diff --git a/index.html b/index.html index 06f3bd4..01a41d6 100644 --- a/index.html +++ b/index.html @@ -79,6 +79,7 @@

Installation and setupIf you want to avoid reading messages from emodnet.wfs such as “WFS client created successfully”, set the "emodnet.wfs.quiet" option to TRUE.

 options("emodnet.wfs.quiet" = TRUE)
+

The use of the EMODnet Web Feature Services is not subjet to rate limiting at the moment.

Pre-requisites @@ -99,7 +100,7 @@

Available data sources (services)library(emodnet.wfs) services <- emodnet_wfs() class(services) -#> [1] "data.frame" +#> [1] "tbl_df" "tbl" "data.frame" names(services) #> [1] "service_name" "service_url" services$service_name diff --git a/pkgdown.yml b/pkgdown.yml index 51b1610..fa5dc25 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -5,7 +5,7 @@ articles: articles/ecql_filtering: ecql_filtering.html emodnet.wfs: emodnet.wfs.html articles/request-params: request-params.html -last_built: 2024-11-25T08:40Z +last_built: 2024-11-25T08:53Z urls: reference: https://emodnet.github.io/emodnet.wfs/reference article: https://emodnet.github.io/emodnet.wfs/articles diff --git a/reference/emodnet_get_layers.html b/reference/emodnet_get_layers.html index aae604e..8681845 100644 --- a/reference/emodnet_get_layers.html +++ b/reference/emodnet_get_layers.html @@ -260,42 +260,42 @@

Examples#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. str(data[["abiotic_observations"]]) #> spc_tbl_ [1,000,000 × 37] (S3: spec_tbl_df/tbl_df/tbl/data.frame) -#> $ FID : chr [1:1000000] "abiotic_observations.fid--2efb98bf_19362766137_-4916" "abiotic_observations.fid--2efb98bf_19362766137_-4915" "abiotic_observations.fid--2efb98bf_19362766137_-4914" "abiotic_observations.fid--2efb98bf_19362766137_-4913" ... -#> $ id : num [1:1000000] 32822603 32822703 32822703 32822703 32822703 ... +#> $ FID : chr [1:1000000] "abiotic_observations.fid-6c0eccf5_1936280e682_3fa9" "abiotic_observations.fid-6c0eccf5_1936280e682_3faa" "abiotic_observations.fid-6c0eccf5_1936280e682_3fab" "abiotic_observations.fid-6c0eccf5_1936280e682_3fac" ... +#> $ id : num [1:1000000] 4.59e+08 4.59e+08 4.59e+08 4.59e+08 4.59e+08 ... #> $ aphiaid : logi [1:1000000] NA NA NA NA NA NA ... -#> $ latitude : num [1:1000000] 51.4 51.4 51.4 51.4 51.4 ... -#> $ longitude : num [1:1000000] 4.01 4.01 4.01 4.01 4.01 ... -#> $ depth : num [1:1000000] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 ... -#> $ datetime : POSIXct[1:1000000], format: "1990-12-10 13:52:00" "1991-01-08 12:41:00" ... -#> $ value : chr [1:1000000] "3.73" "86" "86" "86" ... +#> $ latitude : num [1:1000000] 51.3 51.3 51.3 51.3 51.3 ... +#> $ longitude : num [1:1000000] 4.26 4.26 4.26 4.26 4.26 ... +#> $ depth : num [1:1000000] NA NA NA NA NA NA NA NA NA NA ... +#> $ datetime : POSIXct[1:1000000], format: "2009-03-01 00:50:00" "2009-03-01 01:00:00" ... +#> $ value : chr [1:1000000] "-" "-" "-" "-" ... #> $ lod : logi [1:1000000] NA NA NA NA NA NA ... #> $ loq : logi [1:1000000] NA NA NA NA NA NA ... -#> $ standardparameterid: num [1:1000000] 1024 1213 1213 1213 1213 ... -#> $ dataproviderid : num [1:1000000] 8 8 8 8 8 8 8 8 8 8 ... -#> $ imisdatasetid : num [1:1000000] 135 135 135 135 135 135 135 135 135 135 ... -#> $ dataficheid : num [1:1000000] 16 11 11 11 11 11 11 11 11 11 ... -#> $ seriesid : num [1:1000000] 1895 1895 1895 1895 1895 ... +#> $ standardparameterid: num [1:1000000] 272 272 272 272 272 272 272 272 272 272 ... +#> $ dataproviderid : num [1:1000000] 6 6 6 6 6 6 6 6 6 6 ... +#> $ imisdatasetid : num [1:1000000] 5242 5242 5242 5242 5242 ... +#> $ dataficheid : num [1:1000000] 61 61 61 61 61 61 61 61 61 61 ... +#> $ seriesid : num [1:1000000] 2032 2032 2032 2032 2032 ... #> $ datatype : chr [1:1000000] "NC" "NC" "NC" "NC" ... #> $ class : logi [1:1000000] NA NA NA NA NA NA ... #> $ classunit : logi [1:1000000] NA NA NA NA NA NA ... #> $ classcode : logi [1:1000000] NA NA NA NA NA NA ... -#> $ season : chr [1:1000000] "autumn" "winter" "winter" "winter" ... -#> $ parametername : chr [1:1000000] "Stikstof, totaal in mgN/l in oppervlaktewater" "Zuurstof in % in oppervlaktewater" "Zuurstof in % in oppervlaktewater" "Zuurstof in % in oppervlaktewater" ... -#> $ parameterunit : chr [1:1000000] "mgN/l" "%" "%" "%" ... -#> $ dataprovider : chr [1:1000000] "RWS - Rijkswaterstaat" "RWS - Rijkswaterstaat" "RWS - Rijkswaterstaat" "RWS - Rijkswaterstaat" ... -#> $ datasettitle : chr [1:1000000] "MWTL chemical monitoring network Westerschelde" "MWTL chemical monitoring network Westerschelde" "MWTL chemical monitoring network Westerschelde" "MWTL chemical monitoring network Westerschelde" ... -#> $ datafichetitle : chr [1:1000000] "S-FC-N-016 - Organische microverontreinigingen" "S-FC-N-010 - Zuurstof (periodiek)" "S-FC-N-010 - Zuurstof (periodiek)" "S-FC-N-010 - Zuurstof (periodiek)" ... -#> $ stationname : chr [1:1000000] "Hansweert geul" "Hansweert geul" "Hansweert geul" "Hansweert geul" ... -#> $ gid : num [1:1000000] 10 10 10 10 10 10 10 10 10 10 ... -#> $ seasonid : num [1:1000000] 4 1 1 1 1 1 1 1 1 1 ... -#> $ unit : chr [1:1000000] "mgN/l" "%" "%" "%" ... -#> $ category : chr [1:1000000] "opgeloste gassen" "opgeloste gassen" "opgeloste gassen" "opgeloste gassen" ... -#> $ the_geom : chr [1:1000000] "POINT (51.43701536692164 4.01438853410749)" "POINT (51.43701536692164 4.01438853410749)" "POINT (51.43701536692164 4.01438853410749)" "POINT (51.43701536692164 4.01438853410749)" ... +#> $ season : chr [1:1000000] "winter" "winter" "winter" "winter" ... +#> $ parametername : chr [1:1000000] "Geleidendheid (Conductiviteit) in mS/cm in de waterkolom" "Geleidendheid (Conductiviteit) in mS/cm in de waterkolom" "Geleidendheid (Conductiviteit) in mS/cm in de waterkolom" "Geleidendheid (Conductiviteit) in mS/cm in de waterkolom" ... +#> $ parameterunit : chr [1:1000000] "mS/cm" "mS/cm" "mS/cm" "mS/cm" ... +#> $ dataprovider : chr [1:1000000] "MOW MT - Maritieme Toegang" "MOW MT - Maritieme Toegang" "MOW MT - Maritieme Toegang" "MOW MT - Maritieme Toegang" ... +#> $ datasettitle : chr [1:1000000] "Continuous measurements in Deurganckdok" "Continuous measurements in Deurganckdok" "Continuous measurements in Deurganckdok" "Continuous measurements in Deurganckdok" ... +#> $ datafichetitle : chr [1:1000000] "P-FC-V-001 - Geleidbaarheid - Continu" "P-FC-V-001 - Geleidbaarheid - Continu" "P-FC-V-001 - Geleidbaarheid - Continu" "P-FC-V-001 - Geleidbaarheid - Continu" ... +#> $ stationname : chr [1:1000000] "DGD S-Middle Top" "DGD S-Middle Top" "DGD S-Middle Top" "DGD S-Middle Top" ... +#> $ gid : num [1:1000000] 7 7 7 7 7 7 7 7 7 7 ... +#> $ seasonid : num [1:1000000] 1 1 1 1 1 1 1 1 1 1 ... +#> $ unit : chr [1:1000000] "mS/cm" "mS/cm" "mS/cm" "mS/cm" ... +#> $ category : chr [1:1000000] "saliniteit, chloriniteit en geleidendheid" "saliniteit, chloriniteit en geleidendheid" "saliniteit, chloriniteit en geleidendheid" "saliniteit, chloriniteit en geleidendheid" ... +#> $ the_geom : chr [1:1000000] "POINT (51.29098351 4.263097996)" "POINT (51.29098351 4.263097996)" "POINT (51.29098351 4.263097996)" "POINT (51.29098351 4.263097996)" ... #> $ valuesign : chr [1:1000000] "=" "=" "=" "=" ... #> $ dateprecision : logi [1:1000000] NA NA NA NA NA NA ... #> $ standard_name : chr [1:1000000] "BODC" "BODC" "BODC" "BODC" ... -#> $ externalid : chr [1:1000000] "NTOTZZXX" "OXYSSE01" "OXYSZW01" "OXYSZZ01" ... -#> $ external_name : chr [1:1000000] "Concentration of total nitrogen {total_N} per unit volume of the water body [dissolved plus reactive particulate phase]" "Saturation of oxygen {O2 CAS 7782-44-7} in the water body [dissolved plus reactive particulate phase] by YSI in"| __truncated__ "Saturation of oxygen {O2 CAS 7782-44-7} in the water body [dissolved plus reactive particulate phase] by Winkle"| __truncated__ "Saturation of oxygen {O2 CAS 7782-44-7} in the water body [dissolved plus reactive particulate phase]" ... +#> $ externalid : chr [1:1000000] "CNDCST01" "CNDCST01" "CNDCST01" "CNDCST01" ... +#> $ external_name : chr [1:1000000] "Electrical conductivity of the water body by CTD" "Electrical conductivity of the water body by CTD" "Electrical conductivity of the water body by CTD" "Electrical conductivity of the water body by CTD" ... #> $ scientificname : logi [1:1000000] NA NA NA NA NA NA ... #> - attr(*, "spec")= #> .. cols( diff --git a/search.json b/search.json index 6494a55..52cee6a 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to emodnet.wfs","title":"Contributing to emodnet.wfs","text":"outlines propose change emodnet.wfs.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing to emodnet.wfs","text":"can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to emodnet.wfs","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to emodnet.wfs","text":"Fork package clone onto computer. haven’t done , recommend using usethis::create_from_github(\"EMODnet/emodnet.wfs\", fork = TRUE). Install development dependencies pak::pak(), make sure package passes R CMD check running devtools::check(). R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using usethis::pr_init(\"brief-description--change\"). Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number. user-facing changes, add bullet top NEWS.md (.e. just first header). Follow style described https://style.tidyverse.org/news.html.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to emodnet.wfs","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. use roxygen2, Markdown syntax, documentation. use testthat httptest unit tests. Contributions test cases included easier accept.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":"collaborators","dir":"","previous_headings":"","what":"Collaborators","title":"Contributing to emodnet.wfs","text":"Regular contributors listed inst/collaborators.txt ensure user-agent used package flags developers.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2021 European Marine Observation Data Network (EMODnet) Biology project Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"cql-ecql-query-languages-","dir":"Articles","previous_headings":"","what":"CQL & ECQL Query languages.","title":"EQCL feature filtering","text":"CQL (Common Query Language) plain-text language created OGC Catalog specification. GeoServer adapted easy--use filtering mechanism. GeoServer actually implements powerful extension called ECQL (Extended CQL), allows expressing full range filters OGC Filter 1.1 can encode. ECQL accepted many places GeoServer. GeoServer supports use CQL ECQL WFS requests whenever documentation refers CQL, ECQL syntax can used well. examples provided small subset filtering functionality available Geoserver. Full references examples can found following documentation: ECQL Reference: reference syntax ECQL language. Filter Function Reference: OGC Filter Encoding specification provides generic concept filter function. filter function named function number arguments, can used filter expression perform specific calculations. provides much richer expressiveness defining filters.GeoServer provides many different kinds filter functions, covering wide range functionality including mathematics, string formatting, geometric operations. CQL ECQL Tutorial shows examples defining filters.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"initialise-emodnet-wfs-client","dir":"Articles","previous_headings":"","what":"Initialise EMODnet WFS client","title":"EQCL feature filtering","text":"First, let’s load library start new WFS client emodnet_init_wfs_client.","code":"library(emodnet.wfs) wfs <- emodnet_init_wfs_client(service = \"biology\") #> Loading ISO 19139 XML schemas... #> Loading ISO 19115 codelists... #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"inspecting-attributes","dir":"Articles","previous_headings":"","what":"Inspecting attributes","title":"EQCL feature filtering","text":"develop filters, first need information attributes can filter . example, might want know data type range distribution values attributes given layer. Let’s look existing layers.","code":"emodnet_get_wfs_info(wfs) #> # A tibble: 35 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 2 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 3 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Cymodo… WFSF… sf #> 4 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 5 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 6 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 7 emodnet_wfs biology https://geo.… mediseh_h… EMOD… \"Haloph… WFSF… sf #> 8 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 10 emodnet_wfs biology https://geo.… mediseh_p… EMOD… \"This d… WFSF… sf #> # ℹ 25 more rows #> # ℹ 1 more variable: layer_namespace "},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"layer-attribute-names","dir":"Articles","previous_headings":"Inspecting attributes","what":"Layer attribute names","title":"EQCL feature filtering","text":"start, might want know names layer’s attributes. functions can also used providing service name instead wfs object.","code":"layer_attributes_get_names(wfs, layer = \"mediseh_zostera_m_pnt\") #> [1] \"id\" \"country\" \"the_geom\" layer_attributes_get_names(service = \"biology\", layer = \"mediseh_zostera_m_pnt\") #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> [1] \"id\" \"country\" \"the_geom\""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"layer-attribute-descriptions","dir":"Articles","previous_headings":"Inspecting attributes","what":"Layer attribute descriptions","title":"EQCL feature filtering","text":"type filtering might want apply depend data type attribute. can inspect attribute descriptions (metadata) given layer layer_attribute_descriptions().","code":"layer_attribute_descriptions(wfs, layer = \"mediseh_zostera_m_pnt\") #> name type minOccurs maxOccurs nillable geometry #> 1 id integer 0 1 TRUE FALSE #> 2 country character 0 1 TRUE FALSE #> 3 the_geom Point 0 1 TRUE TRUE"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"layer-attribute-summaries","dir":"Articles","previous_headings":"Inspecting attributes","what":"Layer attribute summaries","title":"EQCL feature filtering","text":"can get summaries values attribute layer_attributes_summarise(). function basically runs summary() attribute columns layer.","code":"layer_attributes_summarise(wfs, layer = \"mediseh_zostera_m_pnt\") #> gml_id id country #> Length:54 Min. :0 Length:54 #> Class :character 1st Qu.:0 Class :character #> Mode :character Median :0 Mode :character #> Mean :0 #> 3rd Qu.:0 #> Max. :0"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"inspecting-individual-layer-attributes","dir":"Articles","previous_headings":"Inspecting attributes","what":"Inspecting individual layer attributes","title":"EQCL feature filtering","text":"can also inspect individual attributes , case categorical variables, can give detailed information names distribution categories.","code":"layer_attribute_inspect( wfs, layer = \"mediseh_zostera_m_pnt\", attribute = \"country\" ) #> # A tibble: 7 × 3 #> . n percent #> #> 1 Croazia 4 0.0741 #> 2 Francia 1 0.0185 #> 3 Italia 30 0.556 #> 4 Libia 2 0.0370 #> 5 Slovenia 8 0.148 #> 6 Spagna 8 0.148 #> 7 Tunisia 1 0.0185"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"layer-attributes-table","dir":"Articles","previous_headings":"","what":"Layer attributes table","title":"EQCL feature filtering","text":"Finally, enable full inspection custom processing attribute data, can download full set attributes data.frame, excluding geometry column. geometries usually largest column, much faster downloading full layer can useful developing attribute filtering rules.","code":"attr_tbl <- layer_attributes_tbl(wfs, layer = \"mediseh_zostera_m_pnt\") attr_tbl #> # A tibble: 54 × 3 #> gml_id id country #> #> 1 mediseh_zostera_m_pnt.1 0 Spagna #> 2 mediseh_zostera_m_pnt.2 0 Spagna #> 3 mediseh_zostera_m_pnt.3 0 Spagna #> 4 mediseh_zostera_m_pnt.4 0 Spagna #> 5 mediseh_zostera_m_pnt.5 0 Spagna #> 6 mediseh_zostera_m_pnt.6 0 Spagna #> 7 mediseh_zostera_m_pnt.7 0 Spagna #> 8 mediseh_zostera_m_pnt.8 0 Francia #> 9 mediseh_zostera_m_pnt.9 0 Italia #> 10 mediseh_zostera_m_pnt.10 0 Italia #> # ℹ 44 more rows"},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"filtering-categorical-attributes-values-using-text-comparisons","dir":"Articles","previous_headings":"Filtering by attributes","what":"Filtering categorical attributes values using text comparisons","title":"EQCL feature filtering","text":"know values categorical attribute layer, can use filter features returned query. example, let’s say interested results France. previous interrogation attributes associated mediseh_zostera_m_pnt layer, seen attribute country contains country. can use name attribute value require construct eqcl filter pass request using cql_filter argument. shows basic text comparisons can make use equality operator =. want match one value, can use operator instead provide list values compare . example, request France Spain, use following filter: using filter: text comparisons include text pattern matching using operator LIKE. example, request maritime boundaries countries starting S, can use following filter: CQL/ECQL filters can also include filter functions available GeoServer, including multiple string functions greatly increases power CQL expressions. example, can request countries contain l anywhere, including first letter. make request case independent, can turn country names lowercase use like comparison lowercase l:","code":"emodnet_get_layers( wfs, layers = \"mediseh_zostera_m_pnt\", cql_filter = \"country = 'Francia'\" ) #> $mediseh_zostera_m_pnt #> Simple feature collection with 1 feature and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: 4.84864 ymin: 43.37637 xmax: 4.84864 ymax: 43.37637 #> Geodetic CRS: WGS 84 #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) emodnet_get_layers( wfs, layers = \"mediseh_zostera_m_pnt\", cql_filter = \"country IN ('Francia', 'Spagna')\" ) #> $mediseh_zostera_m_pnt #> Simple feature collection with 9 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 36.71226 xmax: 4.84864 ymax: 43.37637 #> Geodetic CRS: WGS 84 #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> 9 mediseh_zostera_m_pnt.54 0 Spagna POINT (3.291868 42.29132) emodnet_get_layers( wfs, layers = \"mediseh_zostera_m_pnt\", cql_filter = \"country='Francia' OR country='Spagna'\" ) #> $mediseh_zostera_m_pnt #> Simple feature collection with 9 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 36.71226 xmax: 4.84864 ymax: 43.37637 #> Geodetic CRS: WGS 84 #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> 9 mediseh_zostera_m_pnt.54 0 Spagna POINT (3.291868 42.29132) emodnet_get_layers( wfs = wfs, layers = \"mediseh_zostera_m_pnt\", cql_filter = \"country LIKE 'S%'\", simplify = TRUE ) #> Simple feature collection with 16 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 36.71226 xmax: 13.73725 ymax: 45.58252 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.39 0 Slovenia POINT (13.73725 45.56948) #> 9 mediseh_zostera_m_pnt.40 0 Slovenia POINT (13.70701 45.58252) #> 10 mediseh_zostera_m_pnt.41 0 Slovenia POINT (13.71894 45.54535) emodnet_get_layers( wfs = wfs, layers = \"mediseh_zostera_m_pnt\", cql_filter = \"strToLowerCase(country) LIKE '%l%'\", simplify = TRUE ) #> Simple feature collection with 40 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: 11.71682 ymin: 33.07783 xmax: 14.4714 ymax: 45.72451 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.9 0 Italia POINT (13.71831 45.70017) #> 2 mediseh_zostera_m_pnt.10 0 Italia POINT (13.16378 45.72451) #> 3 mediseh_zostera_m_pnt.11 0 Italia POINT (13.35982 45.70508) #> 4 mediseh_zostera_m_pnt.12 0 Italia POINT (12.26722 45.25975) #> 5 mediseh_zostera_m_pnt.13 0 Italia POINT (12.31285 45.362) #> 6 mediseh_zostera_m_pnt.14 0 Italia POINT (12.53509 45.53269) #> 7 mediseh_zostera_m_pnt.15 0 Italia POINT (12.48269 45.5065) #> 8 mediseh_zostera_m_pnt.16 0 Italia POINT (12.77334 43.96751) #> 9 mediseh_zostera_m_pnt.17 0 Italia POINT (13.62604 43.50809) #> 10 mediseh_zostera_m_pnt.18 0 Italia POINT (13.46398 43.60892)"},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"filtering-numeric-variables","dir":"Articles","previous_headings":"Filtering by attributes","what":"Filtering numeric variables","title":"EQCL feature filtering","text":"number additional comparison operators, =, <>, >, >=, <, <= , arithmetic operators +, -, *, / well comparison math functions can used filtering numeric variables. time ’ll use mediseh_posidonia_nodata. can inspect , using interrogative functions get information layer attributes. can see values range 0.23 ~473 mean ~40. Let’s say interested values greater 400. can use operator > create filter: request range can use filter functions .","code":"layer_attributes_get_names( wfs, layer = \"mediseh_posidonia_nodata\" ) #> [1] \"id\" \"km\" \"the_geom\" layer_attribute_inspect( wfs, layer = \"mediseh_posidonia_nodata\", attribute = \"km\" ) #> Min. 1st Qu. Median Mean 3rd Qu. Max. #> 0.2371 6.0306 16.6190 40.1771 42.8958 472.9613 emodnet_get_layers( wfs = wfs, layers = \"mediseh_posidonia_nodata\", cql_filter = \"km > 400\", simplify = TRUE ) #> Simple feature collection with 4 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -1.572609 ymin: 35.24538 xmax: 28.33243 ymax: 38.68017 #> Geodetic CRS: WGS 84 #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.8 0 456.3759 MULTICURVE (LINESTRING (2.3... #> 2 mediseh_posidonia_nodata.227 0 464.6573 MULTICURVE (LINESTRING (26.... #> 3 mediseh_posidonia_nodata.228 0 472.9613 MULTICURVE (LINESTRING (26.... #> 4 mediseh_posidonia_nodata.229 0 463.8207 MULTICURVE (LINESTRING (27.... emodnet_get_layers( wfs = wfs, layers = \"mediseh_posidonia_nodata\", cql_filter = \"km between 40 and 400\", simplify = TRUE ) #> Simple feature collection with 120 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -2.1798 ymin: 30.26623 xmax: 34.59127 ymax: 45.35511 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.50323 MULTICURVE (LINESTRING (27.... #> 2 mediseh_posidonia_nodata.2 0 75.37950 MULTICURVE (LINESTRING (23.... #> 3 mediseh_posidonia_nodata.4 0 110.34480 MULTICURVE (LINESTRING (19.... #> 4 mediseh_posidonia_nodata.13 0 66.99746 MULTICURVE (LINESTRING (9.1... #> 5 mediseh_posidonia_nodata.5 0 222.44651 MULTICURVE (LINESTRING (8.6... #> 6 mediseh_posidonia_nodata.6 0 58.72822 MULTICURVE (LINESTRING (6.8... #> 7 mediseh_posidonia_nodata.7 0 192.50519 MULTICURVE (LINESTRING (6.4... #> 8 mediseh_posidonia_nodata.10 0 65.74354 MULTICURVE (LINESTRING (-1.... #> 9 mediseh_posidonia_nodata.11 0 138.68819 MULTICURVE (LINESTRING (4.8... #> 10 mediseh_posidonia_nodata.17 0 184.05959 MULTICURVE (LINESTRING (10...."