Turn off all examples that call an API

R/collect_media.R

@@ -16,7 +16,8 @@
 #'
 #' @return Available image & media files downloaded to a user local directory.
 #'
-#' @examples \dontrun{
+#' @examples 
+#' \dontrun{
 #' # Use `atlas_media()` to return a `tibble` of records that contain media
 #' galah_call() |> 
 #'   galah_identify("perameles") |>

R/collect_occurrences.R

@@ -15,7 +15,8 @@
 #' @return An object of class `tbl_df` and `data.frame` (aka a tibble) of 
 #' occurrences 
 #' 
-#' @examples \dontrun{
+#' @examples 
+#' \dontrun{
 #' # Download previously retrieved records using an existing DOI or URL
 #' collect_occurrences(doi = "your-doi")
 #' 

R/galah_apply_profile.R

@@ -20,12 +20,14 @@
 #' profile filters.
 #' 
 #' @examples
+#' \dontrun{
 #' # Apply a data quality profile to a query
 #' galah_call() |> 
 #'   galah_identify("reptilia") |>
 #'   galah_filter(year == 2021) |>
 #'   galah_apply_profile(ALA) |>
 #'   atlas_counts()
+#' }
 #' 
 #' @export
 

R/galah_bbox.R

@@ -22,6 +22,7 @@
 #' returned by [atlas_occurrences()] and related functions.
 #'
 #' @examples
+#' \dontrun{
 #' # Search for records using a bounding box of coordinates
 #' b_box <- sf::st_bbox(c(xmin = 143, xmax = 148, ymin = -29, ymax = -28), 
 #'                      crs = sf::st_crs("WGS84"))
@@ -39,7 +40,6 @@
 #'   galah_bbox(b_box) |>
 #'   atlas_counts()
 #'   
-#' \dontrun{
 #' # Search for records within the bounding box of an `sf` object
 #' galah_config(email = "your_email_here")
 #' 

R/galah_config.R

@@ -51,7 +51,8 @@
 #' When `galah_config(...)` is called with arguments, nothing is returned
 #' but the configuration is set.
 #' 
-#' @examples \dontrun{
+#' @examples 
+#' \dontrun{
 #' # To download occurrence records, enter your email in `galah_config()`. 
 #' # This email should be registered with the ALA. 
 #' # You can register at:

R/galah_down_to.R

@@ -10,8 +10,8 @@
 #' [galah_geolocate()] for related methods.
 #' 
 #' @examples
-#' # Return a taxonomic tree of *Chordata* down to the class level
 #' \dontrun{
+#' # Return a taxonomic tree of *Chordata* down to the class level
 #' galah_call() |>
 #'     galah_identify("Vertebrata") |>
 #'     galah_down_to(class) |>

R/galah_filter.R

@@ -59,11 +59,13 @@
 #' `galah_filter(cl22 >= "Tasmania")`
 #' 
 #' @examples
+#' \dontrun{
 #' # Filter query results to return records of interest
 #' galah_call() |>
 #'   galah_filter(year >= 2019,
 #'                basisOfRecord == "HumanObservation") |>
 #'   atlas_counts()
+#' }
 #' 
 #' @importFrom rlang caller_env         
 #' @importFrom rlang enquos

R/galah_group_by.R

@@ -14,9 +14,12 @@
 #' @seealso [galah_select()], [galah_filter()] and
 #' [galah_geolocate()] for related methods.
 #' @examples
+#' \dontrun{
 #' galah_call() |> 
 #'   galah_group_by(basisOfRecord) |>
 #'   atlas_counts()
+#' }
+#' 
 #' @export
 galah_group_by <- function(..., expand = TRUE){
 

R/galah_identify.R

@@ -22,6 +22,7 @@
 #' are already known.
 #' 
 #' @examples
+#' \dontrun{
 #' # Specify a taxon. A valid taxon will return an identifier.
 #' galah_identify("reptilia")
 #' 
@@ -38,6 +39,7 @@
 #'   galah_identify("https://biodiversity.org.au/afd/taxa/009169a9-a916-40ee-866c-669ae0a21c5c", 
 #'                  search = FALSE) |>
 #'   atlas_counts()
+#' }
 #' 
 #' @export
 galah_identify <- function(..., search = TRUE) {

