Uploading examples to include dontrun instead to avoid touching api at all

Author: sedv8808

R/01_classDefinitions.R

@@ -7,8 +7,9 @@ setClassUnion("id", c("character", "integer", "numeric"))
 #' @name contacts_classes
 #' @description An unordered list of individual S4 `contact` objects.
 #' @export
-#' @examples
+#' @examples {
 #' new("contact", familyname = "Goring", givennames = "Simon J.")
+#' }
 #' @returns object of class `contact`
 #' @aliases contact-class
 #' @md

R/clean.R

@@ -16,7 +16,7 @@
 #'   * After: \{site: 1, dataset: \[1, 2\]\}
 #' So the site is gathered, and the datasets are now part of an
 #' array of datasets.
-#' @examples \donttest{
+#' @examples \dontrun{
 #' tryCatch({
 #'   alex <- get_sites(sitename = "Alex%")
 #'   alex2 <- get_sites(24)

R/filter.R

@@ -49,7 +49,7 @@
 #' @param .by (only used for filtering `data.frame` objects)
 #' @param .preserve (only used for filtering `data.frame` objects)
 #' @returns filtered `sites` object
-#' @examples \donttest{
+#' @examples \dontrun{
 #' # Download 10 sites, but only keep the sites that are close to sea level.
 #' tryCatch({
 #'  some_sites <- get_sites(sitename = "Lake%", limit = 3)

R/get_datasets.R

@@ -60,7 +60,7 @@
 #' record.
 #'  * `all_data` The API only downloads the first 25 records of the query. 
 #'  For the complete records, use `all_data=TRUE`
-#' @examples \donttest{
+#' @examples \dontrun{
 #' tryCatch({
 #'   random_sites <- get_sites(1)
 #'   allds <- get_datasets(random_sites, limit=3)

R/get_documentation.R

@@ -4,7 +4,7 @@
 #' @importFrom utils browseURL
 #' @importFrom rlang is_interactive
 #' @returns NULL
-#' @examples \donttest{
+#' @examples \dontrun{
 #' if (interactive()) {
 #'  get_documentation()
 #' }

R/get_downloads.R

@@ -48,7 +48,7 @@
 #' \item{ \code{pi list} }{P.I. info}
 #' \item{ \code{analyst} }{analyst info}
 #' \item{ \code{metadata} }{dataset metadata}
-#' @examples \donttest{
+#' @examples \dontrun{
 #' # To find the downloads object of dataset 24:
 #' tryCatch({
 #'   downloads24 <- get_downloads(24)

R/get_manual.R

@@ -3,7 +3,7 @@
 #' @description Open up the Neotoma manual homepage.
 #' @importFrom utils browseURL
 #' @importFrom rlang is_interactive
-#' @examples {
+#' @examples \dontrun{
 #' # This call does not work from `source()` calls or in testing.
 #' # interactive() just lets us know you are interacting with the console:
 #' if (interactive()) {

R/get_publications.R

@@ -17,7 +17,7 @@
 #' `year` The year the publication was released.
 #' `search` A plain text search string used to search the citation.
 #' @returns `publications` object
-#' @examples \donttest{
+#' @examples \dontrun{
 #' # How old are the papers in Neotoma that include the term "mammut"?
 #' tryCatch({
 #'   mammoth_papers <- get_publications(search="mammut") %>%

R/get_sites.R

@@ -62,42 +62,19 @@
 #'  * `loc` An `sf` object that describes site's location.
 #'  * `description`
 #'  * `collunits` limited information on collunits
-#' @examples
-#' \donttest{
+#' @examples \dontrun{
 #' ## Find sites with a min altitude of 12m and a max altitude of 25m
-#' tryCatch({
-#'   sites_12to25 <- get_sites(altmin=12, altmax=25)
-#' }, error = function(e) {
-#'   message("Neotoma server not responding. Try again later.")
-#' })
-#' ## Return all sites, using a minimum altitude of 2500m (returns >500 sites):
-#' tryCatch({
-#'   sites_2500 <- get_sites(altmin=2500, all_data = TRUE)
-#' }, error = function(e) {
-#'   message("Neotoma server not responding. Try again later.")
-#' })
-#'   ## To find sites in Brazil
+#' sites_12to25 <- get_sites(altmin=12, altmax=25)
+#' sites_2500 <- get_sites(altmin=2500, all_data = TRUE)
+#' ## To find sites in Brazil
 #' brazil <- '{"type": "Polygon",
 #' "coordinates": [[
 #'  [-73.125, -9.102096738726443],
 #'  [-56.953125,-33.137551192346145],
 #'  [-36.5625,-7.710991655433217],
 #'  [-68.203125,13.923403897723347],
 #'  [-73.125,-9.102096738726443]]]}'
-#' tryCatch({
 #' brazil_sites <- get_sites(loc = brazil[1])
-#' # Finding all sites with Liliaceae pollen in 1000 year bins:
-#' lilysites <- c()
-#' for (i in seq(0, 10000, by = 1000)) {
-#'   lily <- get_sites(taxa=c("Liliaceae"),
-#'                     ageyoung = i - 500,
-#'                     ageold = i + 500,
-#'                     all_data = TRUE)
-#'   lilysites <- c(lilysites, length(lily))
-#' }
-#' }, error = function(e) {
-#'   message("Neotoma server not responding. Try again later.")
-#' })
 #' }
 #' @md
 #' @export

R/get_speleothems.R

@@ -58,13 +58,9 @@ speleo_helper <- function(sites) {
 #'  * `x`  The unique dataset ID (integer) in Neotoma. Can be passed as a
 #' vector of dataset IDs.
 #'  * `sites`  A `sites` R object.
-#' @examples {
+#' @examples \dontrun{
 #' ## Find speleothems by numeric datasetid:
-#' tryCatch({
-#'   speleo <- get_speleothems(c(2,5))
-#' }, error = function(e) {
-#'   message("Neotoma server not responding. Try again later.")
-#' })
+#' speleo <- get_speleothems(c(2,5))
 #' }
 #' @md
 #' @export