fix: CRAN requests

1. cran comments explaining dontrun
2. citations
3. removing some dontruns and/or examples

Author: dsweber2

DESCRIPTION

@@ -18,7 +18,7 @@ Authors@R:
   )
 URL: https://cmu-delphi.github.io/epidatr/, https://cmu-delphi.github.io/delphi-epidata/, https://github.com/cmu-delphi/epidatr
 BugReports: https://github.com/cmu-delphi/epidatr/issues
-Description: The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change Healthcare. It is built and maintained by the Carnegie Mellon University Delphi research group.
+Description: The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change Healthcare. It is built and maintained by the Carnegie Mellon University Delphi research group. To cite this API: David C. Farrow, Logan C. Brooks, Aaron Rumack, Ryan J. Tibshirani, Roni Rosenfeld (2015). Delphi Epidata API. <https://github.com/cmu-delphi/delphi-epidata>
 Depends: R (>= 3.5.0)
 License: MIT + file LICENSE
 Encoding: UTF-8

R/cache.R

@@ -68,14 +68,12 @@ cache_environ$epidatr_cache <- NULL
 #'   encoding of the call url. Each file corresponds to a unique epidata-API
 #'   call.
 #' @examples
-#' \dontrun{
 #' set_cache(
-#'   dir = "some/subdir",
+#'   dir = tempdir(),
 #'   days = 14,
 #'   max_size = 512,
-#'   logfile = "some/subdir/logs.txt"
+#'   logfile = "logs.txt"
 #' )
-#' }
 #'
 #' @param cache_dir the directory in which the cache is stored. By default, this
 #'   is `tools::R_user_dir()` if on R 4.0+, but must be specified for earlier
@@ -92,6 +90,8 @@ cache_environ$epidatr_cache <- NULL
 #'   variable is `EPIDATR_CACHE_LOGFILE`.
 #' @param confirm whether to confirm directory creation. default is `TRUE`;
 #'   should only be set in non-interactive scripts
+#' @return [`NULL`] no return value, all effects are stored in the package
+#'         environment
 #' @seealso [`clear_cache`] to delete the old cache while making a new one,
 #'   [`disable_cache`] to disable without deleting, and [`cache_info`]
 #' @export
@@ -176,28 +176,23 @@ set_cache <- function(cache_dir = NULL,
 #'   are using a session unique cache, you will have to pass the arguments you
 #'   used for `set_cache` earlier, otherwise the system-wide `.Renviron`-based
 #'   defaults will be used.
-#' @examples
-#' \dontrun{
-#' clear_cache(
-#'   dir = "some/subdir",
-#'   days = 14,
-#'   max_size = 512,
-#'   logfile = "some/subdir/logs.txt",
-#' )
-#' }
 #' @param disable instead of setting a new cache, disable caching entirely;
 #'   defaults to `FALSE`
 #' @inheritDotParams set_cache
+#' @return [`NULL`] no return value, all effects are stored in the package
+#'         environment
 #' @seealso [`set_cache`] to start a new cache (and general caching info),
 #'   [`disable_cache`] to only disable without deleting, and [`cache_info`]
 #' @export
 #' @import cachem
 clear_cache <- function(disable = FALSE, ...) {
-  cache_environ$epidatr_cache$destroy()
-  if (!disable) {
-    set_cache(...)
-  } else {
+  if (!is.na(cache_environ$epidatr_cache)) {
+    cache_environ$epidatr_cache$destroy()
+  }
+  if (disable) {
     cache_environ$epidatr_cache <- NULL
+  } else {
+    set_cache(...)
   }
 }
 
@@ -207,6 +202,8 @@ clear_cache <- function(disable = FALSE, ...) {
 #'   the cache are untouched. If you are looking to disable the caching more
 #'   permanently, set `EPIDATR_USE_CACHE=FALSE` as environmental variable in
 #'   your `.Renviron`.
+#' @return [`NULL`] no return value, all effects are stored in the package
+#'         environment
 #' @export
 #' @seealso [`set_cache`] to start a new cache (and general caching info),
 #'   [`clear_cache`] to delete the cache and set a new one, and [`cache_info`]
@@ -220,6 +217,7 @@ disable_cache <- function() {
 #' @description
 #' Print out the information about the cache (as would be returned by cachem's
 #' `info()` method).
+#' @return [`list`] containing the info result as created by cachem
 #'
 #' @seealso [`set_cache`] to start a new cache (and general caching info),
 #'   [`clear_cache`] to delete the cache and set a new one, and [`disable_cache`] to

R/covidcast.R

@@ -1,6 +1,7 @@
 #' turn a signal into a callable
 #' @param signal the signal of interest
 #' @param base_url the base url
+#' @keywords internal
 parse_signal <- function(signal, base_url) {
   class(signal) <- c("covidcast_data_signal", class(signal))
   signal$key <- paste(signal$source, signal$signal, sep = ":")

cran-comments.md

@@ -0,0 +1,4 @@
+- Calls in the following files call an API which if queried too frequently without a key would result in CRAN being temporarily locked out of running API calls (so a soft-API key problem)
+  - [`epidatr/R/epidatacall.R`]
+  - [`epidatr/R/request.R`]
+  - [`epidatr/R/endpoints.R`]

inst/CITATION

@@ -0,0 +1,7 @@
+bibentry(
+  "Misc",
+  title = "Delphi Epidata API",
+  author = "David C. Farrow, Logan C. Brooks, Aaron Rumack, Ryan J. Tibshirani, Roni Rosenfeld",
+  year = 2015,
+  url = "https://github.com/cmu-delphi/delphi-epidata"
+)