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"using-or-and-and-statements","dir":"Articles","previous_headings":"Filtering by attributes","what":"Using OR and AND statements","title":"EQCL feature filtering","text":"Filter conditions can also logical combination conditions using , . showed previously use list potential values match attribute . also achieved using statement. example, following query returns features country either Baltic Sea Bulgaria. Let’s say also want restrict features returned shape_length > 1. can include additional condition must met using statement. query returns features country Baltic Sea Bulgaria can see minimum value minimum set filter. ’s filter added country='Bulgaria', features shape_length > 1 returned country also Bulgaria, filter applied shape_length country Baltic Sea. add filter filters, can use parenthesis: Now minimum value indeed 1. However, get features country 'Bulgaria'. ’s single Baltic Sea feature shape_length value smaller 1 filtered . Finally filtering shape_length < 1 returns features shape_length values smaller 1 country values.","code":"wfs <- emodnet_init_wfs_client(service = \"geology_seabed_substrate_maps\") emodnet_get_layers( wfs = wfs, layers = \"seabed_substrate_1m\", cql_filter = \"country='Baltic Sea' OR country='Bulgaria'\", simplify = TRUE ) filter_sf1 <- emodnet_get_layers( wfs = wfs, layers = \"seabed_substrate_1m\", cql_filter = \"country='Baltic Sea' OR country='Bulgaria' AND shape_length>1\", simplify = TRUE ) filter_sf1 unique(filter_sf1$country) min(filter_sf1$shape_length) filter_sf2 <- emodnet_get_layers( wfs = wfs, layers = \"seabed_substrate_1m\", cql_filter = \"(country='Baltic Sea' OR country='Bulgaria') AND shape_length>1\", simplify = TRUE ) min(filter_sf2$shape_length) unique(filter_sf2$country) filter_sf3 <- emodnet_get_layers( wfs = wfs, layers = \"seabed_substrate_1m\", cql_filter = \"(country='Baltic Sea' OR country='Bulgaria') AND shape_length<1\", simplify = TRUE ) max(filter_sf3$shape_length) unique(filter_sf3$country)"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"advanced-use","dir":"Articles","previous_headings":"Filtering by attributes","what":"Advanced use","title":"EQCL feature filtering","text":"can accomplished using EMODnet WFS services downloading data. emodnet.wfs package built top ows4R library, meaning functionalities package available emodnet.wfs. ows4R returns special type R object called R6. can learn Hadley Wickham’s chapter R6 Objects Advance R book. instance: efficient read large dataset R just later subset part . requires longer waiting times bandwidth usage, large datasets simply possible. instance, occurrences data available EMODnet Biology portal stored one table: approximately 30 millions rows! case, suggest access EMODnet Biology occurrence data EMODnet geoviewer eurobis R package. package retrieves occurrences batches, allowing large datasets, uses viewParams, geoserver-specific filtering feature faster requests compared standard OGC CQL filters. addition, one specific filters allow query species traits functional groups.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/emodnet.wfs.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Accessing and mapping EMODnet data","text":"package designed make EMODnet vector data layers easily accessible R. package allows users query information download data available EMODnet Web Feature Service (WFS) endpoints directly R working environment. Data managed sf objects currently state---art handling vector spatial data R. package also allows user specify coordinate reference system imported data.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/emodnet.wfs.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Accessing and mapping EMODnet data","text":"can install development version emodnet.wfs GitHub :","code":"pak::pak(\"EMODnet/emodnet.wfs\")"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/emodnet.wfs.html","id":"explore-the-emodnet-wfs-services-with-r","dir":"Articles","previous_headings":"","what":"Explore the EMODnet WFS services with R","title":"Accessing and mapping EMODnet data","text":"tutorial make use sf mapview packages. simple features sf package well known standard dealing geospatial vector data. visualize geometries, mapview create quick interactive maps. Run line install packages: EMODnet organized seven thematic lots: Bathymetry, Geology, Seabed Habitats, Chemistry, Biology, Physics, Human Activities, focusing specific aspect marine data. emodnet.wfs package, can explore combine data served EMODnet thematic lots OGC Web Feature Services WFS. Imagine interested seabed substrates. first step choose EMODnet thematic lot can provide data. , can check services available emodnet_wfs() function. column service_name shows services available, service_url corresponding base url perform WFS request. Seabed portal data looking . WFS client can created passing corresponding service_name function emodnet_init_wfs_client(). layers available WFS client consulted emodnet_get_wfs_info(). layer explained abstract column. can see several layers information provided EU member states Habitats Directive 92/43/EEC reporting. select layers coastal lagoons, mudflats sandbanks respective layer_name. now ready read layers R emodnet_get_layers(). emodnet.wfs reads geometries simple features (See sf package) transformed 4326 default. Specifying another map projection possible passing EPGS code projection string emodnet_get_layers(crs = \"projection\") crs coordinate reference system (CRS). argument simplify = TRUE stack layers one single tibble. Default FALSE returns list sf objects, one per layer. Note use outputFormat argument example. specifies file type request service, can influence data loaded R. default, data provided GML format geometry type “MULTISURFACE.” However, geometry type widely supported many software tools, including mapview package. address , can request different file type, GeoJSON, delivers geometry “MULTIPOLYGON”—format universally compatible. raised sf community. Run following code quick look layers geometries. plot chunk unnamed-chunk-6 EMODnet provides also physics, chemistry, biological bathymetry data. Explore layers available :","code":"install.packages(c(\"sf\", \"mapview\")) library(emodnet.wfs) library(mapview) library(sf) #> Error in value[[3L]](cond): Package 'sf' version 1.0.18 cannot be unloaded: #> Error in unloadNamespace(package) : namespace 'sf' is imported by 'ows4R', 'mapview', 'leafem', 'leafpop' so cannot be unloaded services <- emodnet_wfs() 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\" seabed_wfs_client <- emodnet_init_wfs_client(service = \"seabed_habitats_general_datasets_and_products\") #> ✔ 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 #> #> 1 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 2 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 3 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 4 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 5 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 6 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 7 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 8 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 9 emodnet_wfs seabed_habitats_gene… https://ow… carib_eus… 2023… \"Output… WFSF… sf #> 10 emodnet_wfs seabed_habitats_gene… https://ow… biogenic_… Biog… \"This l… WFSF… sf #> # ℹ 62 more rows #> # ℹ 1 more variable: layer_namespace 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 abstract class format #> #> 1 emodnet_wfs https://ows.emodnet-s… seabed_hab… art17_hab… 2013… \"Gridde… WFSF… sf #> 2 emodnet_wfs https://ows.emodnet-s… seabed_hab… art17_hab… 2013… \"Gridde… WFSF… sf #> 3 emodnet_wfs https://ows.emodnet-s… seabed_hab… art17_hab… 2013… \"Gridde… WFSF… sf #> # ℹ 1 more variable: layer_namespace habitats_directive_layers <- emodnet_get_layers( wfs = seabed_wfs_client, layers = habitats_directive_layer_names, 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 #> Geometry type: MULTIPOLYGON #> Dimension: XY #> Bounding box: xmin: 950000 ymin: 940000 xmax: 6510000 ymax: 4820000 #> Projected CRS: ETRS89-extended / LAEA Europe #> First 10 features: #> id habitat_code ms region cs_ms country_code #> 1 art17_hab_1110.13 1110 DK ATL U2+ Denmark #> 2 art17_hab_1110.22 1110 ES MAC U1+ Spain #> 3 art17_hab_1110.25 1110 ES MMAC U1+ Spain #> 4 art17_hab_1110.59 1110 PT MMAC XX Portugal #> 5 art17_hab_1110.56 1110 PT MATL U1- Portugal #> 6 art17_hab_1110.53 1110 PL MBAL U1- Poland #> 7 art17_hab_1110.17 1110 DK MBAL U1- Denmark #> 8 art17_hab_1110.31 1110 FR MATL U1x France #> 9 art17_hab_1110.75 1110 UK MATL U1x United Kingdom #> 10 art17_hab_1110.1 1110 BE ATL U1x Belgium #> habitat_code_uri #> 1 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 2 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 3 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 4 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 5 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 6 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 7 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 8 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 9 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 10 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> habitat_description #> 1 Sandbanks which are slightly covered by sea water all the time #> 2 Sandbanks which are slightly covered by sea water all the time #> 3 Sandbanks which are slightly covered by sea water all the time #> 4 Sandbanks which are slightly covered by sea water all the time #> 5 Sandbanks which are slightly covered by sea water all the time #> 6 Sandbanks which are slightly covered by sea water all the time #> 7 Sandbanks which are slightly covered by sea water all the time #> 8 Sandbanks which are slightly covered by sea water all the time #> 9 Sandbanks which are slightly covered by sea water all the time #> 10 Sandbanks which are slightly covered by sea water all the time #> geometry #> 1 MULTIPOLYGON (((4200000 360... #> 2 MULTIPOLYGON (((1950000 950... #> 3 MULTIPOLYGON (((1960000 950... #> 4 MULTIPOLYGON (((1810000 120... #> 5 MULTIPOLYGON (((2730000 173... #> 6 MULTIPOLYGON (((4610000 346... #> 7 MULTIPOLYGON (((4310000 352... #> 8 MULTIPOLYGON (((3790000 314... #> 9 MULTIPOLYGON (((3780000 319... #> 10 MULTIPOLYGON (((3800000 313... mapview(habitats_directive_layers, zcol = \"habitat_description\", burst = TRUE) 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.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 "},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/articles/emodnet.wfs.html","id":"references","dir":"Articles","previous_headings":"More information","what":"References","title":"Accessing and mapping EMODnet data","text":"Blondel, Emmanuel. (2020, May 27). ows4R: R Interface OGC Web-Services (Version 0.1-5). Zenodo. https://doi.org/10.5281/zenodo.3860330 Flanders Marine Institute (2019). Maritime Boundaries Geodatabase, version 11. Available online https://www.marineregions.org/. https://doi.org/10.14284/382. Hadley Wickham, Romain François, Lionel Henry Kirill Müller (2020). dplyr: Grammar Data Manipulation. R package version 1.0.2.https://CRAN.R-project.org/package=dplyr Pebesma E (2018). “Simple Features R: Standardized Support Spatial Vector Data.” 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: language environment statistical computing. R Foundation Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. Tim Appelhans, Florian Detsch, Christoph Reudenbach Stefan Woellauer (2020). mapview: Interactive Viewing Spatial Data R. R package version 2.9.0. https://CRAN.R-project.org/package=mapview","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/emodnet.wfs.html","id":"code","dir":"Articles","previous_headings":"More information","what":"Code","title":"Accessing and mapping EMODnet data","text":"cite emodnet.wfs, please use output citation(package = \"emodnet.wfs\").","code":"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, . #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> 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 2.0.2.9000. 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}, #> url = {https://github.com/EMODnet/emodnet.wfs}, #> doi = {10.14284/679}, #> }"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"initialise-a-wfs-client","dir":"Articles","previous_headings":"","what":"Initialise a WFS client","title":"Using request parameters to limit query results","text":"Let’s start loading emodnet.wfs initialising WFS client human_activities WFS service.","code":"library(emodnet.wfs) wfs <- emodnet_init_wfs_client(\"human_activities\") #> Loading ISO 19139 XML schemas... #> Loading ISO 19115 codelists... #> ✔ WFS client created successfully #> ℹ Service: \"https://ows.emodnet-humanactivities.eu/wfs\" #> ℹ Version: \"2.0.0\""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"return-single-feature-using-feature-id","dir":"Articles","previous_headings":"","what":"Return single feature using feature ID","title":"Using request parameters to limit query results","text":"can restrict query single feature using featureID providing ID specific feature.","code":"emodnet_get_layers( wfs = wfs, layers = \"pipelines\", featureID = \"pipelines.1\", simplify = TRUE ) #> Simple feature collection with 1 feature and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: -5.87186 ymin: 35.99551 xmax: -5.836784 ymax: 36.12588 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year from_loc to_loc #> 1 pipelines.1 Active 15467.17 #> country_co country notes the_geom #> 1 ES Spain MULTILINESTRING ((-5.87186 ..."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"return-specific-number-of-features","dir":"Articles","previous_headings":"","what":"Return specific number of features","title":"Using request parameters to limit query results","text":"ID feature unknown still want limit number features returned, use count parameter WFS 2.0.0 maxFeatures parameter earlier WFS versions restrict number features returned. example restrict query first feature.","code":"emodnet_get_layers( wfs = wfs, layers = \"pipelines\", count = 1L, simplify = TRUE ) #> Simple feature collection with 1 feature and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: 24.98448 ymin: 60.19078 xmax: 25.01292 ymax: 60.19293 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year from_loc #> 1 pipelines.3463 n/a 1628.03 #> to_loc country_co country notes #> 1 FI Finland Finnish Transport Agency #> the_geom #> 1 MULTILINESTRING ((25.01292 ..."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"order-features","dir":"Articles","previous_headings":"","what":"Order features","title":"Using request parameters to limit query results","text":"Exactly features returned depends internal structure data. However, can sort returned selection based attribute value using sortBy parameter. Say wanted return 5 longest marine pipelines. following example, sort \"length_m\" attribute combine count parameter restrict number features returned. returns first 5 features data ordered \"length_m\". pipelines lengths recorded, skip CQL Filter. default sort operation sort ascending order. WFS servers require sort order specified. case, append +attribute character string passed sortBy. Conversely, add +D sort descending order.","code":"emodnet_get_layers( wfs = wfs, layers = \"pipelines\", sortBy = \"length_m+D\", count = 5L, simplify = TRUE, cql_filter = \"length_m IS NOT NULL\" ) #> Simple feature collection with 5 features and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: 2.249597 ymin: 51.04064 xmax: 28.14228 ymax: 60.52758 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m #> 1 pipelines.3423 Active Gas Nord Stream AG 48 2443360.2 #> 2 pipelines.3424 Planned Gas Nord Stream 2 AG 48 1210867.9 #> 3 pipelines.52 PL0187_PR Active Gas Statoil ASA 42 836155.4 #> 4 pipelines.517 326374 Active Gas GASSCO AS 42 832197.9 #> 5 pipelines.53 PL0186_PR Active Gas Statoil ASA 40 807749.5 #> year from_loc to_loc country_co country notes #> 1 2011 Vyborg, RU Lubmin, GE DE, RU Germany, Russia Schematic Route #> 2 2021 Kurgalsky, RU Lubmin, GE DE, RU Germany, Russia Schematic Route #> 3 Draupner (N) Duinkerken (F) NL Netherlands #> 4 DRAUPNER E DUNKERQUE NO Norway #> 5 Sleipner (N) Zeebrugge (B) NL Netherlands #> the_geom #> 1 MULTILINESTRING ((18.00045 ... #> 2 MULTILINESTRING ((28.14228 ... #> 3 MULTILINESTRING ((2.249597 ... #> 4 MULTILINESTRING ((2.458616 ... #> 5 MULTILINESTRING ((3.298373 ..."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"return-blocks-of-features-from-specific-starting-point","dir":"Articles","previous_headings":"","what":"Return blocks of features from specific starting point","title":"Using request parameters to limit query results","text":"Finally WFS version 2.0.0 (also available earlier versions GeoServer) startIndex parameter introduced, allowing users specify starting index features returned. example, full \"pipelines\" layer contains 3951 features. Setting startIndex n_features - 4 (3947) returns last 4 features. can also combine startIndex count return specific blocks features. example, following query request features 5-9 supplying startIndex 4 count 5. Note startIndex uses 0 starting index (0 indicates first feature), hence set 4 order start 5th feature. combination , example, loop, can used download process large layer might able handled R smaller, manageable blocks features.","code":"#> [1] 3951 n_features <- layer_attributes_tbl(wfs = wfs, layer = \"pipelines\") %>% nrow() n_features startIndex <- n_features - 4L startIndex #> [1] 3947 emodnet_get_layers( wfs = wfs, layers = \"pipelines\", startIndex = startIndex, simplify = TRUE ) #> Simple feature collection with 4 features and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: 3.990801 ymin: 53.53329 xmax: 14.4857 ymax: 55.81712 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year #> 1 pipelines.3948 154802 Not in use Gas NA #> 2 pipelines.3949 154812 Not in use Gas NA #> 3 pipelines.3950 154982 Active Gas NA #> 4 pipelines.3951 155942 Active Gas NA #> from_loc to_loc country_co country notes the_geom #> 1 DE Germany MULTILINESTRING ((14.48506 ... #> 2 DE Germany MULTILINESTRING ((14.4857 5... #> 3 DE Germany MULTILINESTRING ((4.058202 ... #> 4 DE Germany MULTILINESTRING ((4.019116 ... emodnet_get_layers( wfs = wfs, layers = \"pipelines\", startIndex = 4L, count = 6L, simplify = TRUE ) #> Simple feature collection with 6 features and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: -8.336029 ymin: 51.19448 xmax: -7.947595 ymax: 51.8236 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year from_loc #> 1 pipelines.5 F43__3 n/a 10038.745 Kinsale #> 2 pipelines.6 F43__4 n/a 20011.185 Ballycotton #> 3 pipelines.7 F43__5 n/a 10853.853 Kinsale #> 4 pipelines.8 F43__6 n/a 5397.224 Kinsale #> 5 pipelines.9 F43__7 n/a 73853.753 Kinsale #> 6 pipelines.10 F43__8 n/a 56242.374 Seven Heads #> to_loc country_co country notes the_geom #> 1 IE Ireland MULTILINESTRING ((-8.186204... #> 2 IE Ireland MULTILINESTRING ((-8.017066... #> 3 IE Ireland MULTILINESTRING ((-8.017356... #> 4 IE Ireland MULTILINESTRING ((-8.179044... #> 5 IE Ireland MULTILINESTRING ((-7.947595... #> 6 IE Ireland MULTILINESTRING ((-8.217298..."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"return-data-for-specific-attributes","dir":"Articles","previous_headings":"","what":"Return data for specific attributes","title":"Using request parameters to limit query results","text":"Finally, can specify specific attributes want data returned using parameter propertyName. limit data returned single attribute \"country\" just 3 features, use parameters propertyName = \"country\" count = 3. Note limiting data specific attributes, columns returned NA (including spatial, case the_geom, column). limit multiple attributes, separate attribute name character string supplied propertyName comma.","code":"emodnet_get_layers( wfs = wfs, layers = \"pipelines\", propertyName = \"country\", count = 3L, simplify = TRUE ) #> Simple feature collection with 3 features and 13 fields (with 3 geometries empty) #> Geometry type: GEOMETRYCOLLECTION #> Dimension: XY #> Bounding box: xmin: NA ymin: NA xmax: NA ymax: NA #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year from_loc #> 1 pipelines.3463 NA #> 2 pipelines.3702 NA #> 3 pipelines.3707 NA #> to_loc country_co country notes the_geom #> 1 Finland GEOMETRYCOLLECTION EMPTY #> 2 Finland GEOMETRYCOLLECTION EMPTY #> 3 Finland GEOMETRYCOLLECTION EMPTY emodnet_get_layers( wfs = wfs, layers = \"pipelines\", propertyName = \"country,the_geom\", count = 3L, simplify = TRUE ) #> Simple feature collection with 3 features and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: 24.90736 ymin: 60.1819 xmax: 27.11348 ymax: 60.5359 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year from_loc #> 1 pipelines.3463 NA #> 2 pipelines.3702 NA #> 3 pipelines.3707 NA #> to_loc country_co country notes the_geom #> 1 Finland MULTILINESTRING ((25.01292 ... #> 2 Finland MULTILINESTRING ((27.11348 ... #> 3 Finland MULTILINESTRING ((24.90967 ..."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"limit-spatial-extent-using-a-boundary-box","dir":"Articles","previous_headings":"","what":"Limit spatial extent using a boundary box","title":"Using request parameters to limit query results","text":"bbox parameter allows us search features contained (partially contained) inside box user-defined coordinates. format bbox parameter EMODnet WFS cases (assuming using version 2.0.0) bbox=a1,b1,a2,b2,[crs] a1, b1, a2, b2 represent coordinate values. optional crs parameter used name coordinate reference system (CRS) bbox coordinates (different featureTypes native CRS.) order coordinates passed bbox parameter depends coordinate system used (coordinate syntax isn’t represented x y). following example, specify bounding box proving coordinates order xmin,ymin,xmax,ymax specifying coordinates given EPSG:4326 coordinate reference system.","code":"bbox_response <- emodnet_get_layers( service = \"biology\", layers = \"mediseh_posidonia_nodata\", bbox = \"22.9,34.4,26.8,35.8,EPSG:4326\", simplify = TRUE ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" bbox_response %>% sf::st_cast(to = \"MULTILINESTRING\") %>% mapview::mapview(burst = TRUE, legend = FALSE)"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"non-standard-vendor-parameters","dir":"Articles","previous_headings":"","what":"Non-standard Vendor Parameters","title":"Using request parameters to limit query results","text":"WFS vendor parameters additional, non-standard request parameters defined implementation provide enhanced capabilities. majority EMODnet services GeoServer WFS implementations support variety vendor-specific WFS parameters. One cql_filters. handled explicitly emodnet.wfs package cql_filter argument emodnet_get_layers() documented detail article(\"ecql_filtering\"). additional vendor parameters available GeoServer implementations please refer WFS vendor parameters documentatio Exceptions Chemistry (Eutrophication sea region, Eutrophication) services uses Python Chemistry (Litter) uses MapServer vendor parameters services might differ.