diff --git a/404.html b/404.html index fcfd52e7..3fb1c1be 100644 --- a/404.html +++ b/404.html @@ -6,26 +6,26 @@ Page not found (404) • emodnet.wfs - - - - - - - - - - - - + + + + + + + + + + + + - Skip to contents + Skip to contents
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diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 29883601..43be118c 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -1,5 +1,5 @@ -Contributing to EMODnetWFS • emodnet.wfs +Contributing to emodnet.wfs • emodnet.wfs Skip to contents @@ -19,7 +19,7 @@
  • Changelog
    • @@ -33,13 +33,13 @@
    -

    Contributing to EMODnetWFS

    +

    Contributing to emodnet.wfs

    Source: .github/CONTRIBUTING.md
    -

    This outlines how to propose a change to EMODnetWFS.

    +

    This outlines how to propose a change to emodnet.wfs.

    Fixing typos

    You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the source file. This generally means you’ll need to edit roxygen2 comments in an .R, not a .Rd file. You can find the .R file that generates the .Rd by reading the comment in the first line.

    @@ -49,7 +49,7 @@

    Bigger changesIf you want to make a bigger change, it’s a good idea to first file an issue and make sure someone from the team agrees that it’s needed. If you’ve found a bug, please file an issue that illustrates the bug with a minimal reprex (this will also help you write a unit test, if needed).

    Pull request process

    -
    +library(emodnet.wfs)

     wfs <- emodnet_init_wfs_client(service = "biology")
 #> Loading ISO 19139 XML schemas...
@@ -689,8 +689,8 @@ 
    Using OR and AND
 
    Advanced use
 
    
 
    There is more that can accomplished by using the EMODnet WFS services
-than downloading data. The EMODnetWFS package is built on top of the ows4R library, meaning that
-all the functionalities of this package are available for EMODnetWFS.
+than downloading data. The emodnet.wfs package is built on top of the ows4R library, meaning that
+all the functionalities of this package are available for emodnet.wfs.
 The ows4R returns a special type of R object called R6. You can learn
 more in Hadley Wickham’s chapter on R6 Objects of the Advance R book.
    
 
    For instance: it is not efficient to read a large dataset into R just
diff --git a/articles/emodnet.wfs.html b/articles/emodnet.wfs.html
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+emodnet.wfs Case Study: Accessing and mapping EMODnet data • emodnet.wfs
+
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+    Skip to contents
+
+
+    
    
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+
    
+  
    
+      
    emodnet.wfs Case Study: Accessing and mapping EMODnet data
    
+            
+      
+      Source: vignettes/emodnet.wfs.Rmd
+      
    emodnet.wfs.Rmd
    
+    
    
+
+    
+    
+
    
+
    Introduction
+
    
+
    The package was designed to make EMODnet vector data layers easily
+accessible in R. The package allows users to query information on and
+download data from all available EMODnet
+Web Feature Service (WFS) endpoints directly into their R working
+environment. Data are managed as sf objects which
+are currently the state-of-the-art in handling of vector spatial data in
+R. The package also allows user to specify the coordinate reference
+system of imported data.
    
+
    
+
    
+
    Data Product
+
    
+
    
+
    Installation
+
    
+
    You can install the development version of emodnet.wfs from GitHub
+with:
    
+
    +pak::pak("EMODnet/emodnet.wfs")
    
+
    
+
    
+
    Explore the EMODnet WFS services with R
+
    
+
    For this tutorial we will make use of the sf,
+dplyr and mapview packages. The simple
+features sf package is a well known standard for dealing
+with geospatial vector data. The package dplyr is a strong
+library for data manipulation. This package also loads
+magrittr’s pipe operator %>% (you could
+also use the base
+pipe), which allows to write pipelines in R. To visualize
+geometries, mapview will create quick interactive maps.
    
+
    Run this line to install these packages:
    
+
    +install.packages(c("sf", "dplyr", "mapview"))
    
+
    With the emodnet.wfs package, we can explore and combine the data
+served by the EMODnet
+lots through OGC Web Feature
+Services or WFS.
    
+
    Imagine we are interested in seabed substrates. The first step is to
+choose what EMODnet lot can provide with these data. For that, we can
+check the services available with the emodnet_wfs()
+function.
    
