use example files

R/available.R

@@ -10,7 +10,7 @@
 #' @return A logical indicates FAERS can have data for the `years` and
 #' `quarters` required?
 #' @examples
-#' faers_available(c(2011, 2023), c("q1", "q2"))
+#'  faers_available(c(2011, 2023), c("q1", "q2"))
 #' @export
 faers_available <- function(years, quarters, force = FALSE, internal = FALSE) {
     assert_inclusive(quarters, faers_file_quarters)

R/combine.R

@@ -5,11 +5,16 @@
 #' @param x A list of [FAERSxml] or [FAERSascii] objects.
 #' @return A [FAERSxml] or [FAERSascii] object.
 #' @examples
-#' \donttest{
-#' data1 <- faers(2004, "q1")
-#' data2 <- faers(2004, "q2")
+#' # the files included in the package are sampled
+#' data1 <- faers_parse(
+#'     system.file("extdata", "aers_ascii_2004q1.zip", package = "faers"),
+#'     compress_dir = tempdir()
+#' )
+#' data2 <- faers_parse(
+#'     system.file("extdata", "faers_ascii_2017q2.zip", package = "faers"),
+#'     compress_dir = tempdir()
+#' )
 #' faers_combine(list(data1, data2))
-#' }
 #' @export
 faers_combine <- function(x) {
     assert_(x, is.list, "a list")

R/dedup.R

@@ -2,12 +2,17 @@
 #' @param object A [FAERSascii] object.
 #' @param ... Other arguments passed to specific methods.
 #' @return A [FAERSascii] object.
-#' @examples 
+#' @seealso [faers_standardize]
+#' @examples
 #' \dontrun{
-#'  data <- faers(2004, c("q1", "q2"))
-#'  # you should replace `meddra_path` with yours
-#'  data <- faers_standardize(data, meddra_path)
-#'  faers_dedup(data)
+#' # you must change `dir`, as the files included in the package are sampled
+#' data <- faers(c(2004, 2017), c("q1", "q2"),
+#'     dir = system.file("extdata", package = "faers")
+#' )
+#' # we must standardize firstly
+#' # you should replace `meddra_path` with yours
+#' data <- faers_standardize(data, meddra_path)
+#' faers_dedup(data)
 #' }
 #' @export
 #' @name faers_dedup

R/download.R

@@ -11,9 +11,12 @@
 #'  [new_handle][curl::new_handle].
 #' @return An atomic character for the path of downloaded files.
 #' @examples
-#' \donttest{
-#' faers_download(year = 2004, quarter = "q1", dir = tempdir())
-#' }
+#' # you must change `dir`, as the file included in the package is sampled
+#' # in this way, the file will downloaded from FAERS
+#' faers_download(
+#'     year = 2004, quarter = "q1",
+#'     dir = system.file("extdata", package = "faers")
+#' )
 #' @export
 faers_download <- function(years, quarters, format = NULL, dir = getwd(), ...) {
     format <- match.arg(format, faers_file_format)

R/faers.R

@@ -4,10 +4,9 @@
 #' @param handle_opts Extra handle options passed to each request
 #' [new_handle][curl::new_handle].
 #' @return A [FAERSxml] or [FAERSascii] object.
-#' @examples 
-#' \donttest{
-#'  data <- faers(2004, "q1")
-#' }
+#' @examples
+#' # you must change `dir`, as the file included in the package is sampled
+#' data <- faers(2004, "q1", dir = system.file("extdata", package = "faers"))
 #' @export
 faers <- function(years, quarters, format = NULL, dir = getwd(), compress_dir = dir, handle_opts = list()) {
     format <- match.arg(format, faers_file_format)

R/merge.R

@@ -12,11 +12,10 @@
 #'
 #' @return A [data.table][data.table::data.table] object.
 #' @examples 
-#' \donttest{
-#'  data <- faers(2004, "q1")
-#'  faers_merge(data, "indi")
+#'  # you must change `dir`, as the file included in the package is sampled
+#'  data <- faers(2004, "q1", dir = system.file("extdata", package = "faers"))
+#'  faers_merge(data, "indi") # only one field is just like faers_get()
 #'  faers_merge(data, c("demo", "indi"))
-#' }
 #' @export
 #' @name faers_merge
 methods::setGeneric("faers_merge", function(object, ...) {

R/methods-utils.R

@@ -25,16 +25,15 @@
 #'    `faers_keep` to filter.
 #' @export
 #' @examples 
-#' \donttest{
-#'  data <- faers(2004, "q1")
+#'  # you must change `dir`, as the file included in the package is sampled
+#'  data <- faers(2004, "q1", dir = system.file("extdata", package = "faers"))
 #'  faers_get(data, "indi")
 #'  data[["indi"]]
 #'  faers_get(data, "demo")
 #'  data[["demo"]]
 #'  faers_mget(data, c("indi", "drug"))
 #'  faers_mget(data, c("indi", "demo"))
 #'  faers_primaryid(data)
-#' }
 #' @rdname FAERS-methods
 methods::setGeneric("faers_get", function(object, ...) {
     methods::makeStandardGeneric("faers_get")

R/parse.R

@@ -11,6 +11,12 @@
 #' @param compress_dir A string specifies the directory to extract files to. It
 #' will be created if necessary.
 #' @return A [FAERSxml] or [FAERSascii] object.
+#' @examples 
+#' # the files included in the package are sampled
+#' data <- faers_parse(
+#'     system.file("extdata", "aers_ascii_2004q1.zip", package = "faers"),
+#'     compress_dir = tempdir()
+#' )
 #' @export
 faers_parse <- function(path, format = NULL, year = NULL, quarter = NULL, compress_dir = getwd()) {
     assert_string(path, empty_ok = FALSE)

R/standardize.R

@@ -6,9 +6,12 @@
 #' <https://www.meddra.org/>
 #' @examples 
 #' \dontrun{
-#'  data <- faers(2004, "q1")
+#' #' # you must change `dir`, as the files included in the package are sampled
+#' data <- faers(c(2004, 2017), c("q1", "q2"),
+#'     dir = system.file("extdata", package = "faers")
+#' )
 #' # you should replace `meddra_path` with yours
-#'  data <- faers_standardize(data, meddra_path)
+#' data <- faers_standardize(data, meddra_path)
 #' }
 #' @export
 #' @name faers_standardize