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anna Krystalli. Author. Salvador Fernández-Bejarano. Author, maintainer. Thomas J Webb. Contributor. European Marine Observation Data Network (EMODnet) Biology project European Commission's Directorate - General Maritime Affairs Fisheries (DG MARE). Copyright holder. VLIZ (VLAAMS INSTITUUT VOOR DE ZEE). Funder. Maëlle Salmon. Author. Alec L. Robitaille. Reviewer. Reviewed package (v2.0.2.9000) rOpenSci, see . Liz Hare. Reviewer. Reviewed package (v2.0.2.9000) rOpenSci, see . François Michonneau. Reviewer. Reviewed package (v2.0.2.9000) rOpenSci, see .","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Krystalli , Fernández-Bejarano S, Salmon M (????). emodnet.wfs: Access EMODnet Web Feature Service data R. doi:10.14284/679, R package version 2.0.2.9000. Integrated data products created European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded European Union Regulation (EU) 508/2014 European Parliament Council 15 May 2014 European Maritime Fisheries Fund, https://github.com/EMODnet/emodnet.wfs.","code":"@Manual{, 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 2.0.2.9000. 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}, url = {https://github.com/EMODnet/emodnet.wfs}, doi = {10.14284/679}, }"},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"emodnetwfs-access-emodnet-web-feature-service-data-through-r","dir":"","previous_headings":"","what":"Access EMODnet Web Feature Service data through R","title":"Access EMODnet Web Feature Service data through R","text":"goal emodnet.wfs allow interrogation access EMODnet’s, European Marine Observation Data Network, geographic vector data R EMODnet Web Feature Services. Web Feature services (WFS) represent change way geographic information created, modified exchanged Internet offer direct fine-grained access geographic information feature feature property level. Features representation geographic entities, coastlines, marine protected areas, offshore platforms, fishing areas. WFS, features geometry (spatial information) attributes (descriptive data). emodnet.wfs aims offering user-friendly interface rich data.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"installation-and-setup","dir":"","previous_headings":"","what":"Installation and setup","title":"Access EMODnet Web Feature Service data through R","text":"can install development version emodnet.wfs GitHub : want avoid reading messages emodnet.wfs “WFS client created successfully”, set \"emodnet.wfs.quiet\" option TRUE.","code":"# install.packages(\"pak\") pak::pak(\"EMODnet/emodnet.wfs\") options(\"emodnet.wfs.quiet\" = TRUE)"},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"pre-requisites","dir":"","previous_headings":"","what":"Pre-requisites","title":"Access EMODnet Web Feature Service data through R","text":"emodnet.wfs designed compatible modern R geospatial stack, particular output geospatial objects sf objects, say, tibble geometry list-column. users familiar yet geospatial data R, recommend following resources: Spatial Data Science Applications R Edzer Pebesma Roger Bivand. Geocomputation R Robin Lovelace, Jakub Nowosad Jannes Muenchow. documentation assume basic familiarity spatial data: knowing coordinates projections / coordinate reference systems (CRS).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"available-data-sources-services","dir":"","previous_headings":"","what":"Available data sources (services)","title":"Access EMODnet Web Feature Service data through R","text":"available data sources, called services, contained tibble returned emodnet_wfs(). explore available services can use View() usual way explore data.frames.","code":"library(emodnet.wfs) services <- emodnet_wfs() class(services) #> [1] \"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\""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"initialise-a-wfs-service-client","dir":"","previous_headings":"","what":"Initialise a WFS Service Client","title":"Access EMODnet Web Feature Service data through R","text":"WFS service client responsible sending requests WFS server processing responses retrieve, display, analyze geospatial features. , initialising client first step interacting EMODnet Web Feature Services. Specify service using service argument.","code":"wfs_bio <- emodnet_init_wfs_client(service = \"biology\") #> Loading ISO 19139 XML schemas... #> Loading ISO 19115 codelists... #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" wfs_bio #> #> ....|-- url: https://geo.vliz.be/geoserver/Emodnetbio/wfs #> ....|-- version: 2.0.0 #> ....|-- capabilities "},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"list-contents-of-a-wfs-get-layer-information-from-a-service-client","dir":"","previous_headings":"","what":"List contents of a WFS: Get layer information from a service client","title":"Access EMODnet Web Feature Service data through R","text":"context Web Feature Service (WFS), layer refers logical grouping geographic features share schema (.e., feature type, geometry, attributes). Layers units data clients can query, retrieve, manipulate WFS. can access information (metadata) layer available EMODnet WFS emodnet_get_wfs_info() can pass wfs client object. can also get info specific layers wfs object: Finally, can get details available services layers server","code":"emodnet_get_wfs_info(service = \"biology\") #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> # A tibble: 35 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 2 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 3 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Cymodo… WFSF… sf #> 4 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 5 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 6 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 7 emodnet_wfs biology https://geo.… mediseh_h… EMOD… \"Haloph… WFSF… sf #> 8 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 10 emodnet_wfs biology https://geo.… mediseh_p… EMOD… \"This d… WFSF… sf #> # ℹ 25 more rows #> # ℹ 1 more variable: layer_namespace emodnet_get_wfs_info(wfs_bio) #> # A tibble: 35 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 2 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 3 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Cymodo… WFSF… sf #> 4 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 5 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 6 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 7 emodnet_wfs biology https://geo.… mediseh_h… EMOD… \"Haloph… WFSF… sf #> 8 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 10 emodnet_wfs biology https://geo.… mediseh_p… EMOD… \"This d… WFSF… sf #> # ℹ 25 more rows #> # ℹ 1 more variable: layer_namespace layers <- c(\"mediseh_zostera_m_pnt\", \"mediseh_posidonia_nodata\") emodnet_get_layer_info(wfs = wfs_bio, layers = layers) #> # A tibble: 2 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs https://geo.vl… biology mediseh_p… EMOD… \"Coastl… WFSF… sf #> 2 emodnet_wfs https://geo.vl… biology mediseh_z… EMOD… \"Zoster… WFSF… sf #> # ℹ 1 more variable: layer_namespace emodnet_get_all_wfs_info()"},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"get-data-from-a-data-source-get-layers","dir":"","previous_headings":"","what":"Get data from a data source: get layers","title":"Access EMODnet Web Feature Service data through R","text":"can extract layers directly wfs object using layer names. layers downloaded sf objects output list named element layer requested. argument simplify = TRUE stack layers one single tibble, possible (instance column names , otherwise fails). default, emodnet_get_layers() returns list sf objects, one per layer. can change output Coordinate Reference System (CRS), defines geographic data mapped Earth’s surface, argument crs. can also extract layers using WFS service name. Layers can also returned single sf object argument simplify. TRUE function try reduce layers single sf. attempting reduce fails, error: Using simplify = TRUE also useful returning sf object rather list single layer request.","code":"emodnet_get_layers(wfs = wfs_bio, layers = layers) #> $mediseh_zostera_m_pnt #> Simple feature collection with 54 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 33.07783 xmax: 15.35766 ymax: 45.72451 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> 9 mediseh_zostera_m_pnt.9 0 Italia POINT (13.71831 45.70017) #> 10 mediseh_zostera_m_pnt.10 0 Italia POINT (13.16378 45.72451) #> #> $mediseh_posidonia_nodata #> Simple feature collection with 465 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -2.1798 ymin: 30.26623 xmax: 34.60767 ymax: 45.47668 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.503233 MULTICURVE (LINESTRING (27.... #> 2 mediseh_posidonia_nodata.2 0 75.379502 MULTICURVE (LINESTRING (23.... #> 3 mediseh_posidonia_nodata.3 0 38.627764 MULTICURVE (LINESTRING (22.... #> 4 mediseh_posidonia_nodata.4 0 110.344802 MULTICURVE (LINESTRING (19.... #> 5 mediseh_posidonia_nodata.13 0 66.997461 MULTICURVE (LINESTRING (9.1... #> 6 mediseh_posidonia_nodata.14 0 18.090640 MULTICURVE (LINESTRING (9.7... #> 7 mediseh_posidonia_nodata.15 0 16.618978 MULTICURVE (LINESTRING (9.8... #> 8 mediseh_posidonia_nodata.16 0 1.913773 MULTICURVE (LINESTRING (10.... #> 9 mediseh_posidonia_nodata.83 0 2.173447 MULTICURVE (LINESTRING (15.... #> 10 mediseh_posidonia_nodata.84 0 2.817453 MULTICURVE (LINESTRING (15.... emodnet_get_layers(wfs = wfs_bio, layers = layers, crs = 3857) #> ℹ crs transformed to 3857. #> ℹ crs transformed to 3857. #> $mediseh_zostera_m_pnt #> Simple feature collection with 54 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -463885.4 ymin: 3905639 xmax: 1709607 ymax: 5736311 #> Projected CRS: WGS 84 / Pseudo-Mercator #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-290893.4 4399707) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-428201.3 4404494) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-440578.6 4400520) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-449698.6 4403229) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-456430.1 4400610) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-463885.4 4399075) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-141193.9 4517168) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (539748.1 5369436) #> 9 mediseh_zostera_m_pnt.9 0 Italia POINT (1527115 5732431) #> 10 mediseh_zostera_m_pnt.10 0 Italia POINT (1465385 5736311) #> #> $mediseh_posidonia_nodata #> Simple feature collection with 465 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -242654.3 ymin: 3537818 xmax: 3852508 ymax: 5696879 #> Projected CRS: WGS 84 / Pseudo-Mercator #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.503233 MULTICURVE (LINESTRING (302... #> 2 mediseh_posidonia_nodata.2 0 75.379502 MULTICURVE (LINESTRING (257... #> 3 mediseh_posidonia_nodata.3 0 38.627764 MULTICURVE (LINESTRING (246... #> 4 mediseh_posidonia_nodata.4 0 110.344802 MULTICURVE (LINESTRING (221... #> 5 mediseh_posidonia_nodata.13 0 66.997461 MULTICURVE (LINESTRING (101... #> 6 mediseh_posidonia_nodata.14 0 18.090640 MULTICURVE (LINESTRING (108... #> 7 mediseh_posidonia_nodata.15 0 16.618978 MULTICURVE (LINESTRING (110... #> 8 mediseh_posidonia_nodata.16 0 1.913773 MULTICURVE (LINESTRING (121... #> 9 mediseh_posidonia_nodata.83 0 2.173447 MULTICURVE (LINESTRING (169... #> 10 mediseh_posidonia_nodata.84 0 2.817453 MULTICURVE (LINESTRING (169... emodnet_get_layers( service = \"biology\", layers = c(\"mediseh_zostera_m_pnt\", \"mediseh_posidonia_nodata\") ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> $mediseh_zostera_m_pnt #> Simple feature collection with 54 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 33.07783 xmax: 15.35766 ymax: 45.72451 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> 9 mediseh_zostera_m_pnt.9 0 Italia POINT (13.71831 45.70017) #> 10 mediseh_zostera_m_pnt.10 0 Italia POINT (13.16378 45.72451) #> #> $mediseh_posidonia_nodata #> Simple feature collection with 465 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -2.1798 ymin: 30.26623 xmax: 34.60767 ymax: 45.47668 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.503233 MULTICURVE (LINESTRING (27.... #> 2 mediseh_posidonia_nodata.2 0 75.379502 MULTICURVE (LINESTRING (23.... #> 3 mediseh_posidonia_nodata.3 0 38.627764 MULTICURVE (LINESTRING (22.... #> 4 mediseh_posidonia_nodata.4 0 110.344802 MULTICURVE (LINESTRING (19.... #> 5 mediseh_posidonia_nodata.13 0 66.997461 MULTICURVE (LINESTRING (9.1... #> 6 mediseh_posidonia_nodata.14 0 18.090640 MULTICURVE (LINESTRING (9.7... #> 7 mediseh_posidonia_nodata.15 0 16.618978 MULTICURVE (LINESTRING (9.8... #> 8 mediseh_posidonia_nodata.16 0 1.913773 MULTICURVE (LINESTRING (10.... #> 9 mediseh_posidonia_nodata.83 0 2.173447 MULTICURVE (LINESTRING (15.... #> 10 mediseh_posidonia_nodata.84 0 2.817453 MULTICURVE (LINESTRING (15.... emodnet_get_layers( wfs = wfs_bio, layers = layers, simplify = TRUE ) #> Error in `value[[3L]]()`: #> ! Cannot reduce layers. #> ℹ Try again with `simplify = FALSE` emodnet_get_layers( service = \"biology\", layers = c(\"mediseh_posidonia_nodata\"), simplify = TRUE ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> Simple feature collection with 465 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -2.1798 ymin: 30.26623 xmax: 34.60767 ymax: 45.47668 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.503233 MULTICURVE (LINESTRING (27.... #> 2 mediseh_posidonia_nodata.2 0 75.379502 MULTICURVE (LINESTRING (23.... #> 3 mediseh_posidonia_nodata.3 0 38.627764 MULTICURVE (LINESTRING (22.... #> 4 mediseh_posidonia_nodata.4 0 110.344802 MULTICURVE (LINESTRING (19.... #> 5 mediseh_posidonia_nodata.13 0 66.997461 MULTICURVE (LINESTRING (9.1... #> 6 mediseh_posidonia_nodata.14 0 18.090640 MULTICURVE (LINESTRING (9.7... #> 7 mediseh_posidonia_nodata.15 0 16.618978 MULTICURVE (LINESTRING (9.8... #> 8 mediseh_posidonia_nodata.16 0 1.913773 MULTICURVE (LINESTRING (10.... #> 9 mediseh_posidonia_nodata.83 0 2.173447 MULTICURVE (LINESTRING (15.... #> 10 mediseh_posidonia_nodata.84 0 2.817453 MULTICURVE (LINESTRING (15...."},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"help-needed","dir":"","previous_headings":"","what":"Help needed?","title":"Access EMODnet Web Feature Service data through R","text":"get unexpected error, Look EMODnet monitor; Open issue repository.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"unlock-the-full-potential-of-the-emodnet-web-services-access-raster-and-gridded-datasets","dir":"","previous_headings":"","what":"Unlock the Full Potential of the EMODnet Web Services: Access Raster and Gridded datasets.","title":"Access EMODnet Web Feature Service data through R","text":"EMODnet hosts wealth marine maritime data distributed three complementary web services: WFS, WCS, ERDDAP. Web services allow users retrieve data programmatically remote servers, eliminating need manual downloads. particularly useful handling large datasets conducting dynamic analyses. services tailored different data types research needs, together, ensure seamless access EMODnet vector, raster, gridded datasets. Vector data, shipwrecks boundaries, accessible emodnet.wfs via Web Feature Services (WFS). Complementary, raster gridded datasets available Web Coverage Services (WCS) ERDDAP respectively.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"access-emodnet-raster-data-through-web-coverage-services-with-emodnetwcs-in-r","dir":"","previous_headings":"Unlock the Full Potential of the EMODnet Web Services: Access Raster and Gridded datasets.","what":"Access EMODnet raster data through Web Coverage Services with EMODnetWCS in R","title":"Access EMODnet Web Feature Service data through R","text":"EMODnet raster datasets, habitat maps bathymetry, available Web Coverage Services (WCS). data continuous, gridded, often used spatial visualization environmental modeling. EMODnetWCS R package provides tools retrieve process raser datasets, similar fashion emodnet.wfs. Extensive documentation available EMODnetWCS website.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"access-emodnet-gridded-and-tabular-datasets-through-the-erddap-server-and-rerddap-in-r","dir":"","previous_headings":"Unlock the Full Potential of the EMODnet Web Services: Access Raster and Gridded datasets.","what":"Access EMODnet gridded and tabular datasets through the ERDDAP Server and rerddap in R","title":"Access EMODnet Web Feature Service data through R","text":"WFS WCS EMODnet services based federated system: EMODnet thematic lot manages servers data, ensuring data exposed via WFS WCS. twin R packages emodnet.wfs EMODnetWCS simplify access entry points collecting single places, packages . contrast, EMODnet ERDDAP Server centrally managed EMODnet Central Portal, offering single access point gridded tabular datasets. ERDDAP simplifies access datasets digital terrain models, vessel density environmental data. particularly suited large-scale, multidimensional data analysis. R, rerddap package allows users query subset ERDDAP data programmatically, enabling efficient analysis integration workflows. example, researchers can retrieve datasets vessel density. functionalities available rerddap. Feel free explore rerddap website find else can EMODnet datasets ERDDAP.","code":"# install.packages(\"rerrdap\") library(rerddap) #> Registered S3 method overwritten by 'hoardr': #> method from #> print.cache_info httr # This is the url where the EMODnet ERDDAP server is located erddap_url <- \"https://erddap.emodnet.eu/erddap/\" # Inspect all available datasets ed_datasets(url = erddap_url) #> # A tibble: 8 × 16 #> griddap Subset tabledap Make.A.Graph wms files Title Summary FGDC ISO.19115 #> #> 1 \"\" \"/erd… /erddap… /erddap/tab… \"\" \"\" * Th… \"This … \"\" \"\" #> 2 \"\" \"\" /erddap… /erddap/tab… \"\" \"/er… EMOD… \"The d… \"\" \"\" #> 3 \"\" \"\" /erddap… /erddap/tab… \"\" \"/er… EMOD… \"The d… \"\" \"\" #> 4 \"\" \"/erd… /erddap… /erddap/tab… \"\" \"/er… EMOD… \"The d… \"/er… \"/erddap… #> 5 \"\" \"\" /erddap… /erddap/tab… \"\" \"/er… Pres… \"The p… \"/er… \"/erddap… #> 6 \"\" \"\" /erddap… /erddap/tab… \"\" \"\" PSMS… \"Perma… \"\" \"\" #> 7 \"\" \"\" /erddap… /erddap/tab… \"\" \"/er… PSMS… \"Perma… \"\" \"\" #> 8 \"\" \"/erd… /erddap… /erddap/tab… \"\" \"/er… TAO/… \"This … \"/er… \"/erddap… #> # ℹ 6 more variables: Info , Background.Info , RSS , #> # Email , Institution , Dataset.ID # Find datasets with the key words \"vessel density\" ed_search(query = \"vessel density\", url = erddap_url) #> # A tibble: 16 × 2 #> title dataset_id #> #> 1 Vessel Density humanactivities_9f… #> 2 Vessel Density humanactivities_e9… #> 3 Vessel traffic density, 2019, All EMODPACE_VD_All #> 4 Vessel traffic density, 2019, Cargo EMODPACE_VD_09_Car… #> 5 Vessel traffic density, 2019, Dredging or underwater ops EMODPACE_VD_03_Dre… #> 6 Vessel traffic density, 2019, Fishing EMODPACE_VD_01_Fis… #> 7 Vessel traffic density, 2019, High Speed craft EMODPACE_VD_06_High #> 8 Vessel traffic density, 2019, Miliary and law enforcement EMODPACE_VD_11_Mil… #> 9 Vessel traffic density, 2019, Other EMODPACE_VD_00_Oth… #> 10 Vessel traffic density, 2019, Passenger EMODPACE_VD_08_Pas… #> 11 Vessel traffic density, 2019, Pleasure craft EMODPACE_VD_05_Ple… #> 12 Vessel traffic density, 2019, Sailing EMODPACE_VD_04_Sai… #> 13 Vessel traffic density, 2019, Service EMODPACE_VD_02_Ser… #> 14 Vessel traffic density, 2019, Tanker EMODPACE_VD_10_Tan… #> 15 Vessel traffic density, 2019, Tug and Towing EMODPACE_VD_07_Tug #> 16 Vessel traffic density, 2019, Unknown EMODPACE_VD_12_Unk… # Inspect more info about the vessel density dataset, using its identifier human_activities_data_info <- info(datasetid = \"humanactivities_9f8a_3389_f08a\", url = erddap_url) human_activities_data_info #> humanactivities_9f8a_3389_f08a #> Base URL: https://erddap.emodnet.eu/erddap #> Dataset Type: griddap #> Dimensions (range): #> time: (2017-01-01T00:00:00Z, 2021-12-01T00:00:00Z) #> y: (604500.0, 7034500.0) #> x: (-622500.0, 6884500.0) #> Variables: #> vd: #> Units: seconds # Retrieve the vessel density at a particular time period year_2020_gridded_data <- griddap(datasetx = human_activities_data_info, time = c(\"2020-03-18\", \"2020-03-19\")) #> info() output passed to x; setting base url to: https://erddap.emodnet.eu/erddap head(year_2020_gridded_data$data) #> x y time vd #> 1 -622500 7034500 2020-04-01T00:00:00Z NA #> 2 -621500 7034500 2020-04-01T00:00:00Z NA #> 3 -620500 7034500 2020-04-01T00:00:00Z NA #> 4 -619500 7034500 2020-04-01T00:00:00Z NA #> 5 -618500 7034500 2020-04-01T00:00:00Z NA #> 6 -617500 7034500 2020-04-01T00:00:00Z NA"},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Access EMODnet Web Feature Service data through R","text":"cite emodnet.wfs, please use output citation(package = \"emodnet.wfs\").","code":"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, . #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> 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 2.0.2.9000. 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}, #> url = {https://github.com/EMODnet/emodnet.wfs}, #> doi = {10.14284/679}, #> }"},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"acknowledgements","dir":"","previous_headings":"","what":"Acknowledgements","title":"Access EMODnet Web Feature Service data through R","text":"package started Sheffield University EMODnet Biology WP4 data products workshop June 2020.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet.wfs-package.html","id":null,"dir":"Reference","previous_headings":"","what":"emodnet.wfs: Access EMODnet Web Feature Service data through R — emodnet.wfs-package","title":"emodnet.wfs: Access EMODnet Web Feature Service data through R — emodnet.wfs-package","text":"Access interrogate EMODnet (European Marine Observation Data Network) Web Feature Service data R.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet.wfs-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"emodnet.wfs: Access EMODnet Web Feature Service data through R — emodnet.wfs-package","text":"Maintainer: Salvador Fernández-Bejarano salvador.fernandez@vliz.(ORCID) Authors: Anna Krystalli annakrystalli@googlemail.com (ORCID) Maëlle Salmon msmaellesalmon@gmail.com (ORCID) contributors: Thomas J Webb t.j.webb@sheffield.ac.uk [contributor] European Marine Observation Data Network (EMODnet) Biology project European Commission's Directorate - General Maritime Affairs Fisheries (DG MARE) bio@emodnet.eu [copyright holder] VLIZ (VLAAMS INSTITUUT VOOR DE ZEE) info@vliz.[funder] Alec L. Robitaille (ORCID) (Reviewed package (v2.0.2.9000) rOpenSci, see .) [reviewer] Liz Hare (ORCID) (Reviewed package (v2.0.2.9000) rOpenSci, see .) [reviewer] François Michonneau francois.michonneau@gmail.com (ORCID) (Reviewed package (v2.0.2.9000) rOpenSci, see .) [reviewer]","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":null,"dir":"Reference","previous_headings":"","what":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"Performs WFS getFeature request layers wfs object specified EMODnet Service. Filtering layer features can also handled via ECQL language filters.