docs: work on manual

R/client.R

@@ -1,4 +1,6 @@
-#' Initialise an EMODnet WFS client
+#' @description Initialise an EMODnet WFS client
+#'
+#' @title Connect to a data source (service)
 #'
 #' @param service the EMODnet OGC WFS service name.
 #' For available services, see [`emodnet_wfs()`].
@@ -13,10 +15,8 @@
 #' @export
 #'
 #' @seealso `WFSClient` in package `ows4R`.
-#' @examples
-#' \dontrun{
+#' @examplesIf interactive()
 #' wfs <- emodnet_init_wfs_client(service = "bathymetry")
-#' }
 emodnet_init_wfs_client <- function(service,
                                     service_version = NULL,
                                     logger = NULL) {

R/emodnet_wfs.R

@@ -4,11 +4,13 @@
     stringsAsFactors = FALSE
   )
 }
-#' Available EMODnet Web Feature Services
+#' @description Available EMODnet Web Feature Services
+#'
+#' @title Which data sources (services) are available?
 #'
 #' @return Tibble of available EMODnet Web Feature Services
 #'
-#' @examples
+#' @examplesIf interactive()
 #' emodnet_wfs()
 #' @export
 emodnet_wfs <- memoise::memoise(.emodnet_wfs)

R/info.R

@@ -14,7 +14,7 @@
     service_url = get_service_name(wfs$getUrl()),
     layer_name = purrr::map_chr(wfs_layers, ~ .x$getName()),
     title = purrr::map_chr(wfs_layers, ~ .x$getTitle()),
     abstract = purrr::map_chr(wfs_layers, ~ get_abstract_null(.x)),
     class = purrr::map_chr(wfs_layers, ~ .x$getClassName()),
     format = purrr::map_chr(wfs_layers, guess_layer_format)
   ) %>%
@@ -65,7 +65,7 @@
     title = purrr::map_chr(capabilities$getFeatureTypes(), ~ .x$getTitle()),
     abstract = purrr::map_chr(
       capabilities$getFeatureTypes(),
       ~ get_abstract_null(.x)
     ),
     class = purrr::map_chr(capabilities$getFeatureTypes(), ~ .x$getClassName()),
     format = purrr::map_chr(capabilities$getFeatureTypes(), guess_layer_format)
@@ -76,26 +76,29 @@
       layer_name = strsplit(layer_name, ":", fixed = TRUE)[[1]][2]
     )
 }
-#' Get WFS available layer information
+#' @description Get WFS available layer information
+#'
+#' @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.
 #'
 #' @param wfs A `WFSClient` R6 object with methods for interfacing an
-#'  OGC Web Feature Service.
+#'  OGC Web Feature Service. From [`emodnet_init_wfs_client()`].
 #' @inheritParams emodnet_init_wfs_client
 #' @return a tibble containing metadata on each layer available from the
 #'  service.
 #' @export
 #' @describeIn emodnet_get_wfs_info Get info on all layers from
 #' an EMODnet WFS service.
-#' @examples
-#' \dontrun{
+#' @examplesIf interactive()
 #' emodnet_get_wfs_info(service = "bathymetry")
 #' # Query a wfs object
 #' wfs_bio <- emodnet_init_wfs_client("biology")
 #' emodnet_get_wfs_info(wfs_bio)
 #' # 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)
-#' }
 emodnet_get_wfs_info <- memoise::memoise(.emodnet_get_wfs_info)
 
 #' @describeIn emodnet_get_wfs_info Get metadata on all layers and all available

R/layer_attributes.R

@@ -7,15 +7,14 @@
 #'
 #' @return output of `summary()` on the attributes (variables) in a given layer
 #' for a given service.
+#' @family attributes
 #' @export
 #'
-#' @examples
-#' \dontrun{
+#' @examplesIf interactive()
 #' layer_attributes_summarise(
 #'   service = "biology",
 #'   layer = "mediseh_zostera_m_pnt"
 #' )
-#' }
 layer_attributes_summarise <- function(wfs = NULL,
                                        service = NULL,
                                        service_version = NULL,
@@ -33,22 +32,23 @@ layer_attributes_summarise <- function(wfs = NULL,
   )
 }
 