+
    +library(emodnet.wfs)
+library(mapview)
+library(dplyr)
+library(sf)
+
+emodnet_wfs()
+#>                                                       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
+#>                                                                    service_url
+#> 1                                        https://ows.emodnet-bathymetry.eu/wfs
+#> 2                                 https://geo.vliz.be/geoserver/Emodnetbio/wfs
+#> 3                                 https://geo.vliz.be/geoserver/Dataportal/wfs
+#> 4                           https://geo-service.maris.nl/emodnet_chemistry/wfs
+#> 5                       https://geo-service.maris.nl/emodnet_chemistry_p36/wfs
+#> 6                       https://geoserver.hcmr.gr/geoserver/EMODNET_SHARED/wfs
+#> 7                       https://www.ifremer.fr/services/wfs/emodnet_chemistry2
+#> 8                           https://drive.emodnet-geology.eu/geoserver/tno/wfs
+#> 9                         https://drive.emodnet-geology.eu/geoserver/ispra/wfs
+#> 10                          https://drive.emodnet-geology.eu/geoserver/gsi/wfs
+#> 11                          https://drive.emodnet-geology.eu/geoserver/bgr/wfs
+#> 12                          https://drive.emodnet-geology.eu/geoserver/gtk/wfs
+#> 13                          https://drive.emodnet-geology.eu/geoserver/bgs/wfs
+#> 14                                  https://ows.emodnet-humanactivities.eu/wfs
+#> 15                     https://prod-geoserver.emodnet-physics.eu/geoserver/ows
+#> 16            https://ows.emodnet-seabedhabitats.eu/geoserver/emodnet_open/wfs
+#> 17 https://ows.emodnet-seabedhabitats.eu/geoserver/emodnet_open_maplibrary/wfs
    
+
    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().
    
+
    +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: 71 × 9
+#> # Rowwise: 
+#>    data_source service_name        service_url layer_name title
+#>    <chr>       <chr>               <chr>       <chr>      <chr>
+#>  1 emodnet_wfs seabed_habitats_ge… https://ow… art17_hab… 2013…
+#>  2 emodnet_wfs seabed_habitats_ge… https://ow… art17_hab… 2013…
+#>  3 emodnet_wfs seabed_habitats_ge… https://ow… art17_hab… 2013…
+#>  4 emodnet_wfs seabed_habitats_ge… https://ow… art17_hab… 2013…
+#>  5 emodnet_wfs seabed_habitats_ge… https://ow… art17_hab… 2013…
+#>  6 emodnet_wfs seabed_habitats_ge… https://ow… art17_hab… 2013…
+#>  7 emodnet_wfs seabed_habitats_ge… https://ow… art17_hab… 2013…
+#>  8 emodnet_wfs seabed_habitats_ge… https://ow… art17_hab… 2013…
+#>  9 emodnet_wfs seabed_habitats_ge… https://ow… carib_eus… 2023…
+#> 10 emodnet_wfs seabed_habitats_ge… https://ow… biogenic_… Biog…
+#> # ℹ 61 more rows
+#> # ℹ 4 more variables: abstract <chr>, class <chr>,
+#> #   format <chr>, layer_namespace <chr>
    
+
    Each layer is explained in the abstract column. We can
+see several layers with the information provided by the EU member states
+for the Habitats
+Directive 92/43/EEC reporting. We will select the layers about
+coastal lagoons, mudflats and sandbanks with their respective
+layer_name.
    
+
    +habitats_directive_layer_names <- c("art17_hab_1110", "art17_hab_1140", "art17_hab_1150")
+
+emodnet_get_layer_info(
+  wfs = seabed_wfs_client,
+  layers = habitats_directive_layer_names
+)
+#> # A tibble: 3 × 9
+#> # Rowwise: 
+#>   data_source service_name         service_url layer_name title
+#>   <chr>       <chr>                <chr>       <chr>      <chr>
+#> 1 emodnet_wfs https://ows.emodnet… seabed_hab… art17_hab… 2013…
+#> 2 emodnet_wfs https://ows.emodnet… seabed_hab… art17_hab… 2013…
+#> 3 emodnet_wfs https://ows.emodnet… seabed_hab… art17_hab… 2013…
+#> # ℹ 4 more variables: abstract <chr>, class <chr>,
+#> #   format <chr>, layer_namespace <chr>
    
+
    We are now ready to read the layers into R with
+emodnet_get_layers(). emodnet.wfs reads the geometries as
+simple features (See sf package) transformed to 4326 by default. Specifying another map
+projection is possible by passing a EPGS code or projection string with
+emodnet_get_layers(crs = "your projection"). The argument
+reduce_layers = TRUE stack all the layers in one single
+tibble. Default is FALSE and returns a list of sf objects, one per
+layer.
    