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"","code":"emodnet_get_layers( wfs = NULL, service = NULL, service_version = NULL, layers, crs = NULL, cql_filter = NULL, simplify = FALSE, reduce_layers = deprecated(), ... )"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layers character vector layer names. get info layers, including layer_name use emodnet_get_wfs_info(). crs integer. EPSG code output crs. NULL (default), layers returned original crs. cql_filter character. Features returned can filtered using valid Extended Common Query Language (ECQL) filtering statements (https://docs.geoserver.org/stable/en/user/filter/ecql_reference.html). one : character string character vector length 1. Filter recycled across layers requested. character vector length equal length layers. Filter matched layers sequentially. Elements containing NA ignored named character vector. filter applied layer corresponding filter name. Filters names correspond layers ignored. Layers without corresponding filters returned whole. simplify whether reduce output layers single sf object. works column names . reduce_layers use simplify. ... additional vendor parameter arguments passed ows4R::GetFeature(). example, including count = 1 returns first available feature. outputFormat = \"CSV\" (outputFormat = \"JSON\") might help downloading bigger datasets.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"simplify = FALSE (default), list sf objects, one element layer. layers download unsuccessful NULL. simplify = TRUE, layers reduced (possible: column names ) single sf containing data layers. NULL layers ignored. simplify = TRUE can also used return sf single layer request instead list length 1.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":"big-downloads","dir":"Reference","previous_headings":"","what":"Big downloads","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"layer really big (like \"abiotic_observations\" \"biology_occurrence_data\" service), might consider combination ideas: using outputFormat = \"CSV\"; filtering using cql_filters bounding boxes (possibly splitting area interests several requests); Using EMODnet's download toolbox.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"","code":"# Layers as character vector emodnet_get_layers( service = \"biology\", layers = c(\"mediseh_zostera_m_pnt\", \"mediseh_posidonia_nodata\") ) #> Loading ISO 19139 XML schemas... #> Loading ISO 19115 codelists... #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> $mediseh_zostera_m_pnt #> Simple feature collection with 54 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 33.07783 xmax: 15.35766 ymax: 45.72451 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> 9 mediseh_zostera_m_pnt.9 0 Italia POINT (13.71831 45.70017) #> 10 mediseh_zostera_m_pnt.10 0 Italia POINT (13.16378 45.72451) #> #> $mediseh_posidonia_nodata #> Simple feature collection with 465 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -2.1798 ymin: 30.26623 xmax: 34.60767 ymax: 45.47668 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.503233 MULTICURVE (LINESTRING (27.... #> 2 mediseh_posidonia_nodata.2 0 75.379502 MULTICURVE (LINESTRING (23.... #> 3 mediseh_posidonia_nodata.3 0 38.627764 MULTICURVE (LINESTRING (22.... #> 4 mediseh_posidonia_nodata.4 0 110.344802 MULTICURVE (LINESTRING (19.... #> 5 mediseh_posidonia_nodata.13 0 66.997461 MULTICURVE (LINESTRING (9.1... #> 6 mediseh_posidonia_nodata.14 0 18.090640 MULTICURVE (LINESTRING (9.7... #> 7 mediseh_posidonia_nodata.15 0 16.618978 MULTICURVE (LINESTRING (9.8... #> 8 mediseh_posidonia_nodata.16 0 1.913773 MULTICURVE (LINESTRING (10.... #> 9 mediseh_posidonia_nodata.83 0 2.173447 MULTICURVE (LINESTRING (15.... #> 10 mediseh_posidonia_nodata.84 0 2.817453 MULTICURVE (LINESTRING (15.... #> # Usage of cql_filter emodnet_get_layers( service = \"biology\", layers = \"mediseh_zostera_m_pnt\", cql_filter = \"country = 'Francia'\" ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> $mediseh_zostera_m_pnt #> Simple feature collection with 1 feature and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: 4.84864 ymin: 43.37637 xmax: 4.84864 ymax: 43.37637 #> Geodetic CRS: WGS 84 #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> # Usage of vendor parameter emodnet_get_layers( service = \"biology\", layers = \"mediseh_zostera_m_pnt\", count = 1 ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> $mediseh_zostera_m_pnt #> Simple feature collection with 1 feature and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -2.61314 ymin: 36.71681 xmax: -2.61314 ymax: 36.71681 #> Geodetic CRS: WGS 84 #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> # Usage of csv output data <- emodnet_get_layers( service = \"biology_occurrence_data\", layers = \"abiotic_observations\", outputFormat = \"CSV\" ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Dataportal/wfs\" #> ℹ Version: \"2.0.0\" #> Rows: 1000000 Columns: 37 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (17): FID, value, datatype, season, parametername, parameterunit, datap... #> dbl (11): id, latitude, longitude, depth, standardparameterid, dataprovider... #> lgl (8): aphiaid, lod, loq, class, classunit, classcode, dateprecision, sc... #> dttm (1): datetime #> #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. str(data[[\"abiotic_observations\"]]) #> spc_tbl_ [1,000,000 × 37] (S3: spec_tbl_df/tbl_df/tbl/data.frame) #> $ FID : chr [1:1000000] \"abiotic_observations.fid--2efb98bf_19362766137_-4916\" \"abiotic_observations.fid--2efb98bf_19362766137_-4915\" \"abiotic_observations.fid--2efb98bf_19362766137_-4914\" \"abiotic_observations.fid--2efb98bf_19362766137_-4913\" ... #> $ id : num [1:1000000] 32822603 32822703 32822703 32822703 32822703 ... #> $ aphiaid : logi [1:1000000] NA NA NA NA NA NA ... #> $ latitude : num [1:1000000] 51.4 51.4 51.4 51.4 51.4 ... #> $ longitude : num [1:1000000] 4.01 4.01 4.01 4.01 4.01 ... #> $ depth : num [1:1000000] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 ... #> $ datetime : POSIXct[1:1000000], format: \"1990-12-10 13:52:00\" \"1991-01-08 12:41:00\" ... #> $ value : chr [1:1000000] \"3.73\" \"86\" \"86\" \"86\" ... #> $ lod : logi [1:1000000] NA NA NA NA NA NA ... #> $ loq : logi [1:1000000] NA NA NA NA NA NA ... #> $ standardparameterid: num [1:1000000] 1024 1213 1213 1213 1213 ... #> $ dataproviderid : num [1:1000000] 8 8 8 8 8 8 8 8 8 8 ... #> $ imisdatasetid : num [1:1000000] 135 135 135 135 135 135 135 135 135 135 ... #> $ dataficheid : num [1:1000000] 16 11 11 11 11 11 11 11 11 11 ... #> $ seriesid : num [1:1000000] 1895 1895 1895 1895 1895 ... #> $ datatype : chr [1:1000000] \"NC\" \"NC\" \"NC\" \"NC\" ... #> $ class : logi [1:1000000] NA NA NA NA NA NA ... #> $ classunit : logi [1:1000000] NA NA NA NA NA NA ... #> $ classcode : logi [1:1000000] NA NA NA NA NA NA ... #> $ season : chr [1:1000000] \"autumn\" \"winter\" \"winter\" \"winter\" ... #> $ parametername : chr [1:1000000] \"Stikstof, totaal in mgN/l in oppervlaktewater\" \"Zuurstof in % in oppervlaktewater\" \"Zuurstof in % in oppervlaktewater\" \"Zuurstof in % in oppervlaktewater\" ... #> $ parameterunit : chr [1:1000000] \"mgN/l\" \"%\" \"%\" \"%\" ... #> $ dataprovider : chr [1:1000000] \"RWS - Rijkswaterstaat\" \"RWS - Rijkswaterstaat\" \"RWS - Rijkswaterstaat\" \"RWS - Rijkswaterstaat\" ... #> $ datasettitle : chr [1:1000000] \"MWTL chemical monitoring network Westerschelde\" \"MWTL chemical monitoring network Westerschelde\" \"MWTL chemical monitoring network Westerschelde\" \"MWTL chemical monitoring network Westerschelde\" ... #> $ datafichetitle : chr [1:1000000] \"S-FC-N-016 - Organische microverontreinigingen\" \"S-FC-N-010 - Zuurstof (periodiek)\" \"S-FC-N-010 - Zuurstof (periodiek)\" \"S-FC-N-010 - Zuurstof (periodiek)\" ... #> $ stationname : chr [1:1000000] \"Hansweert geul\" \"Hansweert geul\" \"Hansweert geul\" \"Hansweert geul\" ... #> $ gid : num [1:1000000] 10 10 10 10 10 10 10 10 10 10 ... #> $ seasonid : num [1:1000000] 4 1 1 1 1 1 1 1 1 1 ... #> $ unit : chr [1:1000000] \"mgN/l\" \"%\" \"%\" \"%\" ... #> $ category : chr [1:1000000] \"opgeloste gassen\" \"opgeloste gassen\" \"opgeloste gassen\" \"opgeloste gassen\" ... #> $ the_geom : chr [1:1000000] \"POINT (51.43701536692164 4.01438853410749)\" \"POINT (51.43701536692164 4.01438853410749)\" \"POINT (51.43701536692164 4.01438853410749)\" \"POINT (51.43701536692164 4.01438853410749)\" ... #> $ valuesign : chr [1:1000000] \"=\" \"=\" \"=\" \"=\" ... #> $ dateprecision : logi [1:1000000] NA NA NA NA NA NA ... #> $ standard_name : chr [1:1000000] \"BODC\" \"BODC\" \"BODC\" \"BODC\" ... #> $ externalid : chr [1:1000000] \"NTOTZZXX\" \"OXYSSE01\" \"OXYSZW01\" \"OXYSZZ01\" ... #> $ external_name : chr [1:1000000] \"Concentration of total nitrogen {total_N} per unit volume of the water body [dissolved plus reactive particulate phase]\" \"Saturation of oxygen {O2 CAS 7782-44-7} in the water body [dissolved plus reactive particulate phase] by YSI in\"| __truncated__ \"Saturation of oxygen {O2 CAS 7782-44-7} in the water body [dissolved plus reactive particulate phase] by Winkle\"| __truncated__ \"Saturation of oxygen {O2 CAS 7782-44-7} in the water body [dissolved plus reactive particulate phase]\" ... #> $ scientificname : logi [1:1000000] NA NA NA NA NA NA ... #> - attr(*, \"spec\")= #> .. cols( #> .. FID = col_character(), #> .. id = col_double(), #> .. aphiaid = col_logical(), #> .. latitude = col_double(), #> .. longitude = col_double(), #> .. depth = col_double(), #> .. datetime = col_datetime(format = \"\"), #> .. value = col_character(), #> .. lod = col_logical(), #> .. loq = col_logical(), #> .. standardparameterid = col_double(), #> .. dataproviderid = col_double(), #> .. imisdatasetid = col_double(), #> .. dataficheid = col_double(), #> .. seriesid = col_double(), #> .. datatype = col_character(), #> .. class = col_logical(), #> .. classunit = col_logical(), #> .. classcode = col_logical(), #> .. season = col_character(), #> .. parametername = col_character(), #> .. parameterunit = col_character(), #> .. dataprovider = col_character(), #> .. datasettitle = col_character(), #> .. datafichetitle = col_character(), #> .. stationname = col_character(), #> .. gid = col_double(), #> .. seasonid = col_double(), #> .. unit = col_character(), #> .. category = col_character(), #> .. the_geom = col_character(), #> .. valuesign = col_character(), #> .. dateprecision = col_logical(), #> .. standard_name = col_character(), #> .. externalid = col_character(), #> .. external_name = col_character(), #> .. scientificname = col_logical() #> .. ) #> - attr(*, \"problems\")="},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"Get WFS available layer information","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"","code":"emodnet_get_layer_info(wfs, layers) emodnet_get_wfs_info(wfs = NULL, service = NULL, service_version = NULL) emodnet_get_all_wfs_info()"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). layers character vector layer names. get info layers, including layer_name use emodnet_get_wfs_info(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\".","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"tibble containing metadata layer available service.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"minimize number requests sent webservices, functions use memoise cache results inside active R session. clear cache, re-start R run memoise::forget(emodnet_get_wfs_info)/ memoise::forget(emodnet_get_layer_info).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"emodnet_get_layer_info(): Get metadata specific layers. Requires wfs object input. emodnet_get_wfs_info(): Get info layers EMODnet WFS service. emodnet_get_all_wfs_info(): Get metadata layers available services server.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"","code":"emodnet_get_wfs_info(service = \"bathymetry\") #> ✔ WFS client created successfully #> ℹ Service: \"https://ows.emodnet-bathymetry.eu/wfs\" #> ℹ Version: \"2.0.0\" #> # A tibble: 7 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs bathymetry https://ows.e… download_… Bath… \"Downlo… WFSF… sf #> 2 emodnet_wfs bathymetry https://ows.e… contours Dept… \"Genera… WFSF… sf #> 3 emodnet_wfs bathymetry https://ows.e… hr_bathym… High… \"Layer … WFSF… sf #> 4 emodnet_wfs bathymetry https://ows.e… quality_i… Qual… \"Repres… WFSF… sf #> 5 emodnet_wfs bathymetry https://ows.e… sea_names Sea … \"Mainta… WFSF… sf #> 6 emodnet_wfs bathymetry https://ows.e… source_re… Sour… \"Covera… WFSF… sf #> 7 emodnet_wfs bathymetry https://ows.e… undersea_… unde… \"\" WFSF… sf #> # ℹ 1 more variable: layer_namespace # Query a wfs object wfs_bio <- emodnet_init_wfs_client(\"biology\") #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" emodnet_get_wfs_info(wfs_bio) #> # A tibble: 35 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 2 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 3 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Cymodo… WFSF… sf #> 4 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 5 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 6 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 7 emodnet_wfs biology https://geo.… mediseh_h… EMOD… \"Haloph… WFSF… sf #> 8 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 10 emodnet_wfs biology https://geo.… mediseh_p… EMOD… \"This d… WFSF… sf #> # ℹ 25 more rows #> # ℹ 1 more variable: layer_namespace # Get info for specific layers from wfs object layers <- c(\"mediseh_zostera_m_pnt\", \"mediseh_posidonia_nodata\") emodnet_get_layer_info(wfs = wfs_bio, layers = layers) #> # A tibble: 2 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs https://geo.vl… biology mediseh_p… EMOD… \"Coastl… WFSF… sf #> 2 emodnet_wfs https://geo.vl… biology mediseh_z… EMOD… \"Zoster… WFSF… sf #> # ℹ 1 more variable: layer_namespace "},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_init_wfs_client.html","id":null,"dir":"Reference","previous_headings":"","what":"Connect to a data source (service) — emodnet_init_wfs_client","title":"Connect to a data source (service) — emodnet_init_wfs_client","text":"Initialise EMODnet WFS client","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_init_wfs_client.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Connect to a data source (service) — emodnet_init_wfs_client","text":"","code":"emodnet_init_wfs_client(service, service_version = NULL, logger = NULL)"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_init_wfs_client.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Connect to a data source (service) — emodnet_init_wfs_client","text":"service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". logger logger. Either NULL (logging info), \"INFO\" (log ows4R requests) \"DEBUG\" (including curl details).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_init_wfs_client.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Connect to a data source (service) — emodnet_init_wfs_client","text":"ows4R::WFSClient R6 object methods interfacing OGC Web Feature Service.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_init_wfs_client.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Connect to a data source (service) — emodnet_init_wfs_client","text":"","code":"wfs <- emodnet_init_wfs_client(service = \"bathymetry\") #> ✔ WFS client created successfully #> ℹ Service: \"https://ows.emodnet-bathymetry.eu/wfs\" #> ℹ Version: \"2.0.0\""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_wfs.html","id":null,"dir":"Reference","previous_headings":"","what":"Which data sources (services) are available? — emodnet_wfs","title":"Which data sources (services) are available? — emodnet_wfs","text":"Available EMODnet Web Feature Services","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_wfs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Which data sources (services) are available? — emodnet_wfs","text":"","code":"emodnet_wfs()"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_wfs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Which data sources (services) are available? — emodnet_wfs","text":"Tibble available EMODnet Web Feature Services","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_wfs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Which data sources (services) are available? — emodnet_wfs","text":"","code":"emodnet_wfs() #> # A tibble: 17 × 2 #> service_name service_url #> #> 1 bathymetry https://ows.… #> 2 biology https://geo.… #> 3 biology_occurrence_data https://geo.… #> 4 chemistry_cdi_data_discovery_and_access_service https://geo-… #> 5 chemistry_cdi_distribution_observations_per_category_and_region https://geo-… #> 6 chemistry_contaminants https://geos… #> 7 chemistry_marine_litter https://www.… #> 8 geology_coastal_behavior https://driv… #> 9 geology_events_and_probabilities https://driv… #> 10 geology_marine_minerals https://driv… #> 11 geology_sea_floor_bedrock https://driv… #> 12 geology_seabed_substrate_maps https://driv… #> 13 geology_submerged_landscapes https://driv… #> 14 human_activities https://ows.… #> 15 physics https://prod… #> 16 seabed_habitats_general_datasets_and_products https://ows.… #> 17 seabed_habitats_individual_habitat_map_and_model_datasets https://ows.…"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_descriptions.html","id":null,"dir":"Reference","previous_headings":"","what":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","title":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","text":"Get layer attribute description","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_descriptions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","text":"","code":"layer_attribute_descriptions( wfs = NULL, service = NULL, service_version = NULL, layer )"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_descriptions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layer character sting layer name. get info layers, including layer_name use emodnet_get_wfs_info().","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_descriptions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","text":"data.frame containing layer attribute descriptions (metadata).","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_descriptions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","text":"","code":"layer_attribute_descriptions( service = \"biology\", layer = \"mediseh_zostera_m_pnt\" ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> name type minOccurs maxOccurs nillable geometry #> 1 id integer 0 1 TRUE FALSE #> 2 country character 0 1 TRUE FALSE #> 3 the_geom Point 0 1 TRUE TRUE"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_inspect.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","title":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","text":"Inspect layer attributes","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_inspect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","text":"","code":"layer_attribute_inspect( wfs = NULL, service = NULL, service_version = NULL, layer, attribute )"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_inspect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layer character sting layer name. get info layers, including layer_name use emodnet_get_wfs_info(). attribute character string, name layer attribute (variable). Use layer_attributes_get_names() get layer attribute names.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_inspect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","text":"Detailed summary individual attribute (variable). Particularly useful inspecting factor character variable levels unique values.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_inspect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","text":"","code":"wfs <- emodnet_init_wfs_client(service = \"biology\") #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" layer_attributes_get_names(wfs, layer = \"mediseh_zostera_m_pnt\") #> [1] \"id\" \"country\" \"the_geom\" layer_attribute_inspect( wfs, layer = \"mediseh_zostera_m_pnt\", attribute = \"country\" ) #> # A tibble: 7 × 3 #> . n percent #> #> 1 Croazia 4 0.0741 #> 2 Francia 1 0.0185 #> 3 Italia 30 0.556 #> 4 Libia 2 0.0370 #> 5 Slovenia 8 0.148 #> 6 Spagna 8 0.148 #> 7 Tunisia 1 0.0185"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_get_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","title":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","text":"Names variables (attributes) available dataset (layer) data source (service).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_get_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","text":"","code":"layer_attributes_get_names( wfs = NULL, service = NULL, service_version = NULL, layer )"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_get_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layer character sting layer name. get info layers, including layer_name use emodnet_get_wfs_info().","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_get_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","text":"character vector layer attribute (variable) names.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_get_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","text":"","code":"layer_attributes_get_names( service = \"biology\", layer = \"mediseh_zostera_m_pnt\" ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> [1] \"id\" \"country\" \"the_geom\""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_summarise.html","id":null,"dir":"Reference","previous_headings":"","what":"Get summaries of layer attributes (variables) — layer_attributes_summarise","title":"Get summaries of layer attributes (variables) — layer_attributes_summarise","text":"Get summaries layer attributes (variables)","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_summarise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get summaries of layer attributes (variables) — layer_attributes_summarise","text":"","code":"layer_attributes_summarise( wfs = NULL, service = NULL, service_version = NULL, layer )"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_summarise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get summaries of layer attributes (variables) — layer_attributes_summarise","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layer character sting layer name. get info layers, including layer_name use emodnet_get_wfs_info().","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_summarise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get summaries of layer attributes (variables) — layer_attributes_summarise","text":"output summary() attributes (variables) given layer given service.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_summarise.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get summaries of layer attributes (variables) — layer_attributes_summarise","text":"","code":"layer_attributes_summarise( service = \"biology\", layer = \"mediseh_zostera_m_pnt\" ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> gml_id id country #> Length:54 Min. :0 Length:54 #> Class :character 1st Qu.:0 Class :character #> Mode :character Median :0 Mode :character #> Mean :0 #> 3rd Qu.:0 #> Max. :0"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"Get layer attribute values tibble","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"","code":"layer_attributes_tbl(wfs = NULL, service = NULL, service_version = NULL, layer)"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layer character sting layer name. get info layers, including layer_name use emodnet_get_wfs_info().","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"tibble layer attribute (variable) values geometry column removed.