-#' Get layer attribute description
+#' @description Get layer attribute description
+#'
+#' @title Variables available in a dataset (layer) from a data source (service).
 #'
 #' @inheritParams emodnet_init_wfs_client
 #' @inheritParams emodnet_get_wfs_info
 #' @inheritParams layer_attributes_summarise
 #'
 #' @return data.frame containing layer attribute descriptions (metadata).
+#' @family attributes
 #' @export
 #'
-#' @examples
-#' \dontrun{
+#' @examplesIf interactive()
 #' layer_attribute_descriptions(
 #'   service = "biology",
 #'   layer = "mediseh_zostera_m_pnt"
 #' )
-#' }
 layer_attribute_descriptions <- function(wfs = NULL,
                                          service = NULL,
                                          service_version = NULL, layer) {
@@ -64,22 +64,23 @@ layer_attribute_descriptions <- function(wfs = NULL,
 }
 
 
-#' Get names of layer attributes
+#' Names of variables (attributes) available from a dataset (layer)
+#' in a data source (service).
 #'
 #' @inheritParams emodnet_init_wfs_client
 #' @inheritParams emodnet_get_wfs_info
 #' @inheritParams layer_attributes_summarise
 #'
+#' @family attributes
+#'
 #' @return character vector of layer attribute (variable) names.
 #' @export
 #'
-#' @examples
-#' \dontrun{
+#' @examplesIf interactive()
 #' layer_attributes_get_names(
 #'   service = "biology",
 #'   layer = "mediseh_zostera_m_pnt"
 #' )
-#' }
 layer_attributes_get_names <- function(wfs = NULL,
                                        service = NULL,
                                        service_version = NULL,
@@ -96,7 +97,10 @@ layer_attributes_get_names <- function(wfs = NULL,
   )$name
 }
 
-#' Inspect layer attributes
+#' @description Inspect layer attributes
+#'
+#' @title Summary of individual variable (attribute) in a dataset (layer) from a
+#' data source (service).
 #'
 #' @inheritParams layer_attributes_summarise
 #' @param attribute character string, name of layer attribute (variable). Use
@@ -107,17 +111,16 @@ layer_attributes_get_names <- function(wfs = NULL,
 #' @return Detailed summary of individual attribute (variable). Particularly
 #' useful for inspecting
 #' factor or character variable levels or unique values.
+#' @family attributes
 #' @export
 #'
-#' @examples
-#' \dontrun{
+#' @examplesIf interactive()
 #' wfs <- emodnet_init_wfs_client(service = "biology")
 #' layer_attributes_get_names(wfs, layer = "mediseh_zostera_m_pnt")
 #' layer_attribute_inspect(
 #'   wfs, layer = "mediseh_zostera_m_pnt",
 #'   attribute = "country"
 #' )
-#' }
 layer_attribute_inspect <- function(wfs = NULL,
                                     service = NULL,
                                     service_version = NULL,
@@ -161,7 +164,10 @@ layer_attribute_inspect <- function(wfs = NULL,
   )
 }
 
-#' Get layer attribute values tibble
+#' @description Get layer attribute values tibble
+#'
+#' @title Possible values of variables (attributes) in a dataset (layer)
+#' from a data source (service).
 #'
 #' @inheritParams emodnet_init_wfs_client
 #' @inheritParams emodnet_get_wfs_info
@@ -174,12 +180,11 @@ layer_attribute_inspect <- function(wfs = NULL,
 #' useful for inspecting attribute values and constructing feature filters
 #' for more
 #' targeted and faster layer download.
+#' @family attributes
 #' @export
 #'
-#' @examples
-#' \dontrun{
+#' @examplesIf interactive()
 #' layer_attributes_tbl(service = "biology", layer = "mediseh_zostera_m_pnt")
-#' }
 layer_attributes_tbl <- function(wfs = NULL,
                                  service = NULL,
                                  service_version = NULL, layer) {

R/layers.R

@@ -1,4 +1,4 @@
-#' Get EMODnet WFS layers
+#' Get EMODnet WFS datasets (layers)
 #'
 #' Performs an WFS getFeature request for layers from a `wfs` object or
 #' specified EMODnet Service. Filtering
@@ -160,7 +160,7 @@
   # if reduce_layers = T, reduce to single sf --------------------------------
   if (reduce_layers) {
     tryCatch(
       out <- purrr::reduce(out, rbind),
       error = function(e) {
         cli::cli_abort(
           c(