr>   <chr> <chr>   <chr> <chr> 
#>  1 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Coral… WFSF… sf    
#>  2 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Coral… WFSF… sf    
#>  3 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Cymod… WFSF… sf    
#>  4 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  5 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  6 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  7 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  8 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Halop… WFSF… sf    
#>  9 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Maërl… WFSF… sf    
#> 10 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Maërl… WFSF… sf    
#> # … with 23 more rows, and abbreviated variable names ¹service_url,
#> #   ²layer_namespace, ³layer_name, ⁴abstract

or you can pass a wfs client object.

emodnet_get_wfs_info(wfs_bio)
#> # A tibble: 33 × 9
#>    data_source service_name service…¹ layer…² layer…³ title abstr…⁴ class format
#>    <chr>       <chr>        <chr>     <chr>   <chr>   <chr> <chr>   <chr> <chr> 
#>  1 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Coral… WFSF… sf    
#>  2 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Coral… WFSF… sf    
#>  3 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Cymod… WFSF… sf    
#>  4 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  5 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  6 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  7 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  8 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Halop… WFSF… sf    
#>  9 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Maërl… WFSF… sf    
#> 10 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Maërl… WFSF… sf    
#> # … with 23 more rows, and abbreviated variable names ¹service_url,
#> #   ²layer_namespace, ³layer_name, ⁴abstract

You can also get info for specific layers from wfs object:

emodnet_get_wfs_info(wfs_bio)
#> # A tibble: 33 × 9
#>    data_source service_name service…¹ layer…² layer…³ title abstr…⁴ class format
#>    <chr>       <chr>        <chr>     <chr>   <chr>   <chr> <chr>   <chr> <chr> 
#>  1 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Coral… WFSF… sf    
#>  2 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Coral… WFSF… sf    
#>  3 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Cymod… WFSF… sf    
#>  4 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  5 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  6 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  7 emodnet_wfs biology      https://… Emodne… Specie… EMOD… "This … WFSF… sf    
#>  8 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Halop… WFSF… sf    
#>  9 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Maërl… WFSF… sf    
#> 10 emodnet_wfs biology      https://… Emodne… medise… EMOD… "Maërl… WFSF… sf    
#> # … with 23 more rows, and abbreviated variable names ¹service_url,
#> #   ²layer_namespace, ³layer_name, ⁴abstract

layers <- c("mediseh_zostera_m_pnt", "mediseh_posidonia_nodata")

emodnet_get_layer_info(wfs = wfs_bio, layers = layers)
#> # A tibble: 2 × 9
#>   data_source service_name    servi…¹ layer…² layer…³ title abstr…⁴ class format
#>   <chr>       <chr>           <chr>   <chr>   <chr>   <chr> <chr>   <chr> <chr> 
#> 1 emodnet_wfs https://geo.vl… biology Emodne… medise… EMOD… "Coast… WFSF… sf    
#> 2 emodnet_wfs https://geo.vl… biology Emodne… medise… EMOD… "Zoste… WFSF… sf    
#> # … with abbreviated variable names ¹service_url, ²layer_namespace,
#> #   ³layer_name, ⁴abstract

Finally, you can get details on all available services and layers from the server

emodnet_get_all_wfs_info()

Get WFS layers

You can extract layers directly from a wfs object using layer names. All layers are downloaded as sf objects and output as a list with a named element for each layer requested.