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"Request excluding spatial information can significantly faster. Can useful inspecting attribute values constructing feature filters targeted faster layer download.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"","code":"layer_attributes_tbl(service = \"biology\", layer = \"mediseh_zostera_m_pnt\") #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> # A tibble: 54 × 3 #> gml_id id country #> #> 1 mediseh_zostera_m_pnt.1 0 Spagna #> 2 mediseh_zostera_m_pnt.2 0 Spagna #> 3 mediseh_zostera_m_pnt.3 0 Spagna #> 4 mediseh_zostera_m_pnt.4 0 Spagna #> 5 mediseh_zostera_m_pnt.5 0 Spagna #> 6 mediseh_zostera_m_pnt.6 0 Spagna #> 7 mediseh_zostera_m_pnt.7 0 Spagna #> 8 mediseh_zostera_m_pnt.8 0 Francia #> 9 mediseh_zostera_m_pnt.9 0 Italia #> 10 mediseh_zostera_m_pnt.10 0 Italia #> # ℹ 44 more rows"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::[\\%>\\%][magrittr::pipe] details.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://emodnet.github.io/emodnet.wfs/news/index.html","id":"emodnetwfs-development-version","dir":"Changelog","previous_headings":"","what":"emodnet.wfs (development version)","title":"emodnet.wfs (development version)","text":"Improved documentation following rOpenSci reviews: manual pages, README, vignettes. Renamed reduce_layers argument simplify. emodnet_wfs() now really returns tibble, data.frame. Listed reviewers DESCRIPTION. Set better escape mechanism examples fail services , ensure rendered pkgdown website.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/news/index.html","id":"emodnetwfs-202","dir":"Changelog","previous_headings":"","what":"emodnet.wfs 2.0.2","title":"emodnet.wfs 2.0.2","text":"Added ability pass vendor parameter emodnet.wfs::emodnet_get_layers() queries (#88). Added memoising (caching R session) functions getting services layers information (#52).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/news/index.html","id":"emodnetwfs-201","dir":"Changelog","previous_headings":"","what":"emodnet.wfs 2.0.1","title":"emodnet.wfs 2.0.1","text":"Introduced better handling server response errors.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/news/index.html","id":"emodnetwfs-200","dir":"Changelog","previous_headings":"","what":"emodnet.wfs 2.0.0","title":"emodnet.wfs 2.0.0","text":"NEW FEATURE: Added ecql filtering capability ability interrogate feature attribute (see relevant vignette). Bug fix: corrected service namespace definition using wfs object Breaking Change: set extract default CRS service information (getDeafultCRS method) Breaking change: Removed default service value. Updated new EMODnet Seabed Habitats endpoints Added NEWS.md file track changes package.","code":""}] +[{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to emodnet.wfs","title":"Contributing to emodnet.wfs","text":"outlines propose change emodnet.wfs.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing to emodnet.wfs","text":"can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to emodnet.wfs","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to emodnet.wfs","text":"Fork package clone onto computer. haven’t done , recommend using usethis::create_from_github(\"EMODnet/emodnet.wfs\", fork = TRUE). Install development dependencies pak::pak(), make sure package passes R CMD check running devtools::check(). R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using usethis::pr_init(\"brief-description--change\"). Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number. user-facing changes, add bullet top NEWS.md (.e. just first header). Follow style described https://style.tidyverse.org/news.html.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to emodnet.wfs","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. use roxygen2, Markdown syntax, documentation. use testthat httptest unit tests. Contributions test cases included easier accept.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/CONTRIBUTING.html","id":"collaborators","dir":"","previous_headings":"","what":"Collaborators","title":"Contributing to emodnet.wfs","text":"Regular contributors listed inst/collaborators.txt ensure user-agent used package flags developers.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2021 European Marine Observation Data Network (EMODnet) Biology project Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"cql-ecql-query-languages-","dir":"Articles","previous_headings":"","what":"CQL & ECQL Query languages.","title":"EQCL feature filtering","text":"CQL (Common Query Language) plain-text language created OGC Catalog specification. GeoServer adapted easy--use filtering mechanism. GeoServer actually implements powerful extension called ECQL (Extended CQL), allows expressing full range filters OGC Filter 1.1 can encode. ECQL accepted many places GeoServer. GeoServer supports use CQL ECQL WFS requests whenever documentation refers CQL, ECQL syntax can used well. examples provided small subset filtering functionality available Geoserver. Full references examples can found following documentation: ECQL Reference: reference syntax ECQL language. Filter Function Reference: OGC Filter Encoding specification provides generic concept filter function. filter function named function number arguments, can used filter expression perform specific calculations. provides much richer expressiveness defining filters.GeoServer provides many different kinds filter functions, covering wide range functionality including mathematics, string formatting, geometric operations. CQL ECQL Tutorial shows examples defining filters.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"initialise-emodnet-wfs-client","dir":"Articles","previous_headings":"","what":"Initialise EMODnet WFS client","title":"EQCL feature filtering","text":"First, let’s load library start new WFS client emodnet_init_wfs_client.","code":"library(emodnet.wfs) wfs <- emodnet_init_wfs_client(service = \"biology\") #> Loading ISO 19139 XML schemas... #> Loading ISO 19115 codelists... #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"inspecting-attributes","dir":"Articles","previous_headings":"","what":"Inspecting attributes","title":"EQCL feature filtering","text":"develop filters, first need information attributes can filter . example, might want know data type range distribution values attributes given layer. Let’s look existing layers.","code":"emodnet_get_wfs_info(wfs) #> # A tibble: 35 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 2 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 3 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Cymodo… WFSF… sf #> 4 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 5 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 6 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 7 emodnet_wfs biology https://geo.… mediseh_h… EMOD… \"Haloph… WFSF… sf #> 8 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 10 emodnet_wfs biology https://geo.… mediseh_p… EMOD… \"This d… WFSF… sf #> # ℹ 25 more rows #> # ℹ 1 more variable: layer_namespace "},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"layer-attribute-names","dir":"Articles","previous_headings":"Inspecting attributes","what":"Layer attribute names","title":"EQCL feature filtering","text":"start, might want know names layer’s attributes. functions can also used providing service name instead wfs object.","code":"layer_attributes_get_names(wfs, layer = \"mediseh_zostera_m_pnt\") #> [1] \"id\" \"country\" \"the_geom\" layer_attributes_get_names(service = \"biology\", layer = \"mediseh_zostera_m_pnt\") #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> [1] \"id\" \"country\" \"the_geom\""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"layer-attribute-descriptions","dir":"Articles","previous_headings":"Inspecting attributes","what":"Layer attribute descriptions","title":"EQCL feature filtering","text":"type filtering might want apply depend data type attribute. can inspect attribute descriptions (metadata) given layer layer_attribute_descriptions().","code":"layer_attribute_descriptions(wfs, layer = \"mediseh_zostera_m_pnt\") #> name type minOccurs maxOccurs nillable geometry #> 1 id integer 0 1 TRUE FALSE #> 2 country character 0 1 TRUE FALSE #> 3 the_geom Point 0 1 TRUE TRUE"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"layer-attribute-summaries","dir":"Articles","previous_headings":"Inspecting attributes","what":"Layer attribute summaries","title":"EQCL feature filtering","text":"can get summaries values attribute layer_attributes_summarise(). function basically runs summary() attribute columns layer.","code":"layer_attributes_summarise(wfs, layer = \"mediseh_zostera_m_pnt\") #> gml_id id country #> Length:54 Min. :0 Length:54 #> Class :character 1st Qu.:0 Class :character #> Mode :character Median :0 Mode :character #> Mean :0 #> 3rd Qu.:0 #> Max. :0"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"inspecting-individual-layer-attributes","dir":"Articles","previous_headings":"Inspecting attributes","what":"Inspecting individual layer attributes","title":"EQCL feature filtering","text":"can also inspect individual attributes , case categorical variables, can give detailed information names distribution categories.","code":"layer_attribute_inspect( wfs, layer = \"mediseh_zostera_m_pnt\", attribute = \"country\" ) #> # A tibble: 7 × 3 #> . n percent #> #> 1 Croazia 4 0.0741 #> 2 Francia 1 0.0185 #> 3 Italia 30 0.556 #> 4 Libia 2 0.0370 #> 5 Slovenia 8 0.148 #> 6 Spagna 8 0.148 #> 7 Tunisia 1 0.0185"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"layer-attributes-table","dir":"Articles","previous_headings":"","what":"Layer attributes table","title":"EQCL feature filtering","text":"Finally, enable full inspection custom processing attribute data, can download full set attributes data.frame, excluding geometry column. geometries usually largest column, much faster downloading full layer can useful developing attribute filtering rules.","code":"attr_tbl <- layer_attributes_tbl(wfs, layer = \"mediseh_zostera_m_pnt\") attr_tbl #> # A tibble: 54 × 3 #> gml_id id country #> #> 1 mediseh_zostera_m_pnt.1 0 Spagna #> 2 mediseh_zostera_m_pnt.2 0 Spagna #> 3 mediseh_zostera_m_pnt.3 0 Spagna #> 4 mediseh_zostera_m_pnt.4 0 Spagna #> 5 mediseh_zostera_m_pnt.5 0 Spagna #> 6 mediseh_zostera_m_pnt.6 0 Spagna #> 7 mediseh_zostera_m_pnt.7 0 Spagna #> 8 mediseh_zostera_m_pnt.8 0 Francia #> 9 mediseh_zostera_m_pnt.9 0 Italia #> 10 mediseh_zostera_m_pnt.10 0 Italia #> # ℹ 44 more rows"},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"filtering-categorical-attributes-values-using-text-comparisons","dir":"Articles","previous_headings":"Filtering by attributes","what":"Filtering categorical attributes values using text comparisons","title":"EQCL feature filtering","text":"know values categorical attribute layer, can use filter features returned query. example, let’s say interested results France. previous interrogation attributes associated mediseh_zostera_m_pnt layer, seen attribute country contains country. can use name attribute value require construct eqcl filter pass request using cql_filter argument. shows basic text comparisons can make use equality operator =. want match one value, can use operator instead provide list values compare . example, request France Spain, use following filter: using filter: text comparisons include text pattern matching using operator LIKE. example, request maritime boundaries countries starting S, can use following filter: CQL/ECQL filters can also include filter functions available GeoServer, including multiple string functions greatly increases power CQL expressions. example, can request countries contain l anywhere, including first letter. make request case independent, can turn country names lowercase use like comparison lowercase l:","code":"emodnet_get_layers( wfs, layers = \"mediseh_zostera_m_pnt\", cql_filter = \"country = 'Francia'\" ) #> $mediseh_zostera_m_pnt #> Simple feature collection with 1 feature and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: 4.84864 ymin: 43.37637 xmax: 4.84864 ymax: 43.37637 #> Geodetic CRS: WGS 84 #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) emodnet_get_layers( wfs, layers = \"mediseh_zostera_m_pnt\", cql_filter = \"country IN ('Francia', 'Spagna')\" ) #> $mediseh_zostera_m_pnt #> Simple feature collection with 9 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 36.71226 xmax: 4.84864 ymax: 43.37637 #> Geodetic CRS: WGS 84 #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> 9 mediseh_zostera_m_pnt.54 0 Spagna POINT (3.291868 42.29132) emodnet_get_layers( wfs, layers = \"mediseh_zostera_m_pnt\", cql_filter = \"country='Francia' OR country='Spagna'\" ) #> $mediseh_zostera_m_pnt #> Simple feature collection with 9 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 36.71226 xmax: 4.84864 ymax: 43.37637 #> Geodetic CRS: WGS 84 #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> 9 mediseh_zostera_m_pnt.54 0 Spagna POINT (3.291868 42.29132) emodnet_get_layers( wfs = wfs, layers = \"mediseh_zostera_m_pnt\", cql_filter = \"country LIKE 'S%'\", simplify = TRUE ) #> Simple feature collection with 16 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 36.71226 xmax: 13.73725 ymax: 45.58252 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.39 0 Slovenia POINT (13.73725 45.56948) #> 9 mediseh_zostera_m_pnt.40 0 Slovenia POINT (13.70701 45.58252) #> 10 mediseh_zostera_m_pnt.41 0 Slovenia POINT (13.71894 45.54535) emodnet_get_layers( wfs = wfs, layers = \"mediseh_zostera_m_pnt\", cql_filter = \"strToLowerCase(country) LIKE '%l%'\", simplify = TRUE ) #> Simple feature collection with 40 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: 11.71682 ymin: 33.07783 xmax: 14.4714 ymax: 45.72451 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.9 0 Italia POINT (13.71831 45.70017) #> 2 mediseh_zostera_m_pnt.10 0 Italia POINT (13.16378 45.72451) #> 3 mediseh_zostera_m_pnt.11 0 Italia POINT (13.35982 45.70508) #> 4 mediseh_zostera_m_pnt.12 0 Italia POINT (12.26722 45.25975) #> 5 mediseh_zostera_m_pnt.13 0 Italia POINT (12.31285 45.362) #> 6 mediseh_zostera_m_pnt.14 0 Italia POINT (12.53509 45.53269) #> 7 mediseh_zostera_m_pnt.15 0 Italia POINT (12.48269 45.5065) #> 8 mediseh_zostera_m_pnt.16 0 Italia POINT (12.77334 43.96751) #> 9 mediseh_zostera_m_pnt.17 0 Italia POINT (13.62604 43.50809) #> 10 mediseh_zostera_m_pnt.18 0 Italia POINT (13.46398 43.60892)"},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"filtering-numeric-variables","dir":"Articles","previous_headings":"Filtering by attributes","what":"Filtering numeric variables","title":"EQCL feature filtering","text":"number additional comparison operators, =, <>, >, >=, <, <= , arithmetic operators +, -, *, / well comparison math functions can used filtering numeric variables. time ’ll use mediseh_posidonia_nodata. can inspect , using interrogative functions get information layer attributes. can see values range 0.23 ~473 mean ~40. Let’s say interested values greater 400. can use operator > create filter: request range can use filter functions .","code":"layer_attributes_get_names( wfs, layer = \"mediseh_posidonia_nodata\" ) #> [1] \"id\" \"km\" \"the_geom\" layer_attribute_inspect( wfs, layer = \"mediseh_posidonia_nodata\", attribute = \"km\" ) #> Min. 1st Qu. Median Mean 3rd Qu. Max. #> 0.2371 6.0306 16.6190 40.1771 42.8958 472.9613 emodnet_get_layers( wfs = wfs, layers = \"mediseh_posidonia_nodata\", cql_filter = \"km > 400\", simplify = TRUE ) #> Simple feature collection with 4 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -1.572609 ymin: 35.24538 xmax: 28.33243 ymax: 38.68017 #> Geodetic CRS: WGS 84 #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.8 0 456.3759 MULTICURVE (LINESTRING (2.3... #> 2 mediseh_posidonia_nodata.227 0 464.6573 MULTICURVE (LINESTRING (26.... #> 3 mediseh_posidonia_nodata.228 0 472.9613 MULTICURVE (LINESTRING (26.... #> 4 mediseh_posidonia_nodata.229 0 463.8207 MULTICURVE (LINESTRING (27.... emodnet_get_layers( wfs = wfs, layers = \"mediseh_posidonia_nodata\", cql_filter = \"km between 40 and 400\", simplify = TRUE ) #> Simple feature collection with 120 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -2.1798 ymin: 30.26623 xmax: 34.59127 ymax: 45.35511 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.50323 MULTICURVE (LINESTRING (27.... #> 2 mediseh_posidonia_nodata.2 0 75.37950 MULTICURVE (LINESTRING (23.... #> 3 mediseh_posidonia_nodata.4 0 110.34480 MULTICURVE (LINESTRING (19.... #> 4 mediseh_posidonia_nodata.13 0 66.99746 MULTICURVE (LINESTRING (9.1... #> 5 mediseh_posidonia_nodata.5 0 222.44651 MULTICURVE (LINESTRING (8.6... #> 6 mediseh_posidonia_nodata.6 0 58.72822 MULTICURVE (LINESTRING (6.8... #> 7 mediseh_posidonia_nodata.7 0 192.50519 MULTICURVE (LINESTRING (6.4... #> 8 mediseh_posidonia_nodata.10 0 65.74354 MULTICURVE (LINESTRING (-1.... #> 9 mediseh_posidonia_nodata.11 0 138.68819 MULTICURVE (LINESTRING (4.8... #> 10 mediseh_posidonia_nodata.17 0 184.05959 MULTICURVE (LINESTRING (10...."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"using-or-and-and-statements","dir":"Articles","previous_headings":"Filtering by attributes","what":"Using OR and AND statements","title":"EQCL feature filtering","text":"Filter conditions can also logical combination conditions using , . showed previously use list potential values match attribute . also achieved using statement. example, following query returns features country either Baltic Sea Bulgaria. Let’s say also want restrict features returned shape_length > 1. can include additional condition must met using statement. query returns features country Baltic Sea Bulgaria can see minimum value minimum set filter. ’s filter added country='Bulgaria', features shape_length > 1 returned country also Bulgaria, filter applied shape_length country Baltic Sea. add filter filters, can use parenthesis: Now minimum value indeed 1. However, get features country 'Bulgaria'. ’s single Baltic Sea feature shape_length value smaller 1 filtered . Finally filtering shape_length < 1 returns features shape_length values smaller 1 country values.","code":"wfs <- emodnet_init_wfs_client(service = \"geology_seabed_substrate_maps\") emodnet_get_layers( wfs = wfs, layers = \"seabed_substrate_1m\", cql_filter = \"country='Baltic Sea' OR country='Bulgaria'\", simplify = TRUE ) filter_sf1 <- emodnet_get_layers( wfs = wfs, layers = \"seabed_substrate_1m\", cql_filter = \"country='Baltic Sea' OR country='Bulgaria' AND shape_length>1\", simplify = TRUE ) filter_sf1 unique(filter_sf1$country) min(filter_sf1$shape_length) filter_sf2 <- emodnet_get_layers( wfs = wfs, layers = \"seabed_substrate_1m\", cql_filter = \"(country='Baltic Sea' OR country='Bulgaria') AND shape_length>1\", simplify = TRUE ) min(filter_sf2$shape_length) unique(filter_sf2$country) filter_sf3 <- emodnet_get_layers( wfs = wfs, layers = \"seabed_substrate_1m\", cql_filter = \"(country='Baltic Sea' OR country='Bulgaria') AND shape_length<1\", simplify = TRUE ) max(filter_sf3$shape_length) unique(filter_sf3$country)"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html","id":"advanced-use","dir":"Articles","previous_headings":"Filtering by attributes","what":"Advanced use","title":"EQCL feature filtering","text":"can accomplished using EMODnet WFS services downloading data. emodnet.wfs package built top ows4R library, meaning functionalities package available emodnet.wfs. ows4R returns special type R object called R6. can learn Hadley Wickham’s chapter R6 Objects Advance R book. instance: efficient read large dataset R just later subset part . requires longer waiting times bandwidth usage, large datasets simply possible. instance, occurrences data available EMODnet Biology portal stored one table: approximately 30 millions rows! case, suggest access EMODnet Biology occurrence data EMODnet geoviewer eurobis R package. package retrieves occurrences batches, allowing large datasets, uses viewParams, geoserver-specific filtering feature faster requests compared standard OGC CQL filters. addition, one specific filters allow query species traits functional groups.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/emodnet.wfs.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Accessing and mapping EMODnet data","text":"package designed make EMODnet vector data layers easily accessible R. package allows users query information download data available EMODnet Web Feature Service (WFS) endpoints directly R working environment. Data managed sf objects currently state---art handling vector spatial data R. package also allows user specify coordinate reference system imported data.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/emodnet.wfs.