Update docs to remove epidemiology examples

DESCRIPTION

@@ -19,7 +19,6 @@ Suggests:
     dplyr,
     knitr,
     magrittr,
-    outbreaks,
     rmarkdown,
     spelling,
     testthat,

R/datatagr-package.R

@@ -43,73 +43,60 @@
 #'
 #' @examples
 #'
-#' if (require(outbreaks)) {
-#'   # using base R style
+#' # using base R style
+#' x <- make_datatagr(cars[1:50, ],
+#'   mph = "speed",
+#'   distance = "dist"
+#' )
+#' x
 #'
-#'   ## dataset we'll create a datatagr from, only using the first 50 entries
-#'   measles_hagelloch_1861[1:50, ]
+#' ## check tagged variables
+#' tags(x)
 #'
-#'   ## create datatagr
-#'   x <- make_datatagr(measles_hagelloch_1861[1:50, ],
-#'     id = "case_ID",
-#'     date_onset = "date_of_prodrome",
-#'     age = "age",
-#'     gender = "gender"
-#'   )
-#'   x
+#' ## robust renaming
+#' names(x)[1] <- "identifier"
+#' x
 #'
-#'   ## check tagged variables
-#'   tags(x)
+#' ## example of dropping tags by mistake - default: warning
+#' x[, 2]
 #'
-#'   ## robust renaming
-#'   names(x)[1] <- "identifier"
-#'   x
+#' ## to silence warnings when taggs are dropped
+#' lost_tags_action("none")
+#' x[, 2]
 #'
-#'   ## example of dropping tags by mistake - default: warning
-#'   x[, 2:5]
+#' ## to trigger errors when taggs are dropped
+#' # lost_tags_action("error")
+#' # x[, 2:5]
 #'
-#'   ## to silence warnings when taggs are dropped
-#'   lost_tags_action("none")
-#'   x[, 2:5]
+#' ## reset default behaviour
+#' lost_tags_action()
 #'
-#'   ## to trigger errors when taggs are dropped
-#'   # lost_tags_action("error")
-#'   # x[, 2:5]
+#' # using tidyverse style
 #'
-#'   ## reset default behaviour
-#'   lost_tags_action()
+#' ## example of creating a datatagr, adding a new variable, and adding a tag
+#' ## for it
 #'
+#' if (require(dplyr) && require(magrittr)) {
+#'   x <- cars %>%
+#'     tibble() %>%
+#'     make_datatagr(
+#'       mph = "speed",
+#'       distance = "dist"
+#'     ) %>%
+#'     mutate(result = if_else(speed > 50, "fast", "slow")) %>%
+#'     set_tags(ticket = "result")
 #'
-#'   # using tidyverse style
+#'   head(x)
 #'
-#'   ## example of creating a datatagr, adding a new variable, and adding a tag
-#'   ## for it
+#'   ## extract tagged variables
+#'   x %>%
+#'     select(has_tag(c("mph", "distance")))
 #'
-#'   if (require(dplyr) && require(magrittr)) {
-#'     x <- measles_hagelloch_1861 %>%
-#'       tibble() %>%
-#'       make_datatagr(
-#'         id = "case_ID",
-#'         date_onset = "date_of_prodrome",
-#'         age = "age",
-#'         gender = "gender"
-#'       ) %>%
-#'       mutate(result = if_else(is.na(date_of_death), "survived", "died")) %>%
-#'       set_tags(outcome = "result") %>%
-#'       rename(identifier = case_ID)
+#'   x %>%
+#'     tags()
 #'
-#'     head(x)
-#'
-#'     ## extract tagged variables
-#'     x %>%
-#'       select(has_tag(c("gender", "age")))
-#'
-#'     x %>%
-#'       tags()
-#'
-#'     x %>%
-#'       select(starts_with("date"))
-#'   }
+#'   x %>%
+#'     select(starts_with("dist"))
 #' }
 #'
 #' @keywords internal

R/has_tag.R

@@ -9,21 +9,16 @@
 #' @export
 #'
 #' @examples
-#' if (require(outbreaks) && require(dplyr)) {
-#'   ## dataset we'll create a datatagr from
-#'   measles_hagelloch_1861
-#'
-#'   ## create datatagr
-#'   x <- make_datatagr(measles_hagelloch_1861,
-#'     id = "case_ID",
-#'     date_onset = "date_of_prodrome",
-#'     age = "age",
-#'     gender = "gender"
-#'   )
-#'   head(x)
+#' ## create datatagr
+#' x <- make_datatagr(cars,
+#'   mph = "speed",
+#'   distance = "dist"
+#' )
+#' head(x)
 #'
+#' if (require(dplyr) && require(magrittr)) {
 #'   x %>%
-#'     select(has_tag(c("id", "age"))) %>%
+#'     select(has_tag(c("mph", "distance"))) %>%
 #'     head()
 #' }
 has_tag <- function(