+
    +habitats_directive_layers <- emodnet_get_layers(
+  wfs = seabed_wfs_client,
+  layers = habitats_directive_layer_names,
+  reduce_layers = TRUE
+)
+
+class(habitats_directive_layers)
+#> [1] "sf"         "data.frame"
    
+
    +
+glimpse(habitats_directive_layers)
+#> Rows: 221
+#> Columns: 9
+#> $ gml_id              <chr> "art17_hab_1110.13", "art17_hab_1110.22", "art17_hab_1110.25", "ar…
+#> $ habitat_code        <chr> "1110", "1110", "1110", "1110", "1110", "1110", "1110", "1110", "1…
+#> $ ms                  <chr> "DK", "ES", "ES", "PT", "PT", "PL", "DK", "FR", "UK", "BE", "BE", …
+#> $ region              <chr> "ATL", "MAC", "MMAC", "MMAC", "MATL", "MBAL", "MBAL", "MATL", "MAT…
+#> $ cs_ms               <chr> "U2+", "U1+", "U1+", "XX", "U1-", "U1-", "U1-", "U1x", "U1x", "U1x…
+#> $ country_code        <chr> "Denmark", "Spain", "Spain", "Portugal", "Portugal", "Poland", "De…
+#> $ 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 (POLYGON…
    
+
    Run the following code to have a quick look at the layers
+geometries
    
+
    +# Transform to Polygon geometry type from Multisurface
+if (unique(st_geometry_type(habitats_directive_layers)) == "MULTISURFACE") {
+  habitats_directive_layers <- habitats_directive_layers %>%
+    st_cast(to = "GEOMETRYCOLLECTION") %>%
+    st_collection_extract(type = "POLYGON")
+}
+
+# Visualize
+map <- mapview(habitats_directive_layers, zcol = "habitat_description", burst = TRUE)
+
+map
+#> Error in loadNamespace(name): there is no package called 'webshot'
    
+
    EMODnet provides also physics, chemistry, biological or bathymetry
+data. Explore all the layers available with.
    
+
+
    
+
    
+
    
+
    More information
+
    
+
    
+
    References
+
    
+
    Blondel, Emmanuel. (2020, May 27). ows4R: R Interface to OGC
+Web-Services (Version 0.1-5). Zenodo. http://doi.org/10.5281/zenodo.3860330
    
+
    Flanders Marine Institute (2019). Maritime Boundaries Geodatabase,
+version 11. Available online at https://www.marineregions.org/. https://doi.org/10.14284/382.
    
+
    Hadley Wickham, Romain François, Lionel Henry and Kirill Müller
+(2020). dplyr: A Grammar of Data Manipulation. R package version
+1.0.2.https://CRAN.R-project.org/package=dplyr
    
+
    Pebesma E (2018). “Simple Features for R: Standardized Support for
+Spatial Vector Data.” The R Journal, 10(1), 439–446. doi:
+10.32614/RJ-2018-009, https://doi.org/10.32614/RJ-2018-009.
    
+
    R Core Team (2020). R: A language and environment for statistical
+computing. R Foundation for Statistical Computing, Vienna, Austria. URL
+https://www.R-project.org/.
    
+
    Tim Appelhans, Florian Detsch, Christoph Reudenbach and Stefan
+Woellauer (2020). mapview: Interactive Viewing of Spatial Data in R. R
+package version 2.9.0. https://CRAN.R-project.org/package=mapview
    
+
    
+
    
+
    Code
+
    
+
    Please cite this package as:
    
+
    Anna Krystalli (2020). emodnet.wfs: Access EMODnet Web Feature
+Service data through R. R package version 0.0.2. https://github.com/EMODnet/emodnet.wfs. 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.
    
+
    
+
    
+  
    
+
    
+
+
+
+    
+
    
+
+
+
+
+
+  
+
diff --git a/articles/index.html b/articles/index.html
index 52edf866..580af81f 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -1,5 +1,5 @@
 
-Articles • emodnet.wfs
+Articles • emodnet.wfs
     Skip to contents
 
 
@@ -19,7 +19,7 @@
 
  • 
   
   
    • 
 
  • Changelog
    • 
@@ -42,7 +42,7 @@ 
    All vignettes
    
 
       
    EQCL feature filtering
    
         
    
-        
    EMODnetWFS Case Study: Accessing and mapping EMODnet data
    
+        
    emodnet.wfs Case Study: Accessing and mapping EMODnet data
    
         
    
         
    Using request parameters to limit query results
    
         
    
diff --git a/articles/request-params.html b/articles/request-params.html
index 48c6d005..64b6dc4e 100644
--- a/articles/request-params.html
+++ b/articles/request-params.html
@@ -40,7 +40,7 @@
   
   
 
@@ -94,10 +94,10 @@
 
    
 
    Initialise a WFS client
 
    
-
    Let’s start by loading EMODnetWFS and initialising a WFS
-client to the human_activities WFS service.
    
