EMODnetWFS

Allow interrogation of and access to EMODnet(European Marine Observation and Data Network) geographic vector data in R though the EMODnet Web Feature Services.
https://github.com/EMODnet/emodnet.wfs

Category: Hydrosphere
Sub Category: Ocean and Hydrology Data Access

Keywords

biology dataproducts emodnet marine-data rstats wfs

Keywords from Contributors

geo gdal geocoding rspatial book

Last synced: about 15 hours ago
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Repository metadata

Access EMODnet Web Feature Service data through R

• Host: GitHub
• URL: https://github.com/EMODnet/emodnet.wfs
• Owner: EMODnet
• License: other
• Created: 2020-06-08T18:57:56.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2025-04-08T07:17:20.000Z (19 days ago)
• Last Synced: 2025-04-12T23:22:38.308Z (14 days ago)
• Topics: biology, dataproducts, emodnet, marine-data, rstats, wfs
• Language: R
• Homepage: https://docs.ropensci.org/emodnet.wfs/
• Size: 34.2 MB
• Stars: 7
• Watchers: 3
• Forks: 4
• Open Issues: 7
• Releases: 3
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Citation: CITATION.cff
  • Codemeta: codemeta.json

README.Rmd

          ---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
options(timeout = 2000)
```

# emodnet.wfs: Access EMODnet Web Feature Service data through R


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The goal of emodnet.wfs is to allow interrogation of and access to [EMODnet's, European Marine Observation and Data Network, geographic vector data](https://emodnet.ec.europa.eu/en/emodnet-web-service-documentation#inline-nav-3) in R through the [EMODnet Web Feature Services](https://emodnet.ec.europa.eu/en/data-0). 
[Web Feature services (WFS)](https://www.ogc.org/publications/standard/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. 
Features are representation of geographic entities, such as a coastlines, marine protected areas, offshore platforms, or fishing areas. In WFS, features have geometry (spatial information) and attributes (descriptive data).
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 the rOpenSci R-universe with:

``` r
install.packages("emodnet.wfs", repos = c("https://ropensci.r-universe.dev", "https://cloud.r-project.org"))
```

Or from GitHub with:

``` r
# 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`.

```r
options("emodnet.wfs.quiet" = TRUE)
```

The use of the EMODnet Web Feature Services is not subjet to rate limiting at the moment.

## Pre-requisites

The emodnet.wfs is designed to be compatible with the modern R geospatial stack, in particular output geospatial objects are [`sf`](https://r-spatial.github.io/sf/) objects, that is to say, a tibble with a geometry list-column.

For users not familiar yet with geospatial data in R, we recommend the following resources:

- [Spatial Data Science With Applications in R](https://r-spatial.org/book/) by Edzer Pebesma and Roger Bivand.

- [Geocomputation with R](https://r.geocompx.org/) by Robin Lovelace, Jakub Nowosad and Jannes Muenchow.

In the documentation we assume a basic familiarity with spatial data: knowing about coordinates and about projections / [coordinate reference systems (CRS)](https://r.geocompx.org/spatial-class#crs-intro).

## Available data sources (services)

All available data sources, called services, are contained in the [tibble](https://tibble.tidyverse.org/) returned by `emodnet_wfs()`. 
```{r, echo=TRUE}
library(emodnet.wfs)
services <- emodnet_wfs()
class(services)
names(services)
services[, c("emodnet_thematic_lot", "service_name")]
```

EMODnet data covers several disciplines organized in 7 thematic lots: bathymetry, biology, chemistry, geology, human activities, physics, seabed habitats. Some thematic lots organize their data in more than one data source or service.

To explore available services you can use `View()` or your usual way to explore `data.frames`.

## Initialise a WFS Service Client

A WFS service client is responsible for sending requests to a WFS server and processing the responses to retrieve, display, or analyze geospatial features. As such, initialising a client is the first step to interacting with an EMODnet Web Feature Services.

Specify the service using the `service` argument. 

```{r}
wfs_bio <- emodnet_init_wfs_client(service = "biology")

wfs_bio
```

## List contents of a WFS: Get layer information from a service client

In the context of a Web Feature Service (WFS), a layer refers to a logical grouping of geographic features that share the same schema (i.e., the same feature type, geometry, and attributes). Layers are the units of data that clients can query, retrieve, and manipulate through a WFS.

You can access information (metadata) about each layer available from an EMODnet WFS with `emodnet_get_wfs_info()`

```{r}
emodnet_get_wfs_info(service = "biology")
```

or you can pass a wfs client object.

```{r}
emodnet_get_wfs_info(wfs_bio)
```

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

```{r}
layers <- c("mediseh_zostera_m_pnt", "mediseh_posidonia_nodata")

emodnet_get_layer_info(wfs = wfs_bio, layers = layers)
```


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

```{r eval=FALSE}
emodnet_get_all_wfs_info()
```


## Get data from a data source: get 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.
The argument `simplify = TRUE` stack all the layers in one single tibble, if possible (for instance if all column names are the same, otherwise it fails).