emodnet_get_layers(wfs = wfs_bio, layers = layers)
#> $mediseh_zostera_m_pnt
#> Simple feature collection with 54 features and 3 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: -4.167154 ymin: 33.07782 xmax: 15.35766 ymax: 45.72451
#> Geodetic CRS:  WGS 84
#> First 10 features:
#>                      gml_id id country                   the_geom
#> 1   mediseh_zostera_m_pnt.1  0  Spagna  POINT (-2.61314 36.71681)
#> 2   mediseh_zostera_m_pnt.2  0  Spagna POINT (-3.846598 36.75127)
#> 3   mediseh_zostera_m_pnt.3  0  Spagna POINT (-3.957785 36.72266)
#> 4   mediseh_zostera_m_pnt.4  0  Spagna POINT (-4.039712 36.74217)
#> 5   mediseh_zostera_m_pnt.5  0  Spagna POINT (-4.100182 36.72331)
#> 6   mediseh_zostera_m_pnt.6  0  Spagna POINT (-4.167154 36.71226)
#> 7   mediseh_zostera_m_pnt.7  0  Spagna POINT (-1.268366 37.55797)
#> 8   mediseh_zostera_m_pnt.8  0 Francia   POINT (4.84864 43.37637)
#> 9   mediseh_zostera_m_pnt.9  0  Italia  POINT (13.71831 45.70017)
#> 10 mediseh_zostera_m_pnt.10  0  Italia  POINT (13.16378 45.72451)
#> 
#> $mediseh_posidonia_nodata
#> Simple feature collection with 465 features and 3 fields
#> Geometry type: MULTICURVE
#> Dimension:     XY
#> Bounding box:  xmin: -2.1798 ymin: 30.26623 xmax: 34.60767 ymax: 45.47668
#> Geodetic CRS:  WGS 84
#> First 10 features:
#>                         gml_id id         km                       the_geom
#> 1   mediseh_posidonia_nodata.1  0 291.503233 MULTICURVE (LINESTRING (27....
#> 2   mediseh_posidonia_nodata.2  0  75.379502 MULTICURVE (LINESTRING (23....
#> 3   mediseh_posidonia_nodata.3  0  38.627764 MULTICURVE (LINESTRING (22....
#> 4   mediseh_posidonia_nodata.4  0 110.344802 MULTICURVE (LINESTRING (19....
#> 5  mediseh_posidonia_nodata.13  0  66.997461 MULTICURVE (LINESTRING (9.1...
#> 6  mediseh_posidonia_nodata.14  0  18.090640 MULTICURVE (LINESTRING (9.7...
#> 7  mediseh_posidonia_nodata.15  0  16.618978 MULTICURVE (LINESTRING (9.8...
#> 8  mediseh_posidonia_nodata.16  0   1.913773 MULTICURVE (LINESTRING (10....
#> 9  mediseh_posidonia_nodata.83  0   2.173447 MULTICURVE (LINESTRING (15....
#> 10 mediseh_posidonia_nodata.84  0   2.817453 MULTICURVE (LINESTRING (15....

You can change the output crs through the argument crs.

emodnet_get_layers(wfs = wfs_bio, layers = layers, crs = 3857)
#> ℹ crs transformed to 3857.
#> ℹ crs transformed to 3857.
#> $mediseh_zostera_m_pnt
#> Simple feature collection with 54 features and 3 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: -463885.5 ymin: 3905638 xmax: 1709607 ymax: 5736311
#> Projected CRS: WGS 84 / Pseudo-Mercator
#> First 10 features:
#>                      gml_id id country                  the_geom
#> 1   mediseh_zostera_m_pnt.1  0  Spagna POINT (-290893.4 4399707)
#> 2   mediseh_zostera_m_pnt.2  0  Spagna POINT (-428201.3 4404494)
#> 3   mediseh_zostera_m_pnt.3  0  Spagna POINT (-440578.6 4400520)
#> 4   mediseh_zostera_m_pnt.4  0  Spagna POINT (-449698.7 4403229)
#> 5   mediseh_zostera_m_pnt.5  0  Spagna POINT (-456430.2 4400610)
#> 6   mediseh_zostera_m_pnt.6  0  Spagna POINT (-463885.5 4399075)
#> 7   mediseh_zostera_m_pnt.7  0  Spagna POINT (-141193.9 4517168)
#> 8   mediseh_zostera_m_pnt.8  0 Francia  POINT (539748.1 5369436)
#> 9   mediseh_zostera_m_pnt.9  0  Italia   POINT (1527115 5732431)
#> 10 mediseh_zostera_m_pnt.10  0  Italia   POINT (1465385 5736311)
#> 
#> $mediseh_posidonia_nodata
#> Simple feature collection with 465 features and 3 fields
#> Geometry type: MULTICURVE
#> Dimension:     XY
#> Bounding box:  xmin: -242654.2 ymin: 3537818 xmax: 3852508 ymax: 5696879
#> Projected CRS: WGS 84 / Pseudo-Mercator
#> First 10 features:
#>                         gml_id id         km                       the_geom
#> 1   mediseh_posidonia_nodata.1  0 291.503233 MULTICURVE (LINESTRING (302...
#> 2   mediseh_posidonia_nodata.2  0  75.379502 MULTICURVE (LINESTRING (257...
#> 3   mediseh_posidonia_nodata.3  0  38.627764 MULTICURVE (LINESTRING (246...
#> 4   mediseh_posidonia_nodata.4  0 110.344802 MULTICURVE (LINESTRING (221...
#> 5  mediseh_posidonia_nodata.13  0  66.997461 MULTICURVE (LINESTRING (101...
#> 6  mediseh_posidonia_nodata.14  0  18.090640 MULTICURVE (LINESTRING (108...
#> 7  mediseh_posidonia_nodata.15  0  16.618978 MULTICURVE (LINESTRING (110...
#> 8  mediseh_posidonia_nodata.16  0   1.913773 MULTICURVE (LINESTRING (121...
#> 9  mediseh_posidonia_nodata.83  0   2.173447 MULTICURVE (LINESTRING (169...
#> 10 mediseh_posidonia_nodata.84  0   2.817453 MULTICURVE (LINESTRING (169...

