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().
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...
#> ✔ 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 2.0.1.9001 DEV https://github.com/E ...
#> 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: 37 × 9
#> # Rowwise:
#> data_source service_name service_url layer_name title abstract class format
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 emodnet_wfs biology https://geo.… mediseh_c… EMOD… "Coral … WFSF… sf
#> 2 emodnet_wfs biology https://geo.… mediseh_c… EMOD… "Coral … WFSF… sf
#> 3 emodnet_wfs biology https://geo.… mediseh_c… EMOD… "Cymodo… WFSF… sf
#> 4 emodnet_wfs biology https://geo.… Species_g… EMOD… "This d… WFSF… sf
#> 5 emodnet_wfs biology https://geo.… Species_g… EMOD… "This d… WFSF… sf
#> 6 emodnet_wfs biology https://geo.… Species_g… EMOD… "This d… WFSF… sf
#> 7 emodnet_wfs biology https://geo.… Species_g… EMOD… "This d… WFSF… sf
#> 8 emodnet_wfs biology https://geo.… mediseh_h… EMOD… "Haloph… WFSF… sf
#> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf
#> 10 emodnet_wfs biology https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf
#> # ℹ 27 more rows
#> # ℹ 1 more variable: layer_namespace <chr>or you can pass a wfs client object.
emodnet_get_wfs_info(wfs_bio)
#> # A tibble: 37 × 9
#> # Rowwise:
#> data_source service_name service_url layer_name title abstract class format
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 emodnet_wfs biology https://geo.… mediseh_c… EMOD… "Coral … WFSF… sf
#> 2 emodnet_wfs biology https://geo.… mediseh_c… EMOD… "Coral … WFSF… sf
#> 3 emodnet_wfs biology https://geo.… mediseh_c… EMOD… "Cymodo… WFSF… sf
#> 4 emodnet_wfs biology https://geo.… Species_g… EMOD… "This d… WFSF… sf
#> 5 emodnet_wfs biology https://geo.… Species_g… EMOD… "This d… WFSF… sf
#> 6 emodnet_wfs biology https://geo.… Species_g… EMOD… "This d… WFSF… sf
#> 7 emodnet_wfs biology https://geo.… Species_g… EMOD… "This d… WFSF… sf
#> 8 emodnet_wfs biology https://geo.… mediseh_h… EMOD… "Haloph… WFSF… sf
#> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf
#> 10 emodnet_wfs biology https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf
#> # ℹ 27 more rows
#> # ℹ 1 more variable: layer_namespace <chr>You can also get info for specific layers from wfs object:
layers <- c("mediseh_zostera_m_pnt", "mediseh_posidonia_nodata")
emodnet_get_layer_info(wfs = wfs_bio, layers = layers)
#> # A tibble: 2 × 9
#> # Rowwise:
#> data_source service_name service_url layer_name title abstract class format
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 emodnet_wfs https://geo.vl… biology mediseh_p… EMOD… "Coastl… WFSF… sf
#> 2 emodnet_wfs https://geo.vl… biology mediseh_z… EMOD… "Zoster… WFSF… sf
#> # ℹ 1 more variable: layer_namespace <chr>Finally, you can get details on all available services and layers from the server
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: 33.07783 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 37.55796)
#> 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: -463885.4 ymin: 3905639 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 (-449698.6 4403229)
#> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-456430.1 4400610)
#> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-463885.4 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: -242654.3 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: 33.07783 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 37.55796)
#> 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 error:
emodnet_get_layers(
wfs = wfs_bio,
layers = layers,
reduce_layers = TRUE
)
#> Error in `value[[3L]]()`:
#> ! Cannot reduce layers.
#> ℹ 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