docs: add instructions to get data from ERDDAP. Fixes (#147)

DESCRIPTION

@@ -48,6 +48,7 @@ Suggests:
     testthis,
     webmockr,
     withr
+Config/Needs/readme: rerddap
 VignetteBuilder: 
     knitr
 Remotes: 

README.Rmd

@@ -139,6 +139,39 @@ emodnet_get_layers(
 )
 ```
 
+## Other web services
+
+### EMODnet ERDDAP server
+
+The EMODnet data are also published in an [ERDDAP server](https://erddap.emodnet.eu). You can access these data in R using the [rerddap R package](https://docs.ropensci.org/rerddap/):
+
+
+```{r rerddap}
+# install.packages("rerrdap")
+library(rerddap)
+
+erddap_url <- "https://erddap.emodnet.eu/erddap/"
+
+rerddap::ed_datasets(url = erddap_url)
+
+rerddap::ed_search(query = "vessel density", url = erddap_url)
+
+human_activities_data_info <- rerddap::info(datasetid = 'humanactivities_9f8a_3389_f08a', url = erddap_url)
+out
+
+year_2020_gridded_data <- griddap(datasetx = human_activities_data_info, time = c('2020-03-18', '2020-03-19'))
+head(year_2020_gridded_data$data)
+
+```
+
+
+### EMODnetWCS: Access EMODnet Web Coverage Service data
+
+This package EMODnetWFS uses [Web Feature Services](https://www.ogc.org/standard/wfs/), hence it is limited to getting vector data. EMODnet also hosts raster data that can be accessed via [Web Coverage Services (WCS)](https://www.ogc.org/standard/wcs/). The R package [EMODnetWCS](https://github.com/EMODnet/EMODnetWCS) makes these data available in R.
+
+
+
+
 ## Citation
 
 To cite EMODnetWFS, please use the output from `citation(package = "EMODnetWFS")`.

README.md

@@ -78,9 +78,57 @@ wfs_bio <- emodnet_init_wfs_client(service = "biology")
 
 wfs_bio
 #> <WFSClient>
-#> ....|-- url: https://geo.vliz.be/geoserver/Emodnetbio/wfs
-#> ....|-- version: 2.0.0
-#> ....|-- capabilities <WFSCapabilities>
+#>   Inherits from: <OWSClient>
+#>   Public:
+#>     attrs: list
+#>     capabilities: WFSCapabilities, OWSCapabilities, OGCAbstractObject, R6
+#>     clone: function (deep = FALSE) 
+#>     defaults: list
+#>     describeFeatureType: function (typeName) 
+#>     element: AbstractObject
+#>     encode: function (addNS = TRUE, geometa_validate = TRUE, geometa_inspire = FALSE, 
+#>     ERROR: function (text) 
+#>     getCapabilities: function () 
+#>     getCASUrl: function () 
+#>     getClass: function () 
+#>     getClassName: function () 
+#>     getConfig: function () 
+#>     getFeatures: function (typeName, ...) 
+#>     getFeatureTypes: function (pretty = FALSE) 
+#>     getHeaders: function () 
+#>     getNamespaceDefinition: function (recursive = FALSE) 
+#>     getPwd: function () 
+#>     getToken: function () 
+#>     getUrl: function () 
+#>     getUser: function () 
+#>     getVersion: function () 
+#>     INFO: function (text) 
+#>     initialize: function (url, serviceVersion = NULL, user = NULL, pwd = NULL, 
+#>     isFieldInheritedFrom: function (field) 
+#>     logger: function (type, text) 
+#>     loggerType: NULL
+#>     namespace: OWSNamespace, R6
+#>     reloadCapabilities: function () 
+#>     url: https://geo.vliz.be/geoserver/Emodnetbio/wfs
+#>     verbose.debug: FALSE
+#>     verbose.info: FALSE
+#>     version: 2.0.0
+#>     WARN: function (text) 
+#>     wrap: FALSE
+#>   Private:
+#>     cas_url: NULL
+#>     config: request
+#>     fromComplexTypes: function (value) 
+#>     headers: EMODnetWFS R package 2.0.1.9001 https://github.com/EMODn ...
+#>     pwd: NULL
+#>     serviceName: WFS
+#>     system_fields: verbose.info verbose.debug loggerType wrap element names ...
+#>     token: NULL
+#>     user: NULL
+#>     xmlElement: AbstractObject
+#>     xmlExtraNamespaces: NULL
+#>     xmlNamespacePrefix: OWS
+#>     xmlNodeToCharacter: function (x, ..., indent = "", tagSeparator = "\n")
 ```
 