You can also extract layers using a WFS service name.

emodnet_get_layers(
    service = "biology",
    layers = c("mediseh_zostera_m_pnt", "mediseh_posidonia_nodata")
)
#> ✔ WFS client created successfully
#> ℹ Service: 'https://geo.vliz.be/geoserver/Emodnetbio/wfs'
#> ℹ Version: '2.0.0'
#> $mediseh_zostera_m_pnt
#> Simple feature collection with 54 features and 3 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: -4.167154 ymin: 33.07782 xmax: 15.35766 ymax: 45.72451
#> Geodetic CRS:  WGS 84
#> First 10 features:
#>                      gml_id id country                   the_geom
#> 1   mediseh_zostera_m_pnt.1  0  Spagna  POINT (-2.61314 36.71681)
#> 2   mediseh_zostera_m_pnt.2  0  Spagna POINT (-3.846598 36.75127)
#> 3   mediseh_zostera_m_pnt.3  0  Spagna POINT (-3.957785 36.72266)
#> 4   mediseh_zostera_m_pnt.4  0  Spagna POINT (-4.039712 36.74217)
#> 5   mediseh_zostera_m_pnt.5  0  Spagna POINT (-4.100182 36.72331)
#> 6   mediseh_zostera_m_pnt.6  0  Spagna POINT (-4.167154 36.71226)
#> 7   mediseh_zostera_m_pnt.7  0  Spagna POINT (-1.268366 37.55797)
#> 8   mediseh_zostera_m_pnt.8  0 Francia   POINT (4.84864 43.37637)
#> 9   mediseh_zostera_m_pnt.9  0  Italia  POINT (13.71831 45.70017)
#> 10 mediseh_zostera_m_pnt.10  0  Italia  POINT (13.16378 45.72451)
#> 
#> $mediseh_posidonia_nodata
#> Simple feature collection with 465 features and 3 fields
#> Geometry type: MULTICURVE
#> Dimension:     XY
#> Bounding box:  xmin: -2.1798 ymin: 30.26623 xmax: 34.60767 ymax: 45.47668
#> Geodetic CRS:  WGS 84
#> First 10 features:
#>                         gml_id id         km                       the_geom
#> 1   mediseh_posidonia_nodata.1  0 291.503233 MULTICURVE (LINESTRING (27....
#> 2   mediseh_posidonia_nodata.2  0  75.379502 MULTICURVE (LINESTRING (23....
#> 3   mediseh_posidonia_nodata.3  0  38.627764 MULTICURVE (LINESTRING (22....
#> 4   mediseh_posidonia_nodata.4  0 110.344802 MULTICURVE (LINESTRING (19....
#> 5  mediseh_posidonia_nodata.13  0  66.997461 MULTICURVE (LINESTRING (9.1...
#> 6  mediseh_posidonia_nodata.14  0  18.090640 MULTICURVE (LINESTRING (9.7...
#> 7  mediseh_posidonia_nodata.15  0  16.618978 MULTICURVE (LINESTRING (9.8...
#> 8  mediseh_posidonia_nodata.16  0   1.913773 MULTICURVE (LINESTRING (10....
#> 9  mediseh_posidonia_nodata.83  0   2.173447 MULTICURVE (LINESTRING (15....
#> 10 mediseh_posidonia_nodata.84  0   2.817453 MULTICURVE (LINESTRING (15....

