Awesome
<!-- README.md is generated from README.Rmd. Please edit that file -->emodnet.wfs: Access EMODnet Web Feature Service data through R
<!-- badges: start -->
The goal of emodnet.wfs is to allow interrogation of and access to EMODnet’s, European Marine Observation and Data Network, geographic vector data in R through 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. emodnet.wfs aims at offering an user-friendly interface to this rich data.
Installation and setup
You can install the development version of emodnet.wfs from GitHub with:
# install.packages("pak")
pak::pak("EMODnet/emodnet.wfs")
If you want to avoid reading messages from emodnet.wfs such as “WFS
client created successfully”, set the "emodnet.wfs.quiet" option to
TRUE.
options("emodnet.wfs.quiet" = TRUE)
Available services
All available services are contained in the tibble returned by
emodnet_wfs().
#> [1] "data.frame"
#> [1] "service_name" "service_url"
#> [1] "bathymetry"
#> [2] "biology"
#> [3] "biology_occurrence_data"
#> [4] "chemistry_cdi_data_discovery_and_access_service"
#> [5] "chemistry_cdi_distribution_observations_per_category_and_region"
#> [6] "chemistry_contaminants"
#> [7] "chemistry_marine_litter"
#> [8] "geology_coastal_behavior"
#> [9] "geology_events_and_probabilities"
#> [10] "geology_marine_minerals"
#> [11] "geology_sea_floor_bedrock"
#> [12] "geology_seabed_substrate_maps"
#> [13] "geology_submerged_landscapes"
#> [14] "human_activities"
#> [15] "physics"
#> [16] "seabed_habitats_general_datasets_and_products"
#> [17] "seabed_habitats_individual_habitat_map_and_model_datasets"
To explore available services you can use View() or your usual way to
explore data.frames.
Create Service 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>
#> ....|-- url: https://geo.vliz.be/geoserver/Emodnetbio/wfs
#> ....|-- version: 2.0.0
#> ....|-- capabilities <WFSCapabilities>
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: 35 × 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.… mediseh_h… EMOD… "Haloph… WFSF… sf
#> 8 emodnet_wfs biology https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf
#> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf
#> 10 emodnet_wfs biology https://geo.… mediseh_p… EMOD… "This d… WFSF… sf
#> # ℹ 25 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: 35 × 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.… mediseh_h… EMOD… "Haloph… WFSF… sf
#> 8 emodnet_wfs biology https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf
#> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf
#> 10 emodnet_wfs biology https://geo.… mediseh_p… EMOD… "This d… WFSF… sf
#> # ℹ 25 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
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: 33.07783 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....
Help needed?
If you get an unexpected error,
- Look up the EMODnet monitor;
- Open an issue in this repository.
Other web services
There are three ways to access EMODnet data at the moment, that complement each other.
EMODnet ERDDAP server
Some EMODnet data are also published in an ERDDAP server. You can access these data in R using the rerddap R package:
# install.packages("rerrdap")
library(rerddap)
#> Registered S3 method overwritten by 'hoardr':
#> method from
#> print.cache_info httr
erddap_url <- "https://erddap.emodnet.eu/erddap/"
rerddap::ed_datasets(url = erddap_url)
#> # A tibble: 8 × 16
#> griddap Subset tabledap Make.A.Graph wms files Title Summary FGDC ISO.19115
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 "" "/erd… /erddap… /erddap/tab… "" "" * Th… "This … "" ""
#> 2 "" "" /erddap… /erddap/tab… "" "/er… EMOD… "The d… "" ""
#> 3 "" "" /erddap… /erddap/tab… "" "/er… EMOD… "The d… "" ""
