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docs: fix webshot dependency problem
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@maelle
maelle committed Oct 17, 2024
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -50,6 +50,7 @@ VignetteBuilder:
Remotes:
eblondel/ows4R
Config/Needs/readme: rerddap
Config/Needs/website: webshot
Config/testthat/edition: 3
Config/testthat/parallel: true
Encoding: UTF-8
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58 changes: 31 additions & 27 deletions vignettes/emodnet.wfs.Rmd
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Expand Up @@ -94,26 +94,29 @@ The column `service_name` shows services available, while `service_url` has the

``` 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 layer_namespace
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 emodnet_wfs seabed_habitats_general… https://ow… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 2 emodnet_wfs seabed_habitats_general… https://ow… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 3 emodnet_wfs seabed_habitats_general… https://ow… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 4 emodnet_wfs seabed_habitats_general… https://ow… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 5 emodnet_wfs seabed_habitats_general… https://ow… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 6 emodnet_wfs seabed_habitats_general… https://ow… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 7 emodnet_wfs seabed_habitats_general… https://ow… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 8 emodnet_wfs seabed_habitats_general… https://ow… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 9 emodnet_wfs seabed_habitats_general… https://ow… carib_eus… 2023… "Output… WFSF… sf emodnet_open
#> 10 emodnet_wfs seabed_habitats_general… https://ow… biogenic_… Biog… "This l… WFSF… sf emodnet_open
#> 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_general_da… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 2 emodnet_wfs seabed_habitats_general_da… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 3 emodnet_wfs seabed_habitats_general_da… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 4 emodnet_wfs seabed_habitats_general_da… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 5 emodnet_wfs seabed_habitats_general_da… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 6 emodnet_wfs seabed_habitats_general_da… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 7 emodnet_wfs seabed_habitats_general_da… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 8 emodnet_wfs seabed_habitats_general_da… https://ow… art17_hab… 2013… "Gridde… WFSF… sf
#> 9 emodnet_wfs seabed_habitats_general_da… https://ow… carib_eus… 2023… "Output… WFSF… sf
#> 10 emodnet_wfs seabed_habitats_general_da… https://ow… biogenic_… Biog… "This l… WFSF… sf
#> # ℹ 62 more rows
#> # ℹ 1 more variable: layer_namespace <chr>
```


Expand All @@ -130,11 +133,11 @@ emodnet_get_layer_info(
)
#> # A tibble: 3 × 9
#> # Rowwise:
#> data_source service_name service_url layer_name title abstract class format layer_namespace
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 emodnet_wfs https://ows.emodnet-seab… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 2 emodnet_wfs https://ows.emodnet-seab… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 3 emodnet_wfs https://ows.emodnet-seab… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> data_source service_name service_url layer_name title abstract class format layer_namespace
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 emodnet_wfs https://ows… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 2 emodnet_wfs https://ows… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
#> 3 emodnet_wfs https://ows… seabed_hab… art17_hab… 2013… "Gridde… WFSF… sf emodnet_open
```


Expand All @@ -155,15 +158,15 @@ class(habitats_directive_layers)
glimpse(habitats_directive_layers)
#> Rows: 221
#> Columns: 9
#> $ gml_id <chr> "art17_hab_1110.13", "art17_hab_1110.22", "art17_hab_1110.25", "art17_hab_11…
#> $ habitat_code <chr> "1110", "1110", "1110", "1110", "1110", "1110", "1110", "1110", "1110", "111…
#> $ ms <chr> "DK", "ES", "ES", "PT", "PT", "PL", "DK", "FR", "UK", "BE", "BE", "GR", "DE"…
#> $ region <chr> "ATL", "MAC", "MMAC", "MMAC", "MATL", "MBAL", "MBAL", "MATL", "MATL", "ATL",…
#> $ cs_ms <chr> "U2+", "U1+", "U1+", "XX", "U1-", "U1-", "U1-", "U1x", "U1x", "U1x", "U1x", …
#> $ country_code <chr> "Denmark", "Spain", "Spain", "Portugal", "Portugal", "Poland", "Denmark", "F…
#> $ habitat_code_uri <chr> "http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110", "http://dd…
#> $ habitat_description <chr> "Sandbanks which are slightly covered by sea water all the time", "Sandbanks…
#> $ geom <MULTISURFACE [m]> MULTISURFACE (POLYGON ((420..., MULTISURFACE (POLYGON ((195...,…
#> $ gml_id <chr> "art17_hab_1110.13", "art17_hab_1110.22", "art17_hab_1110.25", …
#> $ habitat_code <chr> "1110", "1110", "1110", "1110", "1110", "1110", "1110", "1110",…
#> $ ms <chr> "DK", "ES", "ES", "PT", "PT", "PL", "DK", "FR", "UK", "BE", "BE…
#> $ region <chr> "ATL", "MAC", "MMAC", "MMAC", "MATL", "MBAL", "MBAL", "MATL", "…
#> $ cs_ms <chr> "U2+", "U1+", "U1+", "XX", "U1-", "U1-", "U1-", "U1x", "U1x", "…
#> $ country_code <chr> "Denmark", "Spain", "Spain", "Portugal", "Portugal", "Poland", …
#> $ habitat_code_uri <chr> "http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110…
#> $ habitat_description <chr> "Sandbanks which are slightly covered by sea water all the time…
#> $ geom <MULTISURFACE [m]> MULTISURFACE (POLYGON ((420..., MULTISURFACE (POLY…
```


Expand All @@ -182,9 +185,10 @@ if (unique(st_geometry_type(habitats_directive_layers)) == "MULTISURFACE") {
map <- mapview(habitats_directive_layers, zcol = "habitat_description", burst = TRUE)

map
#> Error in loadNamespace(name): there is no package called 'webshot'
```

![plot of chunk unnamed-chunk-6](emodnet.wfs-unnamed-chunk-6-1.png)

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


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