Layers can also be returned to a single sf object through argument reduce_layers.
If TRUE the function will try to reduce all layers into a single sf.

If attempting to reduce fails, it will return a list with a warning:

emodnet_get_layers(
    wfs = wfs_bio, 
    layers = layers,
    reduce_layers = TRUE
)
#> Error: Cannot reduce layers.
#> Try again with `reduce_layers = FALSE`

Using reduce_layers = TRUE is also useful for returning an sf object rather than a list in single layer request.

emodnet_get_layers(
    service = "biology",
    layers = c("mediseh_posidonia_nodata"), 
    reduce_layers = TRUE
)
#> ✔ WFS client created successfully
#> ℹ Service: 'https://geo.vliz.be/geoserver/Emodnetbio/wfs'
#> ℹ Version: '2.0.0'
#> Simple feature collection with 465 features and 3 fields
#> Geometry type: MULTICURVE
#> Dimension:     XY
#> Bounding box:  xmin: -2.1798 ymin: 30.26623 xmax: 34.60767 ymax: 45.47668
#> Geodetic CRS:  WGS 84
#> First 10 features:
#>                         gml_id id         km                       the_geom
#> 1   mediseh_posidonia_nodata.1  0 291.503233 MULTICURVE (LINESTRING (27....
#> 2   mediseh_posidonia_nodata.2  0  75.379502 MULTICURVE (LINESTRING (23....
#> 3   mediseh_posidonia_nodata.3  0  38.627764 MULTICURVE (LINESTRING (22....
#> 4   mediseh_posidonia_nodata.4  0 110.344802 MULTICURVE (LINESTRING (19....
#> 5  mediseh_posidonia_nodata.13  0  66.997461 MULTICURVE (LINESTRING (9.1...
#> 6  mediseh_posidonia_nodata.14  0  18.090640 MULTICURVE (LINESTRING (9.7...
#> 7  mediseh_posidonia_nodata.15  0  16.618978 MULTICURVE (LINESTRING (9.8...
#> 8  mediseh_posidonia_nodata.16  0   1.913773 MULTICURVE (LINESTRING (10....
#> 9  mediseh_posidonia_nodata.83  0   2.173447 MULTICURVE (LINESTRING (15....
#> 10 mediseh_posidonia_nodata.84  0   2.817453 MULTICURVE (LINESTRING (15....

Citation

To cite EMODnetWFS, please use the output from citation(package = "EMODnetWFS").

citation(package = "EMODnetWFS")
#> 
#> To cite package 'EMODnetWFS' in publications use:
#> 
#>   Krystalli A, Fernández-Bejarano S, Salmon M (????). _EMODnetWFS:
#>   Access EMODnet Web Feature Service data through R_. R package version
#>   2.0.1.9001. Integrated data products created under the European
#>   Marine Observation Data Network (EMODnet) Biology project
#>   (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the by the
#>   European Union under Regulation (EU) No 508/2014 of the European
#>   Parliament and of the Council of 15 May 2014 on the European Maritime
#>   and Fisheries Fund, <https://github.com/EMODnet/EMODnetWFS>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {{EMODnetWFS}: Access EMODnet Web Feature Service data through R},
#>     author = {Anna Krystalli and Salvador Fernández-Bejarano and Maëlle Salmon},
#>     note = {R package version 2.0.1.9001. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund},
#>     url = {https://github.com/EMODnet/EMODnetWFS},
#>   }

Acknowledgements

This package was started by the Sheffield University during the EMODnet Biology WP4 data products workshop in June 2020. You can read the product story on the EMODnet-Biology portal

EMODnetWFS: Access EMODnet Web Feature Service data through R