#> 4 "" "/erd… /erddap… /erddap/tab… "" "/er… EMOD… "The d… "/er… "/erddap…
#> 5 "" "" /erddap… /erddap/tab… "" "/er… Pres… "The p… "/er… "/erddap…
#> 6 "" "" /erddap… /erddap/tab… "" "" PSMS… "Perma… "" ""
#> 7 "" "" /erddap… /erddap/tab… "" "/er… PSMS… "Perma… "" ""
#> 8 "" "/erd… /erddap… /erddap/tab… "" "/er… TAO/… "This … "/er… "/erddap…
#> # ℹ 6 more variables: Info <chr>, Background.Info <chr>, RSS <chr>,
#> # Email <chr>, Institution <chr>, Dataset.ID <chr>
rerddap::ed_search(query = "vessel density", url = erddap_url)
#> # A tibble: 16 × 2
#> title dataset_id
#> <chr> <chr>
#> 1 Vessel Density humanactivities_9f…
#> 2 Vessel Density humanactivities_e9…
#> 3 Vessel traffic density, 2019, All EMODPACE_VD_All
#> 4 Vessel traffic density, 2019, Cargo EMODPACE_VD_09_Car…
#> 5 Vessel traffic density, 2019, Dredging or underwater ops EMODPACE_VD_03_Dre…
#> 6 Vessel traffic density, 2019, Fishing EMODPACE_VD_01_Fis…
#> 7 Vessel traffic density, 2019, High Speed craft EMODPACE_VD_06_High
#> 8 Vessel traffic density, 2019, Miliary and law enforcement EMODPACE_VD_11_Mil…
#> 9 Vessel traffic density, 2019, Other EMODPACE_VD_00_Oth…
#> 10 Vessel traffic density, 2019, Passenger EMODPACE_VD_08_Pas…
#> 11 Vessel traffic density, 2019, Pleasure craft EMODPACE_VD_05_Ple…
#> 12 Vessel traffic density, 2019, Sailing EMODPACE_VD_04_Sai…
#> 13 Vessel traffic density, 2019, Service EMODPACE_VD_02_Ser…
#> 14 Vessel traffic density, 2019, Tanker EMODPACE_VD_10_Tan…
#> 15 Vessel traffic density, 2019, Tug and Towing EMODPACE_VD_07_Tug
#> 16 Vessel traffic density, 2019, Unknown EMODPACE_VD_12_Unk…
human_activities_data_info <- rerddap::info(datasetid = "humanactivities_9f8a_3389_f08a", url = erddap_url)
human_activities_data_info
#> <ERDDAP info> humanactivities_9f8a_3389_f08a
#> Base URL: https://erddap.emodnet.eu/erddap
#> Dataset Type: griddap
#> Dimensions (range):
#> time: (2017-01-01T00:00:00Z, 2021-12-01T00:00:00Z)
#> y: (604500.0, 7034500.0)
#> x: (-622500.0, 6884500.0)
#> Variables:
#> vd:
#> Units: seconds
year_2020_gridded_data <- griddap(datasetx = human_activities_data_info, time = c("2020-03-18", "2020-03-19"))
#> info() output passed to x; setting base url to: https://erddap.emodnet.eu/erddap
head(year_2020_gridded_data$data)
#> x y time vd
#> 1 -622500 7034500 2020-04-01T00:00:00Z NA
#> 2 -621500 7034500 2020-04-01T00:00:00Z NA
#> 3 -620500 7034500 2020-04-01T00:00:00Z NA
#> 4 -619500 7034500 2020-04-01T00:00:00Z NA
#> 5 -618500 7034500 2020-04-01T00:00:00Z NA
#> 6 -617500 7034500 2020-04-01T00:00:00Z NA
EMODnetWCS: Access EMODnet Web Coverage Service data
This package emodnet.wfs uses Web Feature Services, hence it is limited to getting vector data. EMODnet also hosts raster data that can be accessed via Web Coverage Services (WCS). The R package EMODnetWCS makes these data available in R.
Citation
To cite emodnet.wfs, please use the output from
citation(package = "emodnet.wfs").
citation(package = "emodnet.wfs")
#> To cite package 'emodnet.wfs' in publications use:
#>
#> Krystalli A, Fernández-Bejarano S, Salmon M (????). _emodnet.wfs:
#> Access EMODnet Web Feature Service data through R_. doi:10.14284/679
#> <https://doi.org/10.14284/679>, R package version 2.0.2.9000.
#> 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/emodnet.wfs>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {{emodnet.wfs}: Access EMODnet Web Feature Service data through R},
#> author = {Anna Krystalli and Salvador Fernández-Bejarano and Maëlle Salmon},
#> note = {R package version 2.0.2.9000. 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/emodnet.wfs},
#> doi = {10.14284/679},
#> }
Acknowledgements
This package was started by the Sheffield University during the EMODnet Biology WP4 data products workshop in June 2020.