R/galah_polygon.R

@@ -18,14 +18,15 @@
 #' returned by [atlas_occurrences()] and related functions.
 #' 
 #' @examples
+#' \dontrun{
 #' # Search for records within a polygon using an `sf` object
 #' location <- "POLYGON((142.3 -29.0,142.7 -29.1,142.7 -29.4,142.3 -29.0))" |>
 #'   sf::st_as_sfc()
 #' galah_call() |>
 #'   galah_identify("reptilia") |>
 #'   galah_polygon(location) |>
 #'   atlas_counts()
-#' \dontrun{
+#'
 #' # Search for records using a shapefile
 #' galah_config(email = "your_email_here")
 #' location <- galah_geolocate(sf::st_read(path/to/shapefile.shp))

R/galah_select.R

@@ -54,7 +54,8 @@
 #' for how to get counts by levels of variables returned by `galah_select`;
 #' `show_all(fields)` to list available fields.
 #' 
-#' @examples \dontrun{
+#' @examples 
+#' \dontrun{
 #' # Download occurrence records of *Perameles*, 
 #' # Only return scientificName and eventDate columns
 #' galah_config(email = "[email protected]")

R/search_all.R

@@ -57,6 +57,7 @@
 #' arguments to [galah_select()], [galah_filter()], and related functions.
 #' 
 #' @examples
+#' \dontrun{
 #' # Search for fields that include the word "date"
 #' search_all(fields, "date")
 #' 
@@ -77,6 +78,7 @@
 #' 
 #' # Search for a valid taxonomic rank, "subphylum"
 #' search_all(ranks, "subphylum")
+#' }
 #' 
 NULL
 

R/search_identifiers.R

@@ -18,8 +18,10 @@
 #' by [atlas_occurrences()] and related functions.
 #' 
 #' @examples 
+#' \dontrun{
 #' # Look up a unique taxon identifier
 #' search_identifiers(query = "https://id.biodiversity.org.au/node/apni/2914510")
+#' }
 #' 
 #' @export
 search_identifiers <- function(query) {

R/search_media.R

@@ -6,7 +6,8 @@
 #' @param df 
 #'   A `tibble` of species occurrence records or media IDs.
 #' @returns a `tibble` of matching media files of occurrence records or media ids
-#' @examples \dontrun{
+#' @examples 
+#' \dontrun{
 #' # Search for media files for a set of species occurrence records
 #' occs <- galah_call() |>
 #'   galah_identify("perameles") |>

R/search_taxa.R

@@ -28,6 +28,7 @@
 #' up taxonomic trees.
 #' 
 #' @examples 
+#' \dontrun{
 #' # Search using a single string. 
 #' # Note that `search_taxa()` isn't case sensitive
 #' search_taxa("Reptilia")
@@ -53,7 +54,8 @@
 #' galah_call() |>
 #'   galah_identify(taxa) |>
 #'   atlas_counts()
-#'
+#' }
+#' 
 #' @importFrom utils adist 
 #' @importFrom dplyr rename
 #' @export

R/show_all.R

@@ -48,6 +48,7 @@
 #' search for information. These functions are used to pass valid arguments to
 #' [galah_select()], [galah_filter()], and related functions.
 #' @examples
+#' \dontrun{
 #' # See all supported atlases
 #' show_all(atlases)
 #'
@@ -59,7 +60,7 @@
 #' 
 #' # Show a listing of all taxonomic ranks
 #' show_all(ranks)
-#' 
+#' }
 #' 
 #' @md
 NULL

R/show_values.R

@@ -28,7 +28,8 @@
 #' @param df A search result from [search_fields()], [search_profiles()] or 
 #' [search_lists()].
 #' @return A `tibble` of values for a specified field, profile or list.
-#' @examples \donttest{
+#' @examples 
+#' \dontrun{
 #' # Show values in field 'cl22'
 #' search_fields("cl22") |> 
 #'   show_values()