By default, `emodnet_get_layers()` returns a list of sf objects, one per layer.


```{r}
emodnet_get_layers(wfs = wfs_bio, layers = layers)
```

You can change the output Coordinate Reference System (CRS), which defines how geographic data is mapped to the Earth's surface,  through the argument `crs`.

```{r}
emodnet_get_layers(wfs = wfs_bio, layers = layers, crs = 3857)
```

You can also extract layers using a WFS service name.

```{r}
emodnet_get_layers(
  service = "biology",
  layers = c("mediseh_zostera_m_pnt", "mediseh_posidonia_nodata")
)
```


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

If attempting to reduce fails, it will error:
 
```{r, error=TRUE}
emodnet_get_layers(
  wfs = wfs_bio,
  layers = layers,
  simplify = TRUE
)
```

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

```{r}
emodnet_get_layers(
  service = "biology",
  layers = c("mediseh_posidonia_nodata"),
  simplify = TRUE
)
```

## Help needed?

If you get an unexpected error,

- Look up the [EMODnet monitor](https://monitor.emodnet.eu/resources?lang=en&resource_type=OGC:WFS);
- Open an issue in this [repository](https://github.com/EMODnet/emodnet.wfs/issues).

## Unlock the Full Potential of the EMODnet Web Services: Access Raster and Gridded datasets.

EMODnet hosts a wealth of marine and maritime data distributed through three complementary web services: WFS, WCS, and ERDDAP. Web services allow users to retrieve data programmatically from remote servers, eliminating the need for manual downloads. This is particularly useful for handling large datasets or conducting dynamic analyses. These services are tailored to different data types and research needs, but together, they ensure seamless access to all EMODnet vector, raster, and gridded datasets. Vector data, such as shipwrecks or boundaries, are accessible through `emodnet.wfs` via Web Feature Services (WFS). Complementary, raster and gridded datasets are available through Web Coverage Services (WCS) and ERDDAP respectively.

### Access EMODnet raster data through Web Coverage Services with `EMODnetWCS` in R

EMODnet raster datasets, such as habitat maps or bathymetry, are available through [Web Coverage Services (WCS)](https://en.wikipedia.org/wiki/Web_Coverage_Service). These data are continuous, gridded, and often used for spatial visualization or environmental modeling. The EMODnetWCS R package provides tools to retrieve and process these raser datasets, in a similar fashion as `emodnet.wfs`. Extensive documentation is available at the [EMODnetWCS website](https://emodnet.github.io/EMODnetWCS/).


### Access EMODnet gridded and tabular datasets through the ERDDAP Server and `rerddap` in R

Both WFS and WCS EMODnet services are based on a federated system: each EMODnet thematic lot manages their servers and data, ensuring that their data are exposed both via WFS and WCS. The twin R packages `emodnet.wfs` and `EMODnetWCS` simplify the access to all the entry points by collecting them in single places, which are the packages themselves. 

In contrast, the [EMODnet ERDDAP Server](https://erddap.emodnet.eu) is centrally managed by the EMODnet Central Portal, offering a single access point to all gridded and tabular datasets. ERDDAP simplifies access to datasets such as digital terrain models, vessel density or environmental data. It is particularly suited for large-scale, multidimensional data analysis. In R, the `rerddap` package allows users to query and subset ERDDAP data programmatically, enabling efficient analysis and integration into workflows. For example, researchers can retrieve datasets on vessel density. 

```{r rerddap}
# install.packages("rerrdap")
library(rerddap)

# This is the url where the EMODnet ERDDAP server is located
erddap_url <- "https://erddap.emodnet.eu/erddap/"

# Inspect all available datasets
ed_datasets(url = erddap_url)

# Find datasets with the key words "vessel density"
ed_search(query = "vessel density", url = erddap_url)

# Inspect more info about the vessel density dataset, using its identifier
human_activities_data_info <- info(datasetid = "humanactivities_9f8a_3389_f08a", url = erddap_url)
human_activities_data_info

# Retrieve the vessel density at a particular time period
year_2020_gridded_data <- griddap(datasetx = human_activities_data_info, time = c("2020-03-18", "2020-03-19"))
head(year_2020_gridded_data$data)
```

More functionalities are available through `rerddap`. Feel free to explore the [rerddap website](https://docs.ropensci.org/rerddap/) to find out what else can you do with the EMODnet datasets in ERDDAP.

## Citation

To cite emodnet.wfs, please use the output from `citation(package = "emodnet.wfs")`.

```{r}
citation(package = "emodnet.wfs")
```

## Acknowledgements

This package was started by the Sheffield University during the EMODnet Biology WP4 data products workshop in June 2020.