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Accessing and mapping EMODnet data","text":"can install development version emodnet.wfs GitHub :","code":"pak::pak(\"EMODnet/emodnet.wfs\")"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/emodnet.wfs.html","id":"explore-the-emodnet-wfs-services-with-r","dir":"Articles","previous_headings":"","what":"Explore the EMODnet WFS services with R","title":"Accessing and mapping EMODnet data","text":"tutorial make use sf mapview packages. simple features sf package well known standard dealing geospatial vector data. visualize geometries, mapview create quick interactive maps. Run line install packages: EMODnet organized seven thematic lots: Bathymetry, Geology, Seabed Habitats, Chemistry, Biology, Physics, Human Activities, focusing specific aspect marine data. emodnet.wfs package, can explore combine data served EMODnet thematic lots OGC Web Feature Services WFS. Imagine interested seabed substrates. first step choose EMODnet thematic lot can provide data. , can check services available emodnet_wfs() function. column service_name shows services available, service_url corresponding base url perform WFS request. Seabed portal data looking . WFS client can created passing corresponding service_name function emodnet_init_wfs_client(). layers available WFS client consulted emodnet_get_wfs_info(). layer explained abstract column. can see several layers information provided EU member states Habitats Directive 92/43/EEC reporting. select layers coastal lagoons, mudflats sandbanks respective layer_name. now ready read layers R emodnet_get_layers(). emodnet.wfs reads geometries simple features (See sf package) transformed 4326 default. Specifying another map projection possible passing EPGS code projection string emodnet_get_layers(crs = \"projection\") crs coordinate reference system (CRS). argument simplify = TRUE stack layers one single tibble. Default FALSE returns list sf objects, one per layer. Note use outputFormat argument example. specifies file type request service, can influence data loaded R. default, data provided GML format geometry type “MULTISURFACE.” However, geometry type widely supported many software tools, including mapview package. address , can request different file type, GeoJSON, delivers geometry “MULTIPOLYGON”—format universally compatible. raised sf community. Run following code quick look layers geometries. plot chunk unnamed-chunk-6 EMODnet provides also physics, chemistry, biological bathymetry data. Explore layers available :","code":"install.packages(c(\"sf\", \"mapview\")) library(emodnet.wfs) library(mapview) library(sf) #> Error in value[[3L]](cond): Package 'sf' version 1.0.18 cannot be unloaded: #> Error in unloadNamespace(package) : namespace 'sf' is imported by 'ows4R', 'mapview', 'leafem', 'leafpop' so cannot be unloaded services <- emodnet_wfs() 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\" seabed_wfs_client <- emodnet_init_wfs_client(service = \"seabed_habitats_general_datasets_and_products\") #> ✔ 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 #> #> 1 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 2 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 3 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 4 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 5 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 6 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 7 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 8 emodnet_wfs seabed_habitats_gene… https://ow… art17_hab… 2013… \"Gridde… WFSF… sf #> 9 emodnet_wfs seabed_habitats_gene… https://ow… carib_eus… 2023… \"Output… WFSF… sf #> 10 emodnet_wfs seabed_habitats_gene… https://ow… biogenic_… Biog… \"This l… WFSF… sf #> # ℹ 62 more rows #> # ℹ 1 more variable: layer_namespace 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 abstract class format #> #> 1 emodnet_wfs https://ows.emodnet-s… seabed_hab… art17_hab… 2013… \"Gridde… WFSF… sf #> 2 emodnet_wfs https://ows.emodnet-s… seabed_hab… art17_hab… 2013… \"Gridde… WFSF… sf #> 3 emodnet_wfs https://ows.emodnet-s… seabed_hab… art17_hab… 2013… \"Gridde… WFSF… sf #> # ℹ 1 more variable: layer_namespace habitats_directive_layers <- emodnet_get_layers( wfs = seabed_wfs_client, layers = habitats_directive_layer_names, 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 #> Geometry type: MULTIPOLYGON #> Dimension: XY #> Bounding box: xmin: 950000 ymin: 940000 xmax: 6510000 ymax: 4820000 #> Projected CRS: ETRS89-extended / LAEA Europe #> First 10 features: #> id habitat_code ms region cs_ms country_code #> 1 art17_hab_1110.13 1110 DK ATL U2+ Denmark #> 2 art17_hab_1110.22 1110 ES MAC U1+ Spain #> 3 art17_hab_1110.25 1110 ES MMAC U1+ Spain #> 4 art17_hab_1110.59 1110 PT MMAC XX Portugal #> 5 art17_hab_1110.56 1110 PT MATL U1- Portugal #> 6 art17_hab_1110.53 1110 PL MBAL U1- Poland #> 7 art17_hab_1110.17 1110 DK MBAL U1- Denmark #> 8 art17_hab_1110.31 1110 FR MATL U1x France #> 9 art17_hab_1110.75 1110 UK MATL U1x United Kingdom #> 10 art17_hab_1110.1 1110 BE ATL U1x Belgium #> habitat_code_uri #> 1 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 2 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 3 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 4 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 5 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 6 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 7 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 8 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 9 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> 10 http://dd.eionet.europa.eu/vocabulary/art17_2018/habitats/1110 #> habitat_description #> 1 Sandbanks which are slightly covered by sea water all the time #> 2 Sandbanks which are slightly covered by sea water all the time #> 3 Sandbanks which are slightly covered by sea water all the time #> 4 Sandbanks which are slightly covered by sea water all the time #> 5 Sandbanks which are slightly covered by sea water all the time #> 6 Sandbanks which are slightly covered by sea water all the time #> 7 Sandbanks which are slightly covered by sea water all the time #> 8 Sandbanks which are slightly covered by sea water all the time #> 9 Sandbanks which are slightly covered by sea water all the time #> 10 Sandbanks which are slightly covered by sea water all the time #> geometry #> 1 MULTIPOLYGON (((4200000 360... #> 2 MULTIPOLYGON (((1950000 950... #> 3 MULTIPOLYGON (((1960000 950... #> 4 MULTIPOLYGON (((1810000 120... #> 5 MULTIPOLYGON (((2730000 173... #> 6 MULTIPOLYGON (((4610000 346... #> 7 MULTIPOLYGON (((4310000 352... #> 8 MULTIPOLYGON (((3790000 314... #> 9 MULTIPOLYGON (((3780000 319... #> 10 MULTIPOLYGON (((3800000 313... mapview(habitats_directive_layers, zcol = \"habitat_description\", burst = TRUE) 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.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 "},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/articles/emodnet.wfs.html","id":"references","dir":"Articles","previous_headings":"More information","what":"References","title":"Accessing and mapping EMODnet data","text":"Blondel, Emmanuel. (2020, May 27). ows4R: R Interface OGC Web-Services (Version 0.1-5). Zenodo. https://doi.org/10.5281/zenodo.3860330 Flanders Marine Institute (2019). Maritime Boundaries Geodatabase, version 11. Available online https://www.marineregions.org/. https://doi.org/10.14284/382. Hadley Wickham, Romain François, Lionel Henry Kirill Müller (2020). dplyr: Grammar Data Manipulation. R package version 1.0.2.https://CRAN.R-project.org/package=dplyr Pebesma E (2018). “Simple Features R: Standardized Support Spatial Vector Data.” 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: language environment statistical computing. R Foundation Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. Tim Appelhans, Florian Detsch, Christoph Reudenbach Stefan Woellauer (2020). mapview: Interactive Viewing Spatial Data R. R package version 2.9.0. https://CRAN.R-project.org/package=mapview","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/emodnet.wfs.html","id":"code","dir":"Articles","previous_headings":"More information","what":"Code","title":"Accessing and mapping EMODnet data","text":"cite emodnet.wfs, please use output citation(package = \"emodnet.wfs\").","code":"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, . #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> 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 2.0.2.9000. 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}, #> url = {https://github.com/EMODnet/emodnet.wfs}, #> doi = {10.14284/679}, #> }"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"initialise-a-wfs-client","dir":"Articles","previous_headings":"","what":"Initialise a WFS client","title":"Using request parameters to limit query results","text":"Let’s start loading emodnet.wfs initialising WFS client human_activities WFS service.","code":"library(emodnet.wfs) wfs <- emodnet_init_wfs_client(\"human_activities\") #> Loading ISO 19139 XML schemas... #> Loading ISO 19115 codelists... #> ✔ WFS client created successfully #> ℹ Service: \"https://ows.emodnet-humanactivities.eu/wfs\" #> ℹ Version: \"2.0.0\""},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"return-single-feature-using-feature-id","dir":"Articles","previous_headings":"","what":"Return single feature using feature ID","title":"Using request parameters to limit query results","text":"can restrict query single feature using featureID providing ID specific feature.","code":"emodnet_get_layers( wfs = wfs, layers = \"pipelines\", featureID = \"pipelines.1\", simplify = TRUE ) #> Simple feature collection with 1 feature and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: -5.87186 ymin: 35.99551 xmax: -5.836784 ymax: 36.12588 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year from_loc to_loc #> 1 pipelines.1 Active 15467.17 #> country_co country notes the_geom #> 1 ES Spain MULTILINESTRING ((-5.87186 ..."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"return-specific-number-of-features","dir":"Articles","previous_headings":"","what":"Return specific number of features","title":"Using request parameters to limit query results","text":"ID feature unknown still want limit number features returned, use count parameter WFS 2.0.0 maxFeatures parameter earlier WFS versions restrict number features returned. example restrict query first feature.","code":"emodnet_get_layers( wfs = wfs, layers = \"pipelines\", count = 1L, simplify = TRUE ) #> Simple feature collection with 1 feature and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: 24.98448 ymin: 60.19078 xmax: 25.01292 ymax: 60.19293 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year from_loc #> 1 pipelines.3463 n/a 1628.03 #> to_loc country_co country notes #> 1 FI Finland Finnish Transport Agency #> the_geom #> 1 MULTILINESTRING ((25.01292 ..."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"order-features","dir":"Articles","previous_headings":"","what":"Order features","title":"Using request parameters to limit query results","text":"Exactly features returned depends internal structure data. However, can sort returned selection based attribute value using sortBy parameter. Say wanted return 5 longest marine pipelines. following example, sort \"length_m\" attribute combine count parameter restrict number features returned. returns first 5 features data ordered \"length_m\". pipelines lengths recorded, skip CQL Filter. default sort operation sort ascending order. WFS servers require sort order specified. case, append +attribute character string passed sortBy. Conversely, add +D sort descending order.","code":"emodnet_get_layers( wfs = wfs, layers = \"pipelines\", sortBy = \"length_m+D\", count = 5L, simplify = TRUE, cql_filter = \"length_m IS NOT NULL\" ) #> Simple feature collection with 5 features and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: 2.249597 ymin: 51.04064 xmax: 28.14228 ymax: 60.52758 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m #> 1 pipelines.3423 Active Gas Nord Stream AG 48 2443360.2 #> 2 pipelines.3424 Planned Gas Nord Stream 2 AG 48 1210867.9 #> 3 pipelines.52 PL0187_PR Active Gas Statoil ASA 42 836155.4 #> 4 pipelines.517 326374 Active Gas GASSCO AS 42 832197.9 #> 5 pipelines.53 PL0186_PR Active Gas Statoil ASA 40 807749.5 #> year from_loc to_loc country_co country notes #> 1 2011 Vyborg, RU Lubmin, GE DE, RU Germany, Russia Schematic Route #> 2 2021 Kurgalsky, RU Lubmin, GE DE, RU Germany, Russia Schematic Route #> 3 Draupner (N) Duinkerken (F) NL Netherlands #> 4 DRAUPNER E DUNKERQUE NO Norway #> 5 Sleipner (N) Zeebrugge (B) NL Netherlands #> the_geom #> 1 MULTILINESTRING ((18.00045 ... #> 2 MULTILINESTRING ((28.14228 ... #> 3 MULTILINESTRING ((2.249597 ... #> 4 MULTILINESTRING ((2.458616 ... #> 5 MULTILINESTRING ((3.298373 ..."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"return-blocks-of-features-from-specific-starting-point","dir":"Articles","previous_headings":"","what":"Return blocks of features from specific starting point","title":"Using request parameters to limit query results","text":"Finally WFS version 2.0.0 (also available earlier versions GeoServer) startIndex parameter introduced, allowing users specify starting index features returned. example, full \"pipelines\" layer contains 3951 features. Setting startIndex n_features - 4 (3947) returns last 4 features. can also combine startIndex count return specific blocks features. example, following query request features 5-9 supplying startIndex 4 count 5. Note startIndex uses 0 starting index (0 indicates first feature), hence set 4 order start 5th feature. combination , example, loop, can used download process large layer might able handled R smaller, manageable blocks features.","code":"#> [1] 3951 n_features <- layer_attributes_tbl(wfs = wfs, layer = \"pipelines\") %>% nrow() n_features startIndex <- n_features - 4L startIndex #> [1] 3947 emodnet_get_layers( wfs = wfs, layers = \"pipelines\", startIndex = startIndex, simplify = TRUE ) #> Simple feature collection with 4 features and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: 3.990801 ymin: 53.53329 xmax: 14.4857 ymax: 55.81712 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year #> 1 pipelines.3948 154802 Not in use Gas NA #> 2 pipelines.3949 154812 Not in use Gas NA #> 3 pipelines.3950 154982 Active Gas NA #> 4 pipelines.3951 155942 Active Gas NA #> from_loc to_loc country_co country notes the_geom #> 1 DE Germany MULTILINESTRING ((14.48506 ... #> 2 DE Germany MULTILINESTRING ((14.4857 5... #> 3 DE Germany MULTILINESTRING ((4.058202 ... #> 4 DE Germany MULTILINESTRING ((4.019116 ... emodnet_get_layers( wfs = wfs, layers = \"pipelines\", startIndex = 4L, count = 6L, simplify = TRUE ) #> Simple feature collection with 6 features and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: -8.336029 ymin: 51.19448 xmax: -7.947595 ymax: 51.8236 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year from_loc #> 1 pipelines.5 F43__3 n/a 10038.745 Kinsale #> 2 pipelines.6 F43__4 n/a 20011.185 Ballycotton #> 3 pipelines.7 F43__5 n/a 10853.853 Kinsale #> 4 pipelines.8 F43__6 n/a 5397.224 Kinsale #> 5 pipelines.9 F43__7 n/a 73853.753 Kinsale #> 6 pipelines.10 F43__8 n/a 56242.374 Seven Heads #> to_loc country_co country notes the_geom #> 1 IE Ireland MULTILINESTRING ((-8.186204... #> 2 IE Ireland MULTILINESTRING ((-8.017066... #> 3 IE Ireland MULTILINESTRING ((-8.017356... #> 4 IE Ireland MULTILINESTRING ((-8.179044... #> 5 IE Ireland MULTILINESTRING ((-7.947595... #> 6 IE Ireland MULTILINESTRING ((-8.217298..."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"return-data-for-specific-attributes","dir":"Articles","previous_headings":"","what":"Return data for specific attributes","title":"Using request parameters to limit query results","text":"Finally, can specify specific attributes want data returned using parameter propertyName. limit data returned single attribute \"country\" just 3 features, use parameters propertyName = \"country\" count = 3. Note limiting data specific attributes, columns returned NA (including spatial, case the_geom, column). limit multiple attributes, separate attribute name character string supplied propertyName comma.","code":"emodnet_get_layers( wfs = wfs, layers = \"pipelines\", propertyName = \"country\", count = 3L, simplify = TRUE ) #> Simple feature collection with 3 features and 13 fields (with 3 geometries empty) #> Geometry type: GEOMETRYCOLLECTION #> Dimension: XY #> Bounding box: xmin: NA ymin: NA xmax: NA ymax: NA #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year from_loc #> 1 pipelines.3463 NA #> 2 pipelines.3702 NA #> 3 pipelines.3707 NA #> to_loc country_co country notes the_geom #> 1 Finland GEOMETRYCOLLECTION EMPTY #> 2 Finland GEOMETRYCOLLECTION EMPTY #> 3 Finland GEOMETRYCOLLECTION EMPTY emodnet_get_layers( wfs = wfs, layers = \"pipelines\", propertyName = \"country,the_geom\", count = 3L, simplify = TRUE ) #> Simple feature collection with 3 features and 13 fields #> Geometry type: MULTILINESTRING #> Dimension: XY #> Bounding box: xmin: 24.90736 ymin: 60.1819 xmax: 27.11348 ymax: 60.5359 #> Geodetic CRS: WGS 84 #> gml_id id status medium operator size_in length_m year from_loc #> 1 pipelines.3463 NA #> 2 pipelines.3702 NA #> 3 pipelines.3707 NA #> to_loc country_co country notes the_geom #> 1 Finland MULTILINESTRING ((25.01292 ... #> 2 Finland MULTILINESTRING ((27.11348 ... #> 3 Finland MULTILINESTRING ((24.90967 ..."},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"limit-spatial-extent-using-a-boundary-box","dir":"Articles","previous_headings":"","what":"Limit spatial extent using a boundary box","title":"Using request parameters to limit query results","text":"bbox parameter allows us search features contained (partially contained) inside box user-defined coordinates. format bbox parameter EMODnet WFS cases (assuming using version 2.0.0) bbox=a1,b1,a2,b2,[crs] a1, b1, a2, b2 represent coordinate values. optional crs parameter used name coordinate reference system (CRS) bbox coordinates (different featureTypes native CRS.) order coordinates passed bbox parameter depends coordinate system used (coordinate syntax isn’t represented x y). following example, specify bounding box proving coordinates order xmin,ymin,xmax,ymax specifying coordinates given EPSG:4326 coordinate reference system.","code":"bbox_response <- emodnet_get_layers( service = \"biology\", layers = \"mediseh_posidonia_nodata\", bbox = \"22.9,34.4,26.8,35.8,EPSG:4326\", simplify = TRUE ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" bbox_response %>% sf::st_cast(to = \"MULTILINESTRING\") %>% mapview::mapview(burst = TRUE, legend = FALSE)"},{"path":"https://emodnet.github.io/emodnet.wfs/articles/request-params.html","id":"non-standard-vendor-parameters","dir":"Articles","previous_headings":"","what":"Non-standard Vendor Parameters","title":"Using request parameters to limit query results","text":"WFS vendor parameters additional, non-standard request parameters defined implementation provide enhanced capabilities. majority EMODnet services GeoServer WFS implementations support variety vendor-specific WFS parameters. One cql_filters. handled explicitly emodnet.wfs package cql_filter argument emodnet_get_layers() documented detail article(\"ecql_filtering\"). additional vendor parameters available GeoServer implementations please refer WFS vendor parameters documentatio Exceptions Chemistry (Eutrophication sea region, Eutrophication) services uses Python Chemistry (Litter) uses MapServer vendor parameters services might differ.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anna Krystalli. Author. Salvador Fernández-Bejarano. Author, maintainer. Thomas J Webb. Contributor. European Marine Observation Data Network (EMODnet) Biology project European Commission's Directorate - General Maritime Affairs Fisheries (DG MARE). Copyright holder. VLIZ (VLAAMS INSTITUUT VOOR DE ZEE). Funder. Maëlle Salmon. Author. Alec L. Robitaille. Reviewer. Reviewed package (v2.0.2.9000) rOpenSci, see . Liz Hare. Reviewer. Reviewed package (v2.0.2.9000) rOpenSci, see . François Michonneau. Reviewer. Reviewed package (v2.0.2.9000) rOpenSci, see .","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Krystalli , Fernández-Bejarano S, Salmon M (????). emodnet.wfs: Access EMODnet Web Feature Service data R. doi:10.14284/679, R package version 2.0.2.9000. Integrated data products created European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded European Union Regulation (EU) 508/2014 European Parliament Council 15 May 2014 European Maritime Fisheries Fund, https://github.com/EMODnet/emodnet.wfs.","code":"@Manual{, 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 2.0.2.9000. 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}, url = {https://github.com/EMODnet/emodnet.wfs}, doi = {10.14284/679}, }"},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"emodnetwfs-access-emodnet-web-feature-service-data-through-r","dir":"","previous_headings":"","what":"Access EMODnet Web Feature Service data through R","title":"Access EMODnet Web Feature Service data through R","text":"goal emodnet.wfs allow interrogation access EMODnet’s, European Marine Observation Data Network, geographic vector data R EMODnet Web Feature Services. Web Feature services (WFS) represent change way geographic information created, modified exchanged Internet offer direct fine-grained access geographic information feature feature property level. Features representation geographic entities, coastlines, marine protected areas, offshore platforms, fishing areas. WFS, features geometry (spatial information) attributes (descriptive data). emodnet.wfs aims offering user-friendly interface rich data.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"installation-and-setup","dir":"","previous_headings":"","what":"Installation and setup","title":"Access EMODnet Web Feature Service data through R","text":"can install development version emodnet.wfs GitHub : want avoid reading messages emodnet.wfs “WFS client created successfully”, set \"emodnet.wfs.quiet\" option TRUE. use EMODnet Web Feature Services subjet rate limiting moment.","code":"# install.packages(\"pak\") pak::pak(\"EMODnet/emodnet.wfs\") options(\"emodnet.wfs.quiet\" = TRUE)"},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"pre-requisites","dir":"","previous_headings":"","what":"Pre-requisites","title":"Access EMODnet Web Feature Service data through R","text":"emodnet.wfs designed compatible modern R geospatial stack, particular output geospatial objects sf objects, say, tibble geometry list-column. users familiar yet geospatial data R, recommend following resources: Spatial Data Science Applications R Edzer Pebesma Roger Bivand. Geocomputation R Robin Lovelace, Jakub Nowosad Jannes Muenchow. documentation assume basic familiarity spatial data: knowing coordinates projections / coordinate reference systems (CRS).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"available-data-sources-services","dir":"","previous_headings":"","what":"Available data sources (services)","title":"Access EMODnet Web Feature Service data through R","text":"available data sources, called services, contained tibble returned emodnet_wfs(). explore available services can use View() usual way explore data.frames.","code":"library(emodnet.wfs) 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\""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"initialise-a-wfs-service-client","dir":"","previous_headings":"","what":"Initialise a WFS Service Client","title":"Access EMODnet Web Feature Service data through R","text":"WFS service client responsible sending requests WFS server processing responses retrieve, display, analyze geospatial features. , initialising client first step interacting EMODnet Web Feature Services. Specify service using service argument.","code":"wfs_bio <- emodnet_init_wfs_client(service = \"biology\") #> Loading ISO 19139 XML schemas... #> Loading ISO 19115 codelists... #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" wfs_bio #> #> ....|-- url: https://geo.vliz.be/geoserver/Emodnetbio/wfs #> ....|-- version: 2.0.0 #> ....|-- capabilities "},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"list-contents-of-a-wfs-get-layer-information-from-a-service-client","dir":"","previous_headings":"","what":"List contents of a WFS: Get layer information from a service client","title":"Access EMODnet Web Feature Service data through R","text":"context Web Feature Service (WFS), layer refers logical grouping geographic features share schema (.e., feature type, geometry, attributes). Layers units data clients can query, retrieve, manipulate WFS. can access information (metadata) layer available EMODnet WFS emodnet_get_wfs_info() can pass wfs client object. can also get info specific layers wfs object: Finally, can get details available services layers server","code":"emodnet_get_wfs_info(service = \"biology\") #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> # A tibble: 35 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 2 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 3 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Cymodo… WFSF… sf #> 4 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 5 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 6 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 7 emodnet_wfs biology https://geo.