 ## Get WFS Layer info
@@ -106,8 +154,7 @@ emodnet_get_wfs_info(service = "biology")
 #>  8 emodnet_wfs biology      https://geo.… mediseh_h… EMOD… "Haloph… WFSF… sf    
 #>  9 emodnet_wfs biology      https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf    
 #> 10 emodnet_wfs biology      https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf    
-#> # ℹ 28 more rows
-#> # ℹ 1 more variable: layer_namespace <chr>
+#> # … with 27 more rows, and 1 more variable: layer_namespace <chr>
 ```
 
 or you can pass a wfs client object.
@@ -128,8 +175,7 @@ emodnet_get_wfs_info(wfs_bio)
 #>  8 emodnet_wfs biology      https://geo.… mediseh_h… EMOD… "Haloph… WFSF… sf    
 #>  9 emodnet_wfs biology      https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf    
 #> 10 emodnet_wfs biology      https://geo.… mediseh_m… EMOD… "Maërl … WFSF… sf    
-#> # ℹ 28 more rows
-#> # ℹ 1 more variable: layer_namespace <chr>
+#> # … with 27 more rows, and 1 more variable: layer_namespace <chr>
 ```
 
 You can also get info for specific layers from wfs object:
@@ -144,7 +190,7 @@ emodnet_get_layer_info(wfs = wfs_bio, layers = layers)
 #>   <chr>       <chr>           <chr>       <chr>      <chr> <chr>    <chr> <chr> 
 #> 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 <chr>
+#> # … with 1 more variable: layer_namespace <chr>
 ```
 
 Finally, you can get details on all available services and layers from
@@ -343,6 +389,104 @@ emodnet_get_layers(
 #> 10 mediseh_posidonia_nodata.84  0   2.817453 MULTICURVE (LINESTRING (15....
 ```
 
+## Other web services
+
+### EMODnet ERDDAP server
+
+The EMODnet data are also published in an [ERDDAP
+server](https://erddap.emodnet.eu). You can access these data in R using
+the [rerddap R package](https://docs.ropensci.org/rerddap/):
+
+``` r
+# install.packages("rerrdap")
+library(rerddap)
+#> Warning: package 'rerddap' was built under R version 4.2.3
+#> Registered S3 method overwritten by 'hoardr':
+#>   method           from
+#>   print.cache_info httr
+
+# Set the URL of the EMODnet ERDDAP server.
+url <- "https://erddap.emodnet.eu/erddap/"
+
+# List all datasets
+ed_datasets(url = url)
+#> # A tibble: 12 × 16
+#>    griddap Subset          tabledap Make.A.Graph wms   files Title Summary FGDC 
+#>    <chr>   <chr>           <chr>    <chr>        <chr> <chr> <chr> <chr>   <chr>
+#>  1 ""      "https://erdda… https:/… https://erd… ""    ""    * Th… "This … ""   
+#>  2 ""      "https://erdda… https:/… https://erd… ""    "htt… Chin… "Chine… "htt…
+#>  3 ""      "https://erdda… https:/… https://erd… ""    ""    Chin… "Chine… "htt…
+#>  4 ""      ""              https:/… https://erd… ""    "htt… EMOD… "The d… ""   
+#>  5 ""      ""              https:/… https://erd… ""    "htt… EMOD… "The d… ""   
+#>  6 ""      "https://erdda… https:/… https://erd… ""    "htt… EMOD… "The d… "htt…
+#>  7 ""      "https://erdda… https:/… https://erd… ""    ""    INDI… "INDIA… "htt…
+#>  8 ""      ""              https:/… https://erd… ""    "htt… Pres… "The p… "htt…
+#>  9 ""      ""              https:/… https://erd… ""    "htt… Pres… "The p… "htt…
+#> 10 ""      ""              https:/… https://erd… ""    ""    PSMS… "Perma… ""   
+#> 11 ""      ""              https:/… https://erd… ""    "htt… PSMS… "Perma… ""   
+#> 12 ""      "https://erdda… https:/… https://erd… ""    "htt… TAO/… "This … "htt…
+#> # … with 7 more variables: ISO.19115 <chr>, Info <chr>, Background.Info <chr>,
+#> #   RSS <chr>, Email <chr>, Institution <chr>, Dataset.ID <chr>
+
+# Search for datasets with "vessel density" in their name
+ed_search("vessel density", url = url)
+#> # A tibble: 17 × 2
+#>    title                                                     dataset_id         
+#>    <chr>                                                     <chr>              
+#>  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…
+#> 17 Test PACE: HA Vessel density                              emodnet_pace_vesse…
+
+# Get information about a specific dataset.
+out <- rerddap::info('humanactivities_9f8a_3389_f08a', url = url)
+out
+#> <ERDDAP 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
+
+# Request data for a certain time range.
+res <- griddap(out, time = c('2020-03-18','2020-03-19'))
+#> info() output passed to x; setting base url to: https://erddap.emodnet.eu/erddap
+head(res$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
+```
+
+### EMODnetWCS: Access EMODnet Web Coverage Service data
+
+This package EMODnetWFS uses [Web Feature
+Services](https://www.ogc.org/standard/wfs/), hence it is limited to
+getting vector data. EMODnet also hosts raster data that can be accessed
+via [Web Coverage Services (WCS)](https://www.ogc.org/standard/wcs/).
+The R package [EMODnetWCS](https://github.com/EMODnet/EMODnetWCS) makes
+these data available in R.
+
 ## Citation
 
 To cite EMODnetWFS, please use the output from