+
    Let’s start by loading emodnet.wfs and initialising a WFS client to
+the human_activities WFS service.
    
 
    -library(EMODnetWFS)
+library(emodnet.wfs)
 
 wfs <- emodnet_init_wfs_client("human_activities")
 #> Loading ISO 19139 XML schemas...
@@ -385,9 +385,9 @@ 
    Non-standard Vendor Parametersemodnet_get_layers() and are documented in detail in
+handled explicitly through the emodnet.wfs package through the
+cql_filter argument in emodnet_get_layers()
+and are documented in detail in
 article("ecql_filtering").
    
 
    For additional vendor parameters available through GeoServer
 implementations please refer to the WFS
diff --git a/authors.html b/authors.html
index 1f3ba49c..2377e6c9 100644
--- a/authors.html
+++ b/authors.html
@@ -1,5 +1,5 @@
 
-Authors and Citation • emodnet.wfs
+Authors and Citation • emodnet.wfs
     Skip to contents
 
 
@@ -19,7 +19,7 @@
 
  • 
   
   
    • 
 
  • Changelog
    • 
diff --git a/index.html b/index.html
index b7ba805a..834df67c 100644
--- a/index.html
+++ b/index.html
@@ -19,7 +19,7 @@
 
 
 
-
+
 
 
     Skip to contents
@@ -43,7 +43,7 @@
   
   
 
@@ -517,22 +517,22 @@ 
    Citationcitation(package = "emodnet.wfs")
 #> To cite package 'emodnet.wfs' in publications use:
 #> 
-#>   Krystalli A, Fernández-Bejarano S, Salmon M (????). _EMODnetWFS:
+#>   Krystalli A, Fernández-Bejarano S, Salmon M (????). _emodnet.wfs:
 #>   Access EMODnet Web Feature Service data through R_. R package version
 #>   2.0.1.9001. 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/EMODnetWFS>.
+#>   and Fisheries Fund, <https://github.com/EMODnet/emodnet.wfs>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
-#>     title = {{EMODnetWFS}: Access EMODnet Web Feature Service data through R},
+#>     title = {{emodnet.wfs}: Access EMODnet Web Feature Service data through R},
 #>     author = {Anna Krystalli and Salvador Fernández-Bejarano and Maëlle Salmon},
 #>     note = {R package version 2.0.1.9001. 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},
-#>     url = {https://github.com/EMODnet/EMODnetWFS},
+#>     url = {https://github.com/EMODnet/emodnet.wfs},
 #>   }
    
 
    
 
    
diff --git a/news/index.html b/news/index.html
index a68e1e0a..3f7135de 100644
--- a/news/index.html
+++ b/news/index.html
@@ -1,5 +1,5 @@
 
-Changelog • emodnet.wfs
+Changelog • emodnet.wfs
     Skip to contents
 
 
@@ -19,7 +19,7 @@
 
  • 
   
   
    • 
 
  • Changelog
    • 
@@ -37,7 +37,26 @@
       Source: NEWS.md
     
    
 
-
    +
    +

    emodnet.wfs (development version)

    +
    • Added ability to pass vendor parameter to emodnet.wfs::emodnet_get_layers() queries (#88).
      • +
    • Added memoising (caching during each R session) of the functions getting services and layers information (#52).
      • +
    +
    +

    emodnet.wfs 2.0.1

    +
    • Introduced better handling of server response errors.
      • +
    +
    +

    emodnet.wfs 2.0.0

    +
    • NEW FEATURE: Added ecql filtering capability and ability to interrogate feature attribute (see relevant vignette).
      • +
    • Bug fix: corrected service namespace definition when using a wfs object
      • +
    • Breaking Change: set to extract default CRS from service information (through getDeafultCRS method)
      • +
    • Breaking change: Removed default service value.
      • +
    • Updated to new EMODnet Seabed Habitats endpoints
      • +
    • Added a NEWS.md file to track changes to the package.
      • +
    +