        

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------

cff-version: 1.2.0
message: 'To cite package "emodnet.wfs" in publications use:'
type: software
license: MIT
title: 'emodnet.wfs: Access EMODnet Web Feature Service data through R'
version: 2.0.2.9000
doi: 10.14284/679
abstract: Access and interrogate EMODnet (European Marine Observation and Data Network)
  Web Feature Service data through R.
authors:
- family-names: Krystalli
  given-names: Anna
  email: [email protected]
  orcid: https://orcid.org/0000-0002-2378-4915
- family-names: Fernández-Bejarano
  given-names: Salvador
  email: [email protected]
  orcid: https://orcid.org/0000-0003-0535-7677
- family-names: Salmon
  given-names: Maëlle
  email: [email protected]
  orcid: https://orcid.org/0000-0002-2815-0399
preferred-citation:
  type: manual
  title: 'emodnet.wfs: Access EMODnet Web Feature Service data through R'
  authors:
  - family-names: Krystalli
    given-names: Anna
    email: [email protected]
    orcid: https://orcid.org/0000-0002-2378-4915
  - family-names: Fernández-Bejarano
    given-names: Salvador
    email: [email protected]
    orcid: https://orcid.org/0000-0003-0535-7677
  - family-names: Salmon
    given-names: Maëlle
    email: [email protected]
    orcid: https://orcid.org/0000-0002-2815-0399
  notes: 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
repository-code: https://github.com/EMODnet/emodnet.wfs
url: https://docs.ropensci.org/emodnet.wfs/
contact:
- family-names: Fernández-Bejarano
  given-names: Salvador
  email: [email protected]
  orcid: https://orcid.org/0000-0003-0535-7677
keywords:
- biology
- dataproducts
- emodnet
- marine-data
- rstats
- wfs
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
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    address: Vienna, Austria
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  authors:
  - family-names: Lang
    given-names: Michel
    email: [email protected]
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  title: cli
  abstract: 'cli: Helpers for Developing Command Line Interfaces'
  notes: Imports
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  repository: https://CRAN.R-project.org/package=cli
  authors:
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    given-names: Gábor
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  doi: 10.32614/CRAN.package.cli
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  notes: Imports
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    given-names: Gábor
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  notes: Suggests
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    given-names: Hadley
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  year: '2024'
  doi: 10.32614/CRAN.package.readr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
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  repository: https://CRAN.R-project.org/package=rmarkdown
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  - family-names: Allaire
    given-names: JJ
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    email: [email protected]
  - family-names: Wickham
    given-names: Hadley
    email: [email protected]
  - family-names: Cheng
    given-names: Joe
    email: [email protected]
  - family-names: Chang
    given-names: Winston
    email: [email protected]
  - family-names: Iannone
    given-names: Richard
    email: [email protected]
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2024'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: [email protected]
  year: '2024'
  doi: 10.32614/CRAN.package.testthat
  version: '>= 3.1.2'
- type: software
  title: testthis
  abstract: 'testthis: Utils and ''RStudio'' Addins to Make Testing Even More Fun'
  notes: Suggests
  url: https://s-fleck.github.io/testthis
  repository: https://CRAN.R-project.org/package=testthis
  authors:
  - family-names: Fleck
    given-names: Stefan
    email: [email protected]
    orcid: https://orcid.org/0000-0003-3344-9851
  year: '2024'
  doi: 10.32614/CRAN.package.testthis
- type: software
  title: withr
  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
  notes: Suggests
  url: https://withr.r-lib.org
  repository: https://CRAN.R-project.org/package=withr
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Henry
    given-names: Lionel
    email: [email protected]
  - family-names: Müller
    given-names: Kirill
    email: [email protected]
  - family-names: Ushey
    given-names: Kevin
    email: [email protected]
  - family-names: Wickham
    given-names: Hadley
    email: [email protected]
  - family-names: Chang
    given-names: Winston
  year: '2024'
  doi: 10.32614/CRAN.package.withr

---

Owner metadata

• Name: EMODnet
• Login: EMODnet
• Email: [email protected]
• Kind: organization
• Description: Your gateway to marine data in Europe
• Website: https://emodnet.ec.europa.eu
• Location: Belgium
• Twitter: EMODnet
• Company:
• Icon url: https://avatars.githubusercontent.com/u/30047227?v=4
• Repositories: 19
• Last ynced at: 2023-03-05T11:57:44.851Z
• Profile URL: https://github.com/EMODnet

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GitHub Events

Total

• Create event: 7
• Commit comment event: 2
• Issues event: 10
• Delete event: 1
• Issue comment event: 49
• Push event: 102
• Pull request review event: 6
• Pull request review comment event: 9
• Pull request event: 15

Last Year

• Create event: 7
• Commit comment event: 2
• Issues event: 10
• Delete event: 1
• Issue comment event: 49
• Push event: 102
• Pull request review event: 6
• Pull request review comment event: 9
• Pull request event: 15

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Committers metadata

Last synced: 6 days ago

Name	Email	Commits
Maëlle Salmon	m****n@y****e	226
Anna Krystalli	a****i@g****m	118
salvafern	s****z@v****e	38
Emmanuel Blondel	e****1@g****m	1

Committer domains:

• vliz.be: 1

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Issue and Pull Request metadata

Last synced: 1 day ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/EMODnet/emodnet.wfs

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Dependencies

Score: 4.025351690735149