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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
options(timeout = 2000)
```
# emodnet.wfs: Access EMODnet Web Feature Service data through R
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[](https://www.repostatus.org/#active)
[](https://github.com/EMODnet/emodnet.wfs/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/EMODnet/emodnet.wfs/tree/main)
[](https://doi.org/10.14284/679)
[](https://github.com/ropensci/software-review/issues/653)
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The goal of emodnet.wfs is to allow interrogation of and access to [EMODnet's, European Marine Observation and Data Network, geographic vector data](https://emodnet.ec.europa.eu/en/emodnet-web-service-documentation#inline-nav-3) in R through the [EMODnet Web Feature Services](https://emodnet.ec.europa.eu/en/data-0).
[Web Feature services (WFS)](https://www.ogc.org/publications/standard/wfs/) represent a change in the way geographic information is created, modified and exchanged on the Internet and offer direct fine-grained access to geographic information at the feature and feature property level.
emodnet.wfs aims at offering an user-friendly interface to this rich data.
## Installation and setup
You can install the development version of emodnet.wfs from GitHub with:
``` r
# install.packages("pak")
pak::pak("EMODnet/emodnet.wfs")
```
If you want to avoid reading messages from emodnet.wfs such as "WFS client created successfully",
set the `"emodnet.wfs.quiet"` option to `TRUE`.
```r
options("emodnet.wfs.quiet" = TRUE)
```
## Available services
All available services are contained in the tibble returned by `emodnet_wfs()`.
```{r, echo=FALSE}
library(emodnet.wfs)
services <- emodnet_wfs()
class(services)
names(services)
services$service_name
```
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.
```{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/publications/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/publications/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.