Add new emodnet_thematic_lot column to emodnet_wfs() and explain …

…what are thematic lots (#182) * feat: add emodnet_thematic_lot column to emodnet_wfs() * Update emodnet.wfs.Rmd * knit --------- Co-authored-by: Maëlle Salmon <[email protected]>
EMODnet · Nov 26, 2024 · d3c1ad2 · d3c1ad2
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diff --git a/R/emodnet_wfs.R b/R/emodnet_wfs.R
@@ -9,6 +9,17 @@
 #'
 #' @title Which data sources (services) are available?
 #'
+#' @format ## `emodnet_wfs`
+#' \describe{
+#'   \item{emodnet_thematic_lot}{EMODnet disciplinary themes - bathymetry,
+#'   biology, chemistry, geology, human activities, physics and seabed habitats}
+#'   \item{service_name}{Name of the specific service.
+#'   Use in [emodnet_init_wfs_client].}
+#'   \item{service_url}{
+#'   [Web Feature Service (WFS)](https://www.ogc.org/publications/standard/wfs/)
+#'    URL endpoint for accessing the service.}
+#' }
+#'
 #' @return Tibble of available EMODnet Web Feature Services
 #'
 #' @examplesIf identical(Sys.getenv("IN_PKGDOWN"), "true") || interactive()

diff --git a/README.Rmd b/README.Rmd
@@ -61,16 +61,17 @@ In the documentation we assume a basic familiarity with spatial data: knowing ab
 
 ## Available data sources (services)
 
-All available data sources, called services, are contained in the [tibble](https://tibble.tidyverse.org/) returned by `emodnet_wfs()`.
-
+All available data sources, called services, are contained in the [tibble](https://tibble.tidyverse.org/) returned by `emodnet_wfs()`. 
 ```{r, echo=TRUE}
 library(emodnet.wfs)
 services <- emodnet_wfs()
 class(services)
 names(services)
-services$service_name
+services[, c("emodnet_thematic_lot", "service_name")]
 ```
 
+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.
+
 To explore available services you can use `View()` or your usual way to explore `data.frames`.
 
 ## Initialise a WFS Service Client

diff --git a/README.md b/README.md
@@ -83,27 +83,35 @@ services <- emodnet_wfs()
 class(services)
 #> [1] "tbl_df"     "tbl"        "data.frame"
 names(services)
-#> [1] "service_name" "service_url"
-services$service_name
-#>  [1] "bathymetry"                                                     
-#>  [2] "biology"                                                        
-#>  [3] "biology_occurrence_data"                                        
-#>  [4] "chemistry_cdi_data_discovery_and_access_service"                
-#>  [5] "chemistry_cdi_distribution_observations_per_category_and_region"
-#>  [6] "chemistry_contaminants"                                         
-#>  [7] "chemistry_marine_litter"                                        
-#>  [8] "geology_coastal_behavior"                                       
-#>  [9] "geology_events_and_probabilities"                               
-#> [10] "geology_marine_minerals"                                        
-#> [11] "geology_sea_floor_bedrock"                                      
-#> [12] "geology_seabed_substrate_maps"                                  
-#> [13] "geology_submerged_landscapes"                                   
-#> [14] "human_activities"                                               
-#> [15] "physics"                                                        
-#> [16] "seabed_habitats_general_datasets_and_products"                  
-#> [17] "seabed_habitats_individual_habitat_map_and_model_datasets"
+#> [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 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.
+
 To explore available services you can use `View()` or your usual way to
 explore `data.frames`.
 

