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https://github.com/EMODnet/emodnet.wfs

Access EMODnet Web Feature Service data through R
https://github.com/EMODnet/emodnet.wfs

biology dataproducts emodnet marine-data rstats wfs

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Access EMODnet Web Feature Service data through R

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README 

        
---

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 though the [EMODnet Web Feature Services](https://emodnet.ec.europa.eu/en/data). 

[Web Feature services (WFS)](https://www.ogc.org/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. 

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:



``` 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)

```



## Available services



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



```{r, echo=FALSE}

library(emodnet.wfs)

knitr::kable(emodnet_wfs())

```



To explore available services you can use:



```r

View(emodnet_wfs())

```



## Create Service Client



Specify the service using the `service` argument. 



```{r}

wfs_bio <- emodnet_init_wfs_client(service = "biology")



wfs_bio

```



## Get WFS Layer info



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



```{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 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.



```{r}

emodnet_get_layers(wfs = wfs_bio, layers = layers)

```



You can change the output `crs` 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 `reduce_layers`.  

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,

  reduce_layers = TRUE

)

```



Using `reduce_layers = 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"),

  reduce_layers = 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).



## 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](https://erddap.emodnet.eu). You can access these data in R using the [rerddap R package](https://docs.ropensci.org/rerddap/):



```{r rerddap}

# install.packages("rerrdap")

library(rerddap)



erddap_url <- "https://erddap.emodnet.eu/erddap/"



rerddap::ed_datasets(url = erddap_url)



rerddap::ed_search(query = "vessel density", url = erddap_url)



human_activities_data_info <- rerddap::info(datasetid = "humanactivities_9f8a_3389_f08a", url = erddap_url)

human_activities_data_info



year_2020_gridded_data <- griddap(datasetx = human_activities_data_info, time = c("2020-03-18", "2020-03-19"))

head(year_2020_gridded_data$data)

```



### EMODnetWCS: Access EMODnet Web Coverage Service data



This package emodnet.wfs uses [Web Feature Services](https://www.ogc.org/standard/wfs/), hence it is limited to getting vector data. EMODnet also hosts raster data that can be accessed via [Web Coverage Services (WCS)](https://www.ogc.org/standard/wcs/). The R package [EMODnetWCS](https://github.com/EMODnet/EMODnetWCS) makes these data available in R.



## 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.