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maelle committed Nov 26, 2024
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126 changes: 65 additions & 61 deletions vignettes/emodnet.wfs.Rmd
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---
title: "Accessing and mapping EMODnet data"
output: rmarkdown::html_vignette
df_print: "tibble"
df_print: "kable"
vignette: >
%\VignetteIndexEntry{API details}
%\VignetteEngine{knitr::rmarkdown}
Expand Down Expand Up @@ -57,53 +57,51 @@ names(services)
#> [1] "emodnet_thematic_lot" "service_name" "service_url"
services[, c("emodnet_thematic_lot", "service_name")]
#> # A tibble: 17 × 2
#> emodnet_thematic_lot service_name
#> <chr> <chr>
#> 1 EMODnet Bathymetry bathymetry
#> 2 EMODnet Biology biology
#> 3 EMODnet Biology biology_occurrence_data
#> 4 EMODnet Chemistry chemistry_cdi_data_discovery_and_access_service
#> 5 EMODnet Chemistry chemistry_cdi_distribution_observations_per_categor…
#> 6 EMODnet Chemistry chemistry_contaminants
#> 7 EMODnet Chemistry chemistry_marine_litter
#> 8 EMODnet Geology geology_coastal_behavior
#> 9 EMODnet Geology geology_events_and_probabilities
#> 10 EMODnet Geology geology_marine_minerals
#> 11 EMODnet Geology geology_sea_floor_bedrock
#> 12 EMODnet Geology geology_seabed_substrate_maps
#> 13 EMODnet Geology geology_submerged_landscapes
#> 14 EMODnet Human Activities human_activities
#> 15 EMODnet Physics physics
#> 16 EMODnet Seabed Habitats seabed_habitats_general_datasets_and_products
#> 17 EMODnet Seabed Habitats seabed_habitats_individual_habitat_map_and_model_da…
#> emodnet_thematic_lot service_name
#> <chr> <chr>
#> 1 EMODnet Bathymetry bathymetry
#> 2 EMODnet Biology biology
#> 3 EMODnet Biology biology_occurrence_data
#> 4 EMODnet Chemistry chemistry_cdi_data_discovery_and_access_service
#> 5 EMODnet Chemistry chemistry_cdi_distribution_observations_per_category_and_re…
#> 6 EMODnet Chemistry chemistry_contaminants
#> 7 EMODnet Chemistry chemistry_marine_litter
#> 8 EMODnet Geology geology_coastal_behavior
#> 9 EMODnet Geology geology_events_and_probabilities
#> 10 EMODnet Geology geology_marine_minerals
#> 11 EMODnet Geology geology_sea_floor_bedrock
#> 12 EMODnet Geology geology_seabed_substrate_maps
#> 13 EMODnet Geology geology_submerged_landscapes
#> 14 EMODnet Human Activities human_activities
#> 15 EMODnet Physics physics
#> 16 EMODnet Seabed Habitats seabed_habitats_general_datasets_and_products
#> 17 EMODnet Seabed Habitats seabed_habitats_individual_habitat_map_and_model_datasets
```

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. The column `service_name` shows services available, while `service_url` has the corresponding base url to perform a WFS request. The Seabed portal should have the data we are looking for. A WFS client can be created by passing the corresponding `service_name` to the function `emodnet_init_wfs_client()`. The layers available to this WFS client are consulted with `emodnet_get_wfs_info()`.


``` r
seabed_wfs_client <- emodnet_init_wfs_client(service = "seabed_habitats_general_datasets_and_products")
#> Loading ISO 19139 XML schemas...
#> Loading ISO 19115 codelists...
#> ✔ WFS client created successfully
#> ℹ Service: "https://ows.emodnet-seabedhabitats.eu/geoserver/emodnet_open/wfs"
#> ℹ Version: "2.0.0"

emodnet_get_wfs_info(wfs = seabed_wfs_client)
#> # A tibble: 72 × 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 seabed_habita… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 2 emodnet_wfs seabed_habita… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 3 emodnet_wfs seabed_habita… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 4 emodnet_wfs seabed_habita… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 5 emodnet_wfs seabed_habita… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 6 emodnet_wfs seabed_habita… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 7 emodnet_wfs seabed_habita… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 8 emodnet_wfs seabed_habita… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 9 emodnet_wfs seabed_habita… https://ow… carib_eus… 2023… "Output… WFSF… sf
#> 10 emodnet_wfs seabed_habita… https://ow… biogenic_… Biog… "This l… WFSF… sf
#> data_source service_name service_url layer_name title abstract class format
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 emodnet_wfs seabed_habitats_gener… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 2 emodnet_wfs seabed_habitats_gener… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 3 emodnet_wfs seabed_habitats_gener… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 4 emodnet_wfs seabed_habitats_gener… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 5 emodnet_wfs seabed_habitats_gener… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 6 emodnet_wfs seabed_habitats_gener… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 7 emodnet_wfs seabed_habitats_gener… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 8 emodnet_wfs seabed_habitats_gener… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 9 emodnet_wfs seabed_habitats_gener… https://ow… carib_eus… 2023… "Output… WFSF… sf
#> 10 emodnet_wfs seabed_habitats_gener… https://ow… biogenic_… Biog… "This l… WFSF… sf
#> # ℹ 62 more rows
#> # ℹ 1 more variable: layer_namespace <chr>
```
Expand All @@ -122,11 +120,11 @@ emodnet_get_layer_info(
)
#> # A tibble: 3 × 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://ows.em… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf
#> 2 emodnet_wfs https://ows.em… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf
#> 3 emodnet_wfs https://ows.em… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf
#> data_source service_name service_url layer_name title abstract class format
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 emodnet_wfs https://ows.emodnet-se… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf
#> 2 emodnet_wfs https://ows.emodnet-se… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf
#> 3 emodnet_wfs https://ows.emodnet-se… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf
#> # ℹ 1 more variable: layer_namespace <chr>
```

