diff --git a/vignettes/emodnet.wfs.Rmd b/vignettes/emodnet.wfs.Rmd index c4d032a..2df8ece 100644 --- a/vignettes/emodnet.wfs.Rmd +++ b/vignettes/emodnet.wfs.Rmd @@ -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} @@ -57,25 +57,25 @@ 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 -#> -#> 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 +#> +#> 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()`. @@ -83,8 +83,6 @@ EMODnet data covers several disciplines organized in 7 thematic lots: bathymetry ``` 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" @@ -92,18 +90,18 @@ seabed_wfs_client <- emodnet_init_wfs_client(service = "seabed_habitats_general_ 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 -#> -#> 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 +#> +#> 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 ``` @@ -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 -#> -#> 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 +#> +#> 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 ``` @@ -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 @@ -204,9 +205,13 @@ 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' ``` +
+Interactive map of layers in the habitat directive +

plot of chunk unnamed-chunk-6

+
+ EMODnet provides also physics, chemistry, biological or bathymetry data. Explore all the layers available with: @@ -214,18 +219,18 @@ EMODnet provides also physics, chemistry, biological or bathymetry data. Explore emodnet_get_all_wfs_info() #> # A tibble: 1,713 × 9 #> # Rowwise: -#> data_source service_name service_url layer_name title abstract class format -#> -#> 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 +#> +#> 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 ``` @@ -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 -#> , 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, . +#> Krystalli A, Fernández-Bejarano S, Salmon M (????). _emodnet.wfs: Access +#> EMODnet Web Feature Service data through R_. doi: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, . #> #> A BibTeX entry for LaTeX users is #> diff --git a/vignettes/emodnet.wfs.Rmd.orig b/vignettes/emodnet.wfs.Rmd.orig index c10772e..6ce5fe8 100644 --- a/vignettes/emodnet.wfs.Rmd.orig +++ b/vignettes/emodnet.wfs.Rmd.orig @@ -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}