… mediseh_h… EMOD… \"Haloph… WFSF… sf #> 8 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 10 emodnet_wfs biology https://geo.… mediseh_p… EMOD… \"This d… WFSF… sf #> # ℹ 25 more rows #> # ℹ 1 more variable: layer_namespace emodnet_get_wfs_info(wfs_bio) #> # A tibble: 35 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 2 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 3 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Cymodo… WFSF… sf #> 4 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 5 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 6 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 7 emodnet_wfs biology https://geo.… mediseh_h… EMOD… \"Haloph… WFSF… sf #> 8 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 10 emodnet_wfs biology https://geo.… mediseh_p… EMOD… \"This d… WFSF… sf #> # ℹ 25 more rows #> # ℹ 1 more variable: layer_namespace layers <- c(\"mediseh_zostera_m_pnt\", \"mediseh_posidonia_nodata\") emodnet_get_layer_info(wfs = wfs_bio, layers = layers) #> # A tibble: 2 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs https://geo.vl… biology mediseh_p… EMOD… \"Coastl… WFSF… sf #> 2 emodnet_wfs https://geo.vl… biology mediseh_z… EMOD… \"Zoster… WFSF… sf #> # ℹ 1 more variable: layer_namespace emodnet_get_all_wfs_info()"},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"get-data-from-a-data-source-get-layers","dir":"","previous_headings":"","what":"Get data from a data source: get layers","title":"Access EMODnet Web Feature Service data through R","text":"can extract layers directly wfs object using layer names. layers downloaded sf objects output list named element layer requested. argument simplify = TRUE stack layers one single tibble, possible (instance column names , otherwise fails). default, emodnet_get_layers() returns list sf objects, one per layer. can change output Coordinate Reference System (CRS), defines geographic data mapped Earth’s surface, argument crs. can also extract layers using WFS service name. Layers can also returned single sf object argument simplify. TRUE function try reduce layers single sf. attempting reduce fails, error: Using simplify = TRUE also useful returning sf object rather list single layer request.","code":"emodnet_get_layers(wfs = wfs_bio, layers = layers) #> $mediseh_zostera_m_pnt #> Simple feature collection with 54 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 33.07783 xmax: 15.35766 ymax: 45.72451 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> 9 mediseh_zostera_m_pnt.9 0 Italia POINT (13.71831 45.70017) #> 10 mediseh_zostera_m_pnt.10 0 Italia POINT (13.16378 45.72451) #> #> $mediseh_posidonia_nodata #> Simple feature collection with 465 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -2.1798 ymin: 30.26623 xmax: 34.60767 ymax: 45.47668 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.503233 MULTICURVE (LINESTRING (27.... #> 2 mediseh_posidonia_nodata.2 0 75.379502 MULTICURVE (LINESTRING (23.... #> 3 mediseh_posidonia_nodata.3 0 38.627764 MULTICURVE (LINESTRING (22.... #> 4 mediseh_posidonia_nodata.4 0 110.344802 MULTICURVE (LINESTRING (19.... #> 5 mediseh_posidonia_nodata.13 0 66.997461 MULTICURVE (LINESTRING (9.1... #> 6 mediseh_posidonia_nodata.14 0 18.090640 MULTICURVE (LINESTRING (9.7... #> 7 mediseh_posidonia_nodata.15 0 16.618978 MULTICURVE (LINESTRING (9.8... #> 8 mediseh_posidonia_nodata.16 0 1.913773 MULTICURVE (LINESTRING (10.... #> 9 mediseh_posidonia_nodata.83 0 2.173447 MULTICURVE (LINESTRING (15.... #> 10 mediseh_posidonia_nodata.84 0 2.817453 MULTICURVE (LINESTRING (15.... emodnet_get_layers(wfs = wfs_bio, layers = layers, crs = 3857) #> ℹ crs transformed to 3857. #> ℹ crs transformed to 3857. #> $mediseh_zostera_m_pnt #> Simple feature collection with 54 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -463885.4 ymin: 3905639 xmax: 1709607 ymax: 5736311 #> Projected CRS: WGS 84 / Pseudo-Mercator #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-290893.4 4399707) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-428201.3 4404494) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-440578.6 4400520) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-449698.6 4403229) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-456430.1 4400610) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-463885.4 4399075) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-141193.9 4517168) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (539748.1 5369436) #> 9 mediseh_zostera_m_pnt.9 0 Italia POINT (1527115 5732431) #> 10 mediseh_zostera_m_pnt.10 0 Italia POINT (1465385 5736311) #> #> $mediseh_posidonia_nodata #> Simple feature collection with 465 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -242654.3 ymin: 3537818 xmax: 3852508 ymax: 5696879 #> Projected CRS: WGS 84 / Pseudo-Mercator #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.503233 MULTICURVE (LINESTRING (302... #> 2 mediseh_posidonia_nodata.2 0 75.379502 MULTICURVE (LINESTRING (257... #> 3 mediseh_posidonia_nodata.3 0 38.627764 MULTICURVE (LINESTRING (246... #> 4 mediseh_posidonia_nodata.4 0 110.344802 MULTICURVE (LINESTRING (221... #> 5 mediseh_posidonia_nodata.13 0 66.997461 MULTICURVE (LINESTRING (101... #> 6 mediseh_posidonia_nodata.14 0 18.090640 MULTICURVE (LINESTRING (108... #> 7 mediseh_posidonia_nodata.15 0 16.618978 MULTICURVE (LINESTRING (110... #> 8 mediseh_posidonia_nodata.16 0 1.913773 MULTICURVE (LINESTRING (121... #> 9 mediseh_posidonia_nodata.83 0 2.173447 MULTICURVE (LINESTRING (169... #> 10 mediseh_posidonia_nodata.84 0 2.817453 MULTICURVE (LINESTRING (169... emodnet_get_layers( service = \"biology\", layers = c(\"mediseh_zostera_m_pnt\", \"mediseh_posidonia_nodata\") ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> $mediseh_zostera_m_pnt #> Simple feature collection with 54 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 33.07783 xmax: 15.35766 ymax: 45.72451 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> 9 mediseh_zostera_m_pnt.9 0 Italia POINT (13.71831 45.70017) #> 10 mediseh_zostera_m_pnt.10 0 Italia POINT (13.16378 45.72451) #> #> $mediseh_posidonia_nodata #> Simple feature collection with 465 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -2.1798 ymin: 30.26623 xmax: 34.60767 ymax: 45.47668 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.503233 MULTICURVE (LINESTRING (27.... #> 2 mediseh_posidonia_nodata.2 0 75.379502 MULTICURVE (LINESTRING (23.... #> 3 mediseh_posidonia_nodata.3 0 38.627764 MULTICURVE (LINESTRING (22.... #> 4 mediseh_posidonia_nodata.4 0 110.344802 MULTICURVE (LINESTRING (19.... #> 5 mediseh_posidonia_nodata.13 0 66.997461 MULTICURVE (LINESTRING (9.1... #> 6 mediseh_posidonia_nodata.14 0 18.090640 MULTICURVE (LINESTRING (9.7... #> 7 mediseh_posidonia_nodata.15 0 16.618978 MULTICURVE (LINESTRING (9.8... #> 8 mediseh_posidonia_nodata.16 0 1.913773 MULTICURVE (LINESTRING (10.... #> 9 mediseh_posidonia_nodata.83 0 2.173447 MULTICURVE (LINESTRING (15.... #> 10 mediseh_posidonia_nodata.84 0 2.817453 MULTICURVE (LINESTRING (15.... emodnet_get_layers( wfs = wfs_bio, layers = layers, simplify = TRUE ) #> Error in `value[[3L]]()`: #> ! Cannot reduce layers. #> ℹ Try again with `simplify = FALSE` emodnet_get_layers( service = \"biology\", layers = c(\"mediseh_posidonia_nodata\"), simplify = TRUE ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> Simple feature collection with 465 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -2.1798 ymin: 30.26623 xmax: 34.60767 ymax: 45.47668 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.503233 MULTICURVE (LINESTRING (27.... #> 2 mediseh_posidonia_nodata.2 0 75.379502 MULTICURVE (LINESTRING (23.... #> 3 mediseh_posidonia_nodata.3 0 38.627764 MULTICURVE (LINESTRING (22.... #> 4 mediseh_posidonia_nodata.4 0 110.344802 MULTICURVE (LINESTRING (19.... #> 5 mediseh_posidonia_nodata.13 0 66.997461 MULTICURVE (LINESTRING (9.1... #> 6 mediseh_posidonia_nodata.14 0 18.090640 MULTICURVE (LINESTRING (9.7... #> 7 mediseh_posidonia_nodata.15 0 16.618978 MULTICURVE (LINESTRING (9.8... #> 8 mediseh_posidonia_nodata.16 0 1.913773 MULTICURVE (LINESTRING (10.... #> 9 mediseh_posidonia_nodata.83 0 2.173447 MULTICURVE (LINESTRING (15.... #> 10 mediseh_posidonia_nodata.84 0 2.817453 MULTICURVE (LINESTRING (15...."},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"help-needed","dir":"","previous_headings":"","what":"Help needed?","title":"Access EMODnet Web Feature Service data through R","text":"get unexpected error, Look EMODnet monitor; Open issue repository.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"unlock-the-full-potential-of-the-emodnet-web-services-access-raster-and-gridded-datasets","dir":"","previous_headings":"","what":"Unlock the Full Potential of the EMODnet Web Services: Access Raster and Gridded datasets.","title":"Access EMODnet Web Feature Service data through R","text":"EMODnet hosts wealth marine maritime data distributed three complementary web services: WFS, WCS, ERDDAP. Web services allow users retrieve data programmatically remote servers, eliminating need manual downloads. particularly useful handling large datasets conducting dynamic analyses. services tailored different data types research needs, together, ensure seamless access EMODnet vector, raster, gridded datasets. Vector data, shipwrecks boundaries, accessible emodnet.wfs via Web Feature Services (WFS). Complementary, raster gridded datasets available Web Coverage Services (WCS) ERDDAP respectively.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"access-emodnet-raster-data-through-web-coverage-services-with-emodnetwcs-in-r","dir":"","previous_headings":"Unlock the Full Potential of the EMODnet Web Services: Access Raster and Gridded datasets.","what":"Access EMODnet raster data through Web Coverage Services with EMODnetWCS in R","title":"Access EMODnet Web Feature Service data through R","text":"EMODnet raster datasets, habitat maps bathymetry, available Web Coverage Services (WCS). data continuous, gridded, often used spatial visualization environmental modeling. EMODnetWCS R package provides tools retrieve process raser datasets, similar fashion emodnet.wfs. Extensive documentation available EMODnetWCS website.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"access-emodnet-gridded-and-tabular-datasets-through-the-erddap-server-and-rerddap-in-r","dir":"","previous_headings":"Unlock the Full Potential of the EMODnet Web Services: Access Raster and Gridded datasets.","what":"Access EMODnet gridded and tabular datasets through the ERDDAP Server and rerddap in R","title":"Access EMODnet Web Feature Service data through R","text":"WFS WCS EMODnet services based federated system: EMODnet thematic lot manages servers data, ensuring data exposed via WFS WCS. twin R packages emodnet.wfs EMODnetWCS simplify access entry points collecting single places, packages . contrast, EMODnet ERDDAP Server centrally managed EMODnet Central Portal, offering single access point gridded tabular datasets. ERDDAP simplifies access datasets digital terrain models, vessel density environmental data. particularly suited large-scale, multidimensional data analysis. R, rerddap package allows users query subset ERDDAP data programmatically, enabling efficient analysis integration workflows. example, researchers can retrieve datasets vessel density. functionalities available rerddap. Feel free explore rerddap website find else can EMODnet datasets ERDDAP.","code":"# install.packages(\"rerrdap\") library(rerddap) #> Registered S3 method overwritten by 'hoardr': #> method from #> print.cache_info httr # This is the url where the EMODnet ERDDAP server is located erddap_url <- \"https://erddap.emodnet.eu/erddap/\" # Inspect all available datasets ed_datasets(url = erddap_url) #> # A tibble: 8 × 16 #> griddap Subset tabledap Make.A.Graph wms files Title Summary FGDC ISO.19115 #> #> 1 \"\" \"/erd… /erddap… /erddap/tab… \"\" \"\" * Th… \"This … \"\" \"\" #> 2 \"\" \"\" /erddap… /erddap/tab… \"\" \"/er… EMOD… \"The d… \"\" \"\" #> 3 \"\" \"\" /erddap… /erddap/tab… \"\" \"/er… EMOD… \"The d… \"\" \"\" #> 4 \"\" \"/erd… /erddap… /erddap/tab… \"\" \"/er… EMOD… \"The d… \"/er… \"/erddap… #> 5 \"\" \"\" /erddap… /erddap/tab… \"\" \"/er… Pres… \"The p… \"/er… \"/erddap… #> 6 \"\" \"\" /erddap… /erddap/tab… \"\" \"\" PSMS… \"Perma… \"\" \"\" #> 7 \"\" \"\" /erddap… /erddap/tab… \"\" \"/er… PSMS… \"Perma… \"\" \"\" #> 8 \"\" \"/erd… /erddap… /erddap/tab… \"\" \"/er… TAO/… \"This … \"/er… \"/erddap… #> # ℹ 6 more variables: Info , Background.Info , RSS , #> # Email , Institution , Dataset.ID # Find datasets with the key words \"vessel density\" ed_search(query = \"vessel density\", url = erddap_url) #> # A tibble: 16 × 2 #> title dataset_id #> #> 1 Vessel Density humanactivities_9f… #> 2 Vessel Density humanactivities_e9… #> 3 Vessel traffic density, 2019, All EMODPACE_VD_All #> 4 Vessel traffic density, 2019, Cargo EMODPACE_VD_09_Car… #> 5 Vessel traffic density, 2019, Dredging or underwater ops EMODPACE_VD_03_Dre… #> 6 Vessel traffic density, 2019, Fishing EMODPACE_VD_01_Fis… #> 7 Vessel traffic density, 2019, High Speed craft EMODPACE_VD_06_High #> 8 Vessel traffic density, 2019, Miliary and law enforcement EMODPACE_VD_11_Mil… #> 9 Vessel traffic density, 2019, Other EMODPACE_VD_00_Oth… #> 10 Vessel traffic density, 2019, Passenger EMODPACE_VD_08_Pas… #> 11 Vessel traffic density, 2019, Pleasure craft EMODPACE_VD_05_Ple… #> 12 Vessel traffic density, 2019, Sailing EMODPACE_VD_04_Sai… #> 13 Vessel traffic density, 2019, Service EMODPACE_VD_02_Ser… #> 14 Vessel traffic density, 2019, Tanker EMODPACE_VD_10_Tan… #> 15 Vessel traffic density, 2019, Tug and Towing EMODPACE_VD_07_Tug #> 16 Vessel traffic density, 2019, Unknown EMODPACE_VD_12_Unk… # Inspect more info about the vessel density dataset, using its identifier human_activities_data_info <- info(datasetid = \"humanactivities_9f8a_3389_f08a\", url = erddap_url) human_activities_data_info #> humanactivities_9f8a_3389_f08a #> Base URL: https://erddap.emodnet.eu/erddap #> Dataset Type: griddap #> Dimensions (range): #> time: (2017-01-01T00:00:00Z, 2021-12-01T00:00:00Z) #> y: (604500.0, 7034500.0) #> x: (-622500.0, 6884500.0) #> Variables: #> vd: #> Units: seconds # Retrieve the vessel density at a particular time period year_2020_gridded_data <- griddap(datasetx = human_activities_data_info, time = c(\"2020-03-18\", \"2020-03-19\")) #> info() output passed to x; setting base url to: https://erddap.emodnet.eu/erddap head(year_2020_gridded_data$data) #> x y time vd #> 1 -622500 7034500 2020-04-01T00:00:00Z NA #> 2 -621500 7034500 2020-04-01T00:00:00Z NA #> 3 -620500 7034500 2020-04-01T00:00:00Z NA #> 4 -619500 7034500 2020-04-01T00:00:00Z NA #> 5 -618500 7034500 2020-04-01T00:00:00Z NA #> 6 -617500 7034500 2020-04-01T00:00:00Z NA"},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Access EMODnet Web Feature Service data through R","text":"cite emodnet.wfs, please use output citation(package = \"emodnet.wfs\").","code":"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, . #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> 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 2.0.2.9000. 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}, #> url = {https://github.com/EMODnet/emodnet.wfs}, #> doi = {10.14284/679}, #> }"},{"path":"https://emodnet.github.io/emodnet.wfs/index.html","id":"acknowledgements","dir":"","previous_headings":"","what":"Acknowledgements","title":"Access EMODnet Web Feature Service data through R","text":"package started Sheffield University EMODnet Biology WP4 data products workshop June 2020.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet.wfs-package.html","id":null,"dir":"Reference","previous_headings":"","what":"emodnet.wfs: Access EMODnet Web Feature Service data through R — emodnet.wfs-package","title":"emodnet.wfs: Access EMODnet Web Feature Service data through R — emodnet.wfs-package","text":"Access interrogate EMODnet (European Marine Observation Data Network) Web Feature Service data R.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet.wfs-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"emodnet.wfs: Access EMODnet Web Feature Service data through R — emodnet.wfs-package","text":"Maintainer: Salvador Fernández-Bejarano salvador.fernandez@vliz.(ORCID) Authors: Anna Krystalli annakrystalli@googlemail.com (ORCID) Maëlle Salmon msmaellesalmon@gmail.com (ORCID) contributors: Thomas J Webb t.j.webb@sheffield.ac.uk [contributor] European Marine Observation Data Network (EMODnet) Biology project European Commission's Directorate - General Maritime Affairs Fisheries (DG MARE) bio@emodnet.eu [copyright holder] VLIZ (VLAAMS INSTITUUT VOOR DE ZEE) info@vliz.[funder] Alec L. Robitaille (ORCID) (Reviewed package (v2.0.2.9000) rOpenSci, see .) [reviewer] Liz Hare (ORCID) (Reviewed package (v2.0.2.9000) rOpenSci, see .) [reviewer] François Michonneau francois.michonneau@gmail.com (ORCID) (Reviewed package (v2.0.2.9000) rOpenSci, see .) [reviewer]","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":null,"dir":"Reference","previous_headings":"","what":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"Performs WFS getFeature request layers wfs object specified EMODnet Service. Filtering layer features can also handled via ECQL language filters.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"","code":"emodnet_get_layers( wfs = NULL, service = NULL, service_version = NULL, layers, crs = NULL, cql_filter = NULL, simplify = FALSE, reduce_layers = deprecated(), ... )"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layers character vector layer names. get info layers, including layer_name use emodnet_get_wfs_info(). crs integer. EPSG code output crs. NULL (default), layers returned original crs. cql_filter character. Features returned can filtered using valid Extended Common Query Language (ECQL) filtering statements (https://docs.geoserver.org/stable/en/user/filter/ecql_reference.html). one : character string character vector length 1. Filter recycled across layers requested. character vector length equal length layers. Filter matched layers sequentially. Elements containing NA ignored named character vector. filter applied layer corresponding filter name. Filters names correspond layers ignored. Layers without corresponding filters returned whole. simplify whether reduce output layers single sf object. works column names . reduce_layers use simplify. ... additional vendor parameter arguments passed ows4R::GetFeature(). example, including count = 1 returns first available feature. outputFormat = \"CSV\" (outputFormat = \"JSON\") might help downloading bigger datasets.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"simplify = FALSE (default), list sf objects, one element layer. layers download unsuccessful NULL. simplify = TRUE, layers reduced (possible: column names ) single sf containing data layers. NULL layers ignored. simplify = TRUE can also used return sf single layer request instead list length 1.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":"big-downloads","dir":"Reference","previous_headings":"","what":"Big downloads","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"layer really big (like \"abiotic_observations\" \"biology_occurrence_data\" service), might consider combination ideas: using outputFormat = \"CSV\"; filtering using cql_filters bounding boxes (possibly splitting area interests several requests); Using EMODnet's download toolbox.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_layers.