diff --git a/inst/services.csv b/inst/services.csv
@@ -1,18 +1,18 @@
-service_name,service_url
-bathymetry,https://ows.emodnet-bathymetry.eu/wfs
-biology,https://geo.vliz.be/geoserver/Emodnetbio/wfs
-biology_occurrence_data,https://geo.vliz.be/geoserver/Dataportal/wfs
-chemistry_cdi_data_discovery_and_access_service,https://geo-service.maris.nl/emodnet_chemistry/wfs
-chemistry_cdi_distribution_observations_per_category_and_region,https://geo-service.maris.nl/emodnet_chemistry_p36/wfs
-chemistry_contaminants,https://geoserver.hcmr.gr/geoserver/EMODNET_SHARED/wfs
-chemistry_marine_litter,https://www.ifremer.fr/services/wfs/emodnet_chemistry2
-geology_coastal_behavior,https://drive.emodnet-geology.eu/geoserver/tno/wfs
-geology_events_and_probabilities,https://drive.emodnet-geology.eu/geoserver/ispra/wfs
-geology_marine_minerals,https://drive.emodnet-geology.eu/geoserver/gsi/wfs
-geology_sea_floor_bedrock,https://drive.emodnet-geology.eu/geoserver/bgr/wfs
-geology_seabed_substrate_maps,https://drive.emodnet-geology.eu/geoserver/gtk/wfs
-geology_submerged_landscapes,https://drive.emodnet-geology.eu/geoserver/bgs/wfs
-human_activities,https://ows.emodnet-humanactivities.eu/wfs
-physics,https://prod-geoserver.emodnet-physics.eu/geoserver/ows
-seabed_habitats_general_datasets_and_products,https://ows.emodnet-seabedhabitats.eu/geoserver/emodnet_open/wfs
-seabed_habitats_individual_habitat_map_and_model_datasets,https://ows.emodnet-seabedhabitats.eu/geoserver/emodnet_open_maplibrary/wfs
+emodnet_thematic_lot,service_name,service_url
+EMODnet Bathymetry,bathymetry,https://ows.emodnet-bathymetry.eu/wfs
+EMODnet Biology,biology,https://geo.vliz.be/geoserver/Emodnetbio/wfs
+EMODnet Biology,biology_occurrence_data,https://geo.vliz.be/geoserver/Dataportal/wfs
+EMODnet Chemistry,chemistry_cdi_data_discovery_and_access_service,https://geo-service.maris.nl/emodnet_chemistry/wfs
+EMODnet Chemistry,chemistry_cdi_distribution_observations_per_category_and_region,https://geo-service.maris.nl/emodnet_chemistry_p36/wfs
+EMODnet Chemistry,chemistry_contaminants,https://geoserver.hcmr.gr/geoserver/EMODNET_SHARED/wfs
+EMODnet Chemistry,chemistry_marine_litter,https://www.ifremer.fr/services/wfs/emodnet_chemistry2
+EMODnet Geology,geology_coastal_behavior,https://drive.emodnet-geology.eu/geoserver/tno/wfs
+EMODnet Geology,geology_events_and_probabilities,https://drive.emodnet-geology.eu/geoserver/ispra/wfs
+EMODnet Geology,geology_marine_minerals,https://drive.emodnet-geology.eu/geoserver/gsi/wfs
+EMODnet Geology,geology_sea_floor_bedrock,https://drive.emodnet-geology.eu/geoserver/bgr/wfs
+EMODnet Geology,geology_seabed_substrate_maps,https://drive.emodnet-geology.eu/geoserver/gtk/wfs
+EMODnet Geology,geology_submerged_landscapes,https://drive.emodnet-geology.eu/geoserver/bgs/wfs
+EMODnet Human Activities,human_activities,https://ows.emodnet-humanactivities.eu/wfs
+EMODnet Physics,physics,https://prod-geoserver.emodnet-physics.eu/geoserver/ows
+EMODnet Seabed Habitats,seabed_habitats_general_datasets_and_products,https://ows.emodnet-seabedhabitats.eu/geoserver/emodnet_open/wfs
+EMODnet Seabed Habitats,seabed_habitats_individual_habitat_map_and_model_datasets,https://ows.emodnet-seabedhabitats.eu/geoserver/emodnet_open_maplibrary/wfs
diff --git a/man/emodnet_wfs.Rd b/man/emodnet_wfs.Rd