Expand All @@ -142,6 +140,9 @@ habitats_directive_layers <- emodnet_get_layers(
simplify = TRUE,
outputFormat = "application/json"
)
#> Start tag expected, '<' not found
#> Start tag expected, '<' not found
#> Start tag expected, '<' not found

habitats_directive_layers
#> Simple feature collection with 221 features and 8 fields
Expand Down Expand Up @@ -204,28 +205,32 @@ Run the following code to have a quick look at the layers geometries.

``` r
mapview(habitats_directive_layers, zcol = "habitat_description", burst = TRUE)
#> Error in loadNamespace(name): there is no package called 'webshot'
```

<div class="figure">
<img src="emodnet.wfs-unnamed-chunk-6-1.png" alt="Interactive map of layers in the habitat directive" />
<p class="caption">plot of chunk unnamed-chunk-6</p>
</div>

EMODnet provides also physics, chemistry, biological or bathymetry data. Explore all the layers available with:


``` r
emodnet_get_all_wfs_info()
#> # A tibble: 1,713 × 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 bathymetry https://ows.… download_… Bath… "Downlo… WFSF… sf
#> 2 emodnet_wfs bathymetry https://ows.… contours Dept… "Genera… WFSF… sf
#> 3 emodnet_wfs bathymetry https://ows.… hr_bathym… High… "Layer … WFSF… sf
#> 4 emodnet_wfs bathymetry https://ows.… quality_i… Qual… "Repres… WFSF… sf
#> 5 emodnet_wfs bathymetry https://ows.… sea_names Sea … "Mainta… WFSF… sf
#> 6 emodnet_wfs bathymetry https://ows.… source_re… Sour… "Covera… WFSF… sf
#> 7 emodnet_wfs bathymetry https://ows.… undersea_… unde… "" WFSF… sf
#> 8 emodnet_wfs biology https://geo.… mediseh_c… EMOD… "Coral … WFSF… sf
#> 9 emodnet_wfs biology https://geo.… mediseh_c… EMOD… "Coral … WFSF… sf
#> 10 emodnet_wfs biology https://geo.… mediseh_c… EMOD… "Cymodo… WFSF… sf
#> data_source service_name service_url layer_name title abstract class format
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 emodnet_wfs bathymetry https://ows.emodnet-… download_… Bath… "Downlo… WFSF… sf
#> 2 emodnet_wfs bathymetry https://ows.emodnet-… contours Dept… "Genera… WFSF… sf
#> 3 emodnet_wfs bathymetry https://ows.emodnet-… hr_bathym… High… "Layer … WFSF… sf
#> 4 emodnet_wfs bathymetry https://ows.emodnet-… quality_i… Qual… "Repres… WFSF… sf
#> 5 emodnet_wfs bathymetry https://ows.emodnet-… sea_names Sea … "Mainta… WFSF… sf
#> 6 emodnet_wfs bathymetry https://ows.emodnet-… source_re… Sour… "Covera… WFSF… sf
#> 7 emodnet_wfs bathymetry https://ows.emodnet-… undersea_… unde… "" WFSF… sf
#> 8 emodnet_wfs biology https://geo.vliz.be/… mediseh_c… EMOD… "Coral … WFSF… sf
#> 9 emodnet_wfs biology https://geo.vliz.be/… mediseh_c… EMOD… "Coral … WFSF… sf
#> 10 emodnet_wfs biology https://geo.vliz.be/… mediseh_c… EMOD… "Cymodo… WFSF… sf
#> # ℹ 1,703 more rows
#> # ℹ 1 more variable: layer_namespace <chr>
```
Expand Down Expand Up @@ -255,15 +260,14 @@ 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>.
#> 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
#>
Expand Down
2 changes: 1 addition & 1 deletion vignettes/emodnet.wfs.Rmd.orig
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
---
title: "Accessing and mapping EMODnet data"
output: rmarkdown::html_vignette
df_print: "tibble"
df_print: "kable"
vignette: >
%\VignetteIndexEntry{API details}
%\VignetteEngine{knitr::rmarkdown}
Expand Down

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