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get EMODnet WFS datasets (layers) — emodnet_get_layers","text":"","code":"# Layers as character vector emodnet_get_layers( service = \"biology\", layers = c(\"mediseh_zostera_m_pnt\", \"mediseh_posidonia_nodata\") ) #> Loading ISO 19139 XML schemas... #> Loading ISO 19115 codelists... #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> $mediseh_zostera_m_pnt #> Simple feature collection with 54 features and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -4.167154 ymin: 33.07783 xmax: 15.35766 ymax: 45.72451 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> 2 mediseh_zostera_m_pnt.2 0 Spagna POINT (-3.846598 36.75127) #> 3 mediseh_zostera_m_pnt.3 0 Spagna POINT (-3.957785 36.72266) #> 4 mediseh_zostera_m_pnt.4 0 Spagna POINT (-4.039712 36.74217) #> 5 mediseh_zostera_m_pnt.5 0 Spagna POINT (-4.100182 36.72331) #> 6 mediseh_zostera_m_pnt.6 0 Spagna POINT (-4.167154 36.71226) #> 7 mediseh_zostera_m_pnt.7 0 Spagna POINT (-1.268366 37.55796) #> 8 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> 9 mediseh_zostera_m_pnt.9 0 Italia POINT (13.71831 45.70017) #> 10 mediseh_zostera_m_pnt.10 0 Italia POINT (13.16378 45.72451) #> #> $mediseh_posidonia_nodata #> Simple feature collection with 465 features and 3 fields #> Geometry type: MULTICURVE #> Dimension: XY #> Bounding box: xmin: -2.1798 ymin: 30.26623 xmax: 34.60767 ymax: 45.47668 #> Geodetic CRS: WGS 84 #> First 10 features: #> gml_id id km the_geom #> 1 mediseh_posidonia_nodata.1 0 291.503233 MULTICURVE (LINESTRING (27.... #> 2 mediseh_posidonia_nodata.2 0 75.379502 MULTICURVE (LINESTRING (23.... #> 3 mediseh_posidonia_nodata.3 0 38.627764 MULTICURVE (LINESTRING (22.... #> 4 mediseh_posidonia_nodata.4 0 110.344802 MULTICURVE (LINESTRING (19.... #> 5 mediseh_posidonia_nodata.13 0 66.997461 MULTICURVE (LINESTRING (9.1... #> 6 mediseh_posidonia_nodata.14 0 18.090640 MULTICURVE (LINESTRING (9.7... #> 7 mediseh_posidonia_nodata.15 0 16.618978 MULTICURVE (LINESTRING (9.8... #> 8 mediseh_posidonia_nodata.16 0 1.913773 MULTICURVE (LINESTRING (10.... #> 9 mediseh_posidonia_nodata.83 0 2.173447 MULTICURVE (LINESTRING (15.... #> 10 mediseh_posidonia_nodata.84 0 2.817453 MULTICURVE (LINESTRING (15.... #> # Usage of cql_filter emodnet_get_layers( service = \"biology\", layers = \"mediseh_zostera_m_pnt\", cql_filter = \"country = 'Francia'\" ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> $mediseh_zostera_m_pnt #> Simple feature collection with 1 feature and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: 4.84864 ymin: 43.37637 xmax: 4.84864 ymax: 43.37637 #> Geodetic CRS: WGS 84 #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.8 0 Francia POINT (4.84864 43.37637) #> # Usage of vendor parameter emodnet_get_layers( service = \"biology\", layers = \"mediseh_zostera_m_pnt\", count = 1 ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> $mediseh_zostera_m_pnt #> Simple feature collection with 1 feature and 3 fields #> Geometry type: POINT #> Dimension: XY #> Bounding box: xmin: -2.61314 ymin: 36.71681 xmax: -2.61314 ymax: 36.71681 #> Geodetic CRS: WGS 84 #> gml_id id country the_geom #> 1 mediseh_zostera_m_pnt.1 0 Spagna POINT (-2.61314 36.71681) #> # Usage of csv output data <- emodnet_get_layers( service = \"biology_occurrence_data\", layers = \"abiotic_observations\", outputFormat = \"CSV\" ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Dataportal/wfs\" #> ℹ Version: \"2.0.0\" #> Rows: 1000000 Columns: 37 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (17): FID, value, datatype, season, parametername, parameterunit, datap... #> dbl (11): id, latitude, longitude, depth, standardparameterid, dataprovider... #> lgl (8): aphiaid, lod, loq, class, classunit, classcode, dateprecision, sc... #> dttm (1): datetime #> #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. str(data[[\"abiotic_observations\"]]) #> spc_tbl_ [1,000,000 × 37] (S3: spec_tbl_df/tbl_df/tbl/data.frame) #> $ FID : chr [1:1000000] \"abiotic_observations.fid-6c0eccf5_1936280e682_3fa9\" \"abiotic_observations.fid-6c0eccf5_1936280e682_3faa\" \"abiotic_observations.fid-6c0eccf5_1936280e682_3fab\" \"abiotic_observations.fid-6c0eccf5_1936280e682_3fac\" ... #> $ id : num [1:1000000] 4.59e+08 4.59e+08 4.59e+08 4.59e+08 4.59e+08 ... #> $ aphiaid : logi [1:1000000] NA NA NA NA NA NA ... #> $ latitude : num [1:1000000] 51.3 51.3 51.3 51.3 51.3 ... #> $ longitude : num [1:1000000] 4.26 4.26 4.26 4.26 4.26 ... #> $ depth : num [1:1000000] NA NA NA NA NA NA NA NA NA NA ... #> $ datetime : POSIXct[1:1000000], format: \"2009-03-01 00:50:00\" \"2009-03-01 01:00:00\" ... #> $ value : chr [1:1000000] \"-\" \"-\" \"-\" \"-\" ... #> $ lod : logi [1:1000000] NA NA NA NA NA NA ... #> $ loq : logi [1:1000000] NA NA NA NA NA NA ... #> $ standardparameterid: num [1:1000000] 272 272 272 272 272 272 272 272 272 272 ... #> $ dataproviderid : num [1:1000000] 6 6 6 6 6 6 6 6 6 6 ... #> $ imisdatasetid : num [1:1000000] 5242 5242 5242 5242 5242 ... #> $ dataficheid : num [1:1000000] 61 61 61 61 61 61 61 61 61 61 ... #> $ seriesid : num [1:1000000] 2032 2032 2032 2032 2032 ... #> $ datatype : chr [1:1000000] \"NC\" \"NC\" \"NC\" \"NC\" ... #> $ class : logi [1:1000000] NA NA NA NA NA NA ... #> $ classunit : logi [1:1000000] NA NA NA NA NA NA ... #> $ classcode : logi [1:1000000] NA NA NA NA NA NA ... #> $ season : chr [1:1000000] \"winter\" \"winter\" \"winter\" \"winter\" ... #> $ parametername : chr [1:1000000] \"Geleidendheid (Conductiviteit) in mS/cm in de waterkolom\" \"Geleidendheid (Conductiviteit) in mS/cm in de waterkolom\" \"Geleidendheid (Conductiviteit) in mS/cm in de waterkolom\" \"Geleidendheid (Conductiviteit) in mS/cm in de waterkolom\" ... #> $ parameterunit : chr [1:1000000] \"mS/cm\" \"mS/cm\" \"mS/cm\" \"mS/cm\" ... #> $ dataprovider : chr [1:1000000] \"MOW MT - Maritieme Toegang\" \"MOW MT - Maritieme Toegang\" \"MOW MT - Maritieme Toegang\" \"MOW MT - Maritieme Toegang\" ... #> $ datasettitle : chr [1:1000000] \"Continuous measurements in Deurganckdok\" \"Continuous measurements in Deurganckdok\" \"Continuous measurements in Deurganckdok\" \"Continuous measurements in Deurganckdok\" ... #> $ datafichetitle : chr [1:1000000] \"P-FC-V-001 - Geleidbaarheid - Continu\" \"P-FC-V-001 - Geleidbaarheid - Continu\" \"P-FC-V-001 - Geleidbaarheid - Continu\" \"P-FC-V-001 - Geleidbaarheid - Continu\" ... #> $ stationname : chr [1:1000000] \"DGD S-Middle Top\" \"DGD S-Middle Top\" \"DGD S-Middle Top\" \"DGD S-Middle Top\" ... #> $ gid : num [1:1000000] 7 7 7 7 7 7 7 7 7 7 ... #> $ seasonid : num [1:1000000] 1 1 1 1 1 1 1 1 1 1 ... #> $ unit : chr [1:1000000] \"mS/cm\" \"mS/cm\" \"mS/cm\" \"mS/cm\" ... #> $ category : chr [1:1000000] \"saliniteit, chloriniteit en geleidendheid\" \"saliniteit, chloriniteit en geleidendheid\" \"saliniteit, chloriniteit en geleidendheid\" \"saliniteit, chloriniteit en geleidendheid\" ... #> $ the_geom : chr [1:1000000] \"POINT (51.29098351 4.263097996)\" \"POINT (51.29098351 4.263097996)\" \"POINT (51.29098351 4.263097996)\" \"POINT (51.29098351 4.263097996)\" ... #> $ valuesign : chr [1:1000000] \"=\" \"=\" \"=\" \"=\" ... #> $ dateprecision : logi [1:1000000] NA NA NA NA NA NA ... #> $ standard_name : chr [1:1000000] \"BODC\" \"BODC\" \"BODC\" \"BODC\" ... #> $ externalid : chr [1:1000000] \"CNDCST01\" \"CNDCST01\" \"CNDCST01\" \"CNDCST01\" ... #> $ external_name : chr [1:1000000] \"Electrical conductivity of the water body by CTD\" \"Electrical conductivity of the water body by CTD\" \"Electrical conductivity of the water body by CTD\" \"Electrical conductivity of the water body by CTD\" ... #> $ scientificname : logi [1:1000000] NA NA NA NA NA NA ... #> - attr(*, \"spec\")= #> .. cols( #> .. FID = col_character(), #> .. id = col_double(), #> .. aphiaid = col_logical(), #> .. latitude = col_double(), #> .. longitude = col_double(), #> .. depth = col_double(), #> .. datetime = col_datetime(format = \"\"), #> .. value = col_character(), #> .. lod = col_logical(), #> .. loq = col_logical(), #> .. standardparameterid = col_double(), #> .. dataproviderid = col_double(), #> .. imisdatasetid = col_double(), #> .. dataficheid = col_double(), #> .. seriesid = col_double(), #> .. datatype = col_character(), #> .. class = col_logical(), #> .. classunit = col_logical(), #> .. classcode = col_logical(), #> .. season = col_character(), #> .. parametername = col_character(), #> .. parameterunit = col_character(), #> .. dataprovider = col_character(), #> .. datasettitle = col_character(), #> .. datafichetitle = col_character(), #> .. stationname = col_character(), #> .. gid = col_double(), #> .. seasonid = col_double(), #> .. unit = col_character(), #> .. category = col_character(), #> .. the_geom = col_character(), #> .. valuesign = col_character(), #> .. dateprecision = col_logical(), #> .. standard_name = col_character(), #> .. externalid = col_character(), #> .. external_name = col_character(), #> .. scientificname = col_logical() #> .. ) #> - attr(*, \"problems\")="},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"Get WFS available layer information","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"","code":"emodnet_get_layer_info(wfs, layers) emodnet_get_wfs_info(wfs = NULL, service = NULL, service_version = NULL) emodnet_get_all_wfs_info()"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). layers character vector layer names. get info layers, including layer_name use emodnet_get_wfs_info(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\".","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"tibble containing metadata layer available service.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"minimize number requests sent webservices, functions use memoise cache results inside active R session. clear cache, re-start R run memoise::forget(emodnet_get_wfs_info)/ memoise::forget(emodnet_get_layer_info).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"emodnet_get_layer_info(): Get metadata specific layers. Requires wfs object input. emodnet_get_wfs_info(): Get info layers EMODnet WFS service. emodnet_get_all_wfs_info(): Get metadata layers available services server.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata about data available from the different services: data (layers) from a data source (service), metadata on layers from a service, metadata on layers from all services. — emodnet_get_layer_info","text":"","code":"emodnet_get_wfs_info(service = \"bathymetry\") #> ✔ WFS client created successfully #> ℹ Service: \"https://ows.emodnet-bathymetry.eu/wfs\" #> ℹ Version: \"2.0.0\" #> # A tibble: 7 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs bathymetry https://ows.e… download_… Bath… \"Downlo… WFSF… sf #> 2 emodnet_wfs bathymetry https://ows.e… contours Dept… \"Genera… WFSF… sf #> 3 emodnet_wfs bathymetry https://ows.e… hr_bathym… High… \"Layer … WFSF… sf #> 4 emodnet_wfs bathymetry https://ows.e… quality_i… Qual… \"Repres… WFSF… sf #> 5 emodnet_wfs bathymetry https://ows.e… sea_names Sea … \"Mainta… WFSF… sf #> 6 emodnet_wfs bathymetry https://ows.e… source_re… Sour… \"Covera… WFSF… sf #> 7 emodnet_wfs bathymetry https://ows.e… undersea_… unde… \"\" WFSF… sf #> # ℹ 1 more variable: layer_namespace # Query a wfs object wfs_bio <- emodnet_init_wfs_client(\"biology\") #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" emodnet_get_wfs_info(wfs_bio) #> # A tibble: 35 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 2 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Coral … WFSF… sf #> 3 emodnet_wfs biology https://geo.… mediseh_c… EMOD… \"Cymodo… WFSF… sf #> 4 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 5 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 6 emodnet_wfs biology https://geo.… Species_g… EMOD… \"This d… WFSF… sf #> 7 emodnet_wfs biology https://geo.… mediseh_h… EMOD… \"Haloph… WFSF… sf #> 8 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 9 emodnet_wfs biology https://geo.… mediseh_m… EMOD… \"Maërl … WFSF… sf #> 10 emodnet_wfs biology https://geo.… mediseh_p… EMOD… \"This d… WFSF… sf #> # ℹ 25 more rows #> # ℹ 1 more variable: layer_namespace # Get info for specific layers from wfs object layers <- c(\"mediseh_zostera_m_pnt\", \"mediseh_posidonia_nodata\") emodnet_get_layer_info(wfs = wfs_bio, layers = layers) #> # A tibble: 2 × 9 #> # Rowwise: #> data_source service_name service_url layer_name title abstract class format #> #> 1 emodnet_wfs https://geo.vl… biology mediseh_p… EMOD… \"Coastl… WFSF… sf #> 2 emodnet_wfs https://geo.vl… biology mediseh_z… EMOD… \"Zoster… WFSF… sf #> # ℹ 1 more variable: layer_namespace "},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_init_wfs_client.html","id":null,"dir":"Reference","previous_headings":"","what":"Connect to a data source (service) — emodnet_init_wfs_client","title":"Connect to a data source (service) — emodnet_init_wfs_client","text":"Initialise EMODnet WFS client","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_init_wfs_client.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Connect to a data source (service) — emodnet_init_wfs_client","text":"","code":"emodnet_init_wfs_client(service, service_version = NULL, logger = NULL)"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_init_wfs_client.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Connect to a data source (service) — emodnet_init_wfs_client","text":"service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". logger logger. Either NULL (logging info), \"INFO\" (log ows4R requests) \"DEBUG\" (including curl details).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_init_wfs_client.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Connect to a data source (service) — emodnet_init_wfs_client","text":"ows4R::WFSClient R6 object methods interfacing OGC Web Feature Service.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_init_wfs_client.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Connect to a data source (service) — emodnet_init_wfs_client","text":"","code":"wfs <- emodnet_init_wfs_client(service = \"bathymetry\") #> ✔ WFS client created successfully #> ℹ Service: \"https://ows.emodnet-bathymetry.eu/wfs\" #> ℹ Version: \"2.0.0\""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_wfs.html","id":null,"dir":"Reference","previous_headings":"","what":"Which data sources (services) are available? — emodnet_wfs","title":"Which data sources (services) are available? — emodnet_wfs","text":"Available EMODnet Web Feature Services","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_wfs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Which data sources (services) are available? — emodnet_wfs","text":"","code":"emodnet_wfs()"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_wfs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Which data sources (services) are available? — emodnet_wfs","text":"Tibble available EMODnet Web Feature Services","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/emodnet_wfs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Which data sources (services) are available? — emodnet_wfs","text":"","code":"emodnet_wfs() #> # A tibble: 17 × 2 #> service_name service_url #> #> 1 bathymetry https://ows.… #> 2 biology https://geo.… #> 3 biology_occurrence_data https://geo.… #> 4 chemistry_cdi_data_discovery_and_access_service https://geo-… #> 5 chemistry_cdi_distribution_observations_per_category_and_region https://geo-… #> 6 chemistry_contaminants https://geos… #> 7 chemistry_marine_litter https://www.… #> 8 geology_coastal_behavior https://driv… #> 9 geology_events_and_probabilities https://driv… #> 10 geology_marine_minerals https://driv… #> 11 geology_sea_floor_bedrock https://driv… #> 12 geology_seabed_substrate_maps https://driv… #> 13 geology_submerged_landscapes https://driv… #> 14 human_activities https://ows.… #> 15 physics https://prod… #> 16 seabed_habitats_general_datasets_and_products https://ows.… #> 17 seabed_habitats_individual_habitat_map_and_model_datasets https://ows.…"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_descriptions.html","id":null,"dir":"Reference","previous_headings":"","what":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","title":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","text":"Get layer attribute description","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_descriptions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","text":"","code":"layer_attribute_descriptions( wfs = NULL, service = NULL, service_version = NULL, layer )"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_descriptions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layer character sting layer name. get info layers, including layer_name use emodnet_get_wfs_info().","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_descriptions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","text":"data.frame containing layer attribute descriptions (metadata).","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_descriptions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Variables available in a dataset (layer) from a data source (service). — layer_attribute_descriptions","text":"","code":"layer_attribute_descriptions( service = \"biology\", layer = \"mediseh_zostera_m_pnt\" ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> name type minOccurs maxOccurs nillable geometry #> 1 id integer 0 1 TRUE FALSE #> 2 country character 0 1 TRUE FALSE #> 3 the_geom Point 0 1 TRUE TRUE"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_inspect.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","title":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","text":"Inspect layer attributes","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_inspect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","text":"","code":"layer_attribute_inspect( wfs = NULL, service = NULL, service_version = NULL, layer, attribute )"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_inspect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layer character sting layer name. get info layers, including layer_name use emodnet_get_wfs_info(). attribute character string, name layer attribute (variable). Use layer_attributes_get_names() get layer attribute names.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_inspect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","text":"Detailed summary individual attribute (variable). Particularly useful inspecting factor character variable levels unique values.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attribute_inspect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summary of individual variable (attribute) in a dataset (layer) from a data source (service). — layer_attribute_inspect","text":"","code":"wfs <- emodnet_init_wfs_client(service = \"biology\") #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" layer_attributes_get_names(wfs, layer = \"mediseh_zostera_m_pnt\") #> [1] \"id\" \"country\" \"the_geom\" layer_attribute_inspect( wfs, layer = \"mediseh_zostera_m_pnt\", attribute = \"country\" ) #> # A tibble: 7 × 3 #> . n percent #> #> 1 Croazia 4 0.0741 #> 2 Francia 1 0.0185 #> 3 Italia 30 0.556 #> 4 Libia 2 0.0370 #> 5 Slovenia 8 0.148 #> 6 Spagna 8 0.148 #> 7 Tunisia 1 0.0185"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_get_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","title":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","text":"Names variables (attributes) available dataset (layer) data source (service).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_get_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","text":"","code":"layer_attributes_get_names( wfs = NULL, service = NULL, service_version = NULL, layer )"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_get_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layer character sting layer name. get info layers, including layer_name use emodnet_get_wfs_info().","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_get_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","text":"character vector layer attribute (variable) names.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_get_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Names of variables (attributes) available from a dataset (layer) in a data source (service). — layer_attributes_get_names","text":"","code":"layer_attributes_get_names( service = \"biology\", layer = \"mediseh_zostera_m_pnt\" ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> [1] \"id\" \"country\" \"the_geom\""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_summarise.html","id":null,"dir":"Reference","previous_headings":"","what":"Get summaries of layer attributes (variables) — layer_attributes_summarise","title":"Get summaries of layer attributes (variables) — layer_attributes_summarise","text":"Get summaries layer attributes (variables)","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_summarise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get summaries of layer attributes (variables) — layer_attributes_summarise","text":"","code":"layer_attributes_summarise( wfs = NULL, service = NULL, service_version = NULL, layer )"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_summarise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get summaries of layer attributes (variables) — layer_attributes_summarise","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layer character sting layer name. get info layers, including layer_name use emodnet_get_wfs_info().","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_summarise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get summaries of layer attributes (variables) — layer_attributes_summarise","text":"output summary() attributes (variables) given layer given service.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_summarise.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get summaries of layer attributes (variables) — layer_attributes_summarise","text":"","code":"layer_attributes_summarise( service = \"biology\", layer = \"mediseh_zostera_m_pnt\" ) #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> gml_id id country #> Length:54 Min. :0 Length:54 #> Class :character 1st Qu.:0 Class :character #> Mode :character Median :0 Mode :character #> Mean :0 #> 3rd Qu.:0 #> Max. :0"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"Get layer attribute values tibble","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"","code":"layer_attributes_tbl(wfs = NULL, service = NULL, service_version = NULL, layer)"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"wfs WFSClient R6 object methods interfacing OGC Web Feature Service. emodnet_init_wfs_client(). service EMODnet OGC WFS service name. available services, see emodnet_wfs(). service_version WFS service version. Now always \"2.0.0\". layer character sting layer name. get info layers, including layer_name use emodnet_get_wfs_info().","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"tibble layer attribute (variable) values geometry column removed.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"Request excluding spatial information can significantly faster. Can useful inspecting attribute values constructing feature filters targeted faster layer download.","code":""},{"path":[]},{"path":"https://emodnet.github.io/emodnet.wfs/reference/layer_attributes_tbl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Possible values of variables (attributes) in a dataset (layer) from a data source (service). — layer_attributes_tbl","text":"","code":"layer_attributes_tbl(service = \"biology\", layer = \"mediseh_zostera_m_pnt\") #> ✔ WFS client created successfully #> ℹ Service: \"https://geo.vliz.be/geoserver/Emodnetbio/wfs\" #> ℹ Version: \"2.0.0\" #> # A tibble: 54 × 3 #> gml_id id country #> #> 1 mediseh_zostera_m_pnt.1 0 Spagna #> 2 mediseh_zostera_m_pnt.2 0 Spagna #> 3 mediseh_zostera_m_pnt.3 0 Spagna #> 4 mediseh_zostera_m_pnt.4 0 Spagna #> 5 mediseh_zostera_m_pnt.5 0 Spagna #> 6 mediseh_zostera_m_pnt.6 0 Spagna #> 7 mediseh_zostera_m_pnt.7 0 Spagna #> 8 mediseh_zostera_m_pnt.8 0 Francia #> 9 mediseh_zostera_m_pnt.9 0 Italia #> 10 mediseh_zostera_m_pnt.10 0 Italia #> # ℹ 44 more rows"},{"path":"https://emodnet.github.io/emodnet.wfs/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::[\\%>\\%][magrittr::pipe] details.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://emodnet.github.io/emodnet.wfs/news/index.html","id":"emodnetwfs-development-version","dir":"Changelog","previous_headings":"","what":"emodnet.wfs (development version)","title":"emodnet.wfs (development version)","text":"Improved documentation following rOpenSci reviews: manual pages, README, vignettes. Renamed reduce_layers argument simplify. emodnet_wfs() now really returns tibble, data.frame. Listed reviewers DESCRIPTION. Set better escape mechanism examples fail services , ensure rendered pkgdown website.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/news/index.html","id":"emodnetwfs-202","dir":"Changelog","previous_headings":"","what":"emodnet.wfs 2.0.2","title":"emodnet.wfs 2.0.2","text":"Added ability pass vendor parameter emodnet.wfs::emodnet_get_layers() queries (#88). Added memoising (caching R session) functions getting services layers information (#52).","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/news/index.html","id":"emodnetwfs-201","dir":"Changelog","previous_headings":"","what":"emodnet.wfs 2.0.1","title":"emodnet.wfs 2.0.1","text":"Introduced better handling server response errors.","code":""},{"path":"https://emodnet.github.io/emodnet.wfs/news/index.html","id":"emodnetwfs-200","dir":"Changelog","previous_headings":"","what":"emodnet.wfs 2.0.0","title":"emodnet.wfs 2.0.0","text":"NEW FEATURE: Added ecql filtering capability ability interrogate feature attribute (see relevant vignette). Bug fix: corrected service namespace definition using wfs object Breaking Change: set extract default CRS service information (getDeafultCRS method) Breaking change: Removed default service value. Updated new EMODnet Seabed Habitats endpoints Added NEWS.md file track changes package.","code":""}]