R/make_datatagr.R

@@ -33,7 +33,7 @@
 #' @examples
 #'
 #' x <- make_datatagr(cars,
-#'   age = "speed",
+#'   mph = "speed",
 #'   distance = "dist"
 #' )
 #'
@@ -45,7 +45,7 @@
 #'
 #' ## Tags can also be passed as a list with the splice operator (!!!)
 #' my_tags <- list(
-#'   age = "speed",
+#'   mph = "speed",
 #'   distance = "dist"
 #' )
 #' new_x <- make_datatagr(cars, !!!my_tags)

R/names.R

@@ -12,34 +12,27 @@
 #' @export
 #'
 #' @examples
-#' if (require(outbreaks)) {
-#'   ## dataset to create a datatagr from
-#'   measles_hagelloch_1861
+#' ## create datatagr
+#' x <- make_datatagr(cars,
+#'   mph = "speed",
+#'   distance = "dist"
+#' )
+#' head(x)
 #'
-#'   ## create datatagr
-#'   x <- make_datatagr(measles_hagelloch_1861,
-#'     id = "case_ID",
-#'     date_onset = "date_of_prodrome",
-#'     age = "age",
-#'     gender = "gender"
-#'   )
-#'   head(x)
+#' ## change names
+#' names(x)[1] <- "speed in miles"
 #'
-#'   ## change names
-#'   names(x)[1] <- "case_label"
+#' ## see results: tags have been updated
+#' head(x)
+#' tags(x)
 #'
-#'   ## see results: tags have been updated
+#' # This also works with using `dplyr::rename()` because it uses names<-()
+#' # under the hood
+#' if (require(dplyr) && require(magrittr)) {
+#'   x <- x %>%
+#'     rename(speed = "speed in miles")
 #'   head(x)
 #'   tags(x)
-#'
-#'   # This also works with using `dplyr::rename()` because it uses names<-()
-#'   # under hood
-#'   if (require(dplyr)) {
-#'     x <- x %>%
-#'       rename(case_id = case_label)
-#'     head(x)
-#'     tags(x)
-#'   }
 #' }
 `names<-.datatagr` <- function(x, value) {
   # Strategy for renaming

R/print.datatagr.R

@@ -11,32 +11,23 @@
 #' @export
 #'
 #' @examples
-#' if (require(outbreaks)) {
-#'   ## dataset we'll create a datatagr from
-#'   measles_hagelloch_1861
-#'
-#'   ## create datatagr
-#'   x <- make_datatagr(measles_hagelloch_1861,
-#'     id = "case_ID",
-#'     date_onset = "date_of_prodrome",
-#'     age = "age",
-#'     gender = "gender"
-#'   )
-#'
-#'   ## print object - using only the first few entries
-#'   head(x)
-#'
-#'   # version with a tibble
-#'   if (require(tibble) && require(magrittr)) {
-#'     measles_hagelloch_1861 %>%
-#'       tibble() %>%
-#'       make_datatagr(
-#'         id = "case_ID",
-#'         date_onset = "date_of_prodrome",
-#'         age = "age",
-#'         gender = "gender"
-#'       )
-#'   }
+#' ## create datatagr
+#' x <- make_datatagr(cars,
+#'   mph = "speed",
+#'   distance = "dist"
+#' )
+#'
+#' ## print object - using only the first few entries
+#' head(x)
+#'
+#' # version with a tibble
+#' if (require(tibble) && require(magrittr)) {
+#'   cars %>%
+#'     tibble() %>%
+#'     make_datatagr(
+#'       mph = "speed",
+#'       distance = "dist"
+#'     )
 #' }
 print.datatagr <- function(x, ...) {
   cat("\n// datatagr object\n")

R/set_tags.R

@@ -14,33 +14,22 @@
 #'
 #' @examples
 #'
-#' if (require(outbreaks)) {
-#'   ## create a datatagr
-#'   x <- make_datatagr(measles_hagelloch_1861, date_onset = "date_of_rash")
-#'   tags(x)
-#'
-#'   ## add new tags and fix an existing one
-#'   x <- set_tags(x,
-#'     age = "age",
-#'     gender = "gender",
-#'     date_onset = "date_of_prodrome"
-#'   )
-#'   tags(x)
-#'
-#'   ## add non-default tags using allow_extra
-#'   x <- set_tags(x, severe = "complications", allow_extra = TRUE)
-#'   tags(x)
-#'
-#'   ## remove tags by setting them to NULL
-#'   old_tags <- tags(x)
-#'   x <- set_tags(x, age = NULL, gender = NULL)
-#'   tags(x)
-#'
-#'   ## setting tags providing a list (used to restore old tags here)
-#'   x <- set_tags(x, !!!old_tags)
-#'   tags(x)
-#' }
-#'
+#' ## create a datatagr
+#' x <- make_datatagr(cars, mph = "speed")
+#' tags(x)
+#'
+#' ## add new tags and fix an existing one
+#' x <- set_tags(x, distance = "dist")
+#' tags(x)
+#'
+#' ## remove tags by setting them to NULL
+#' old_tags <- tags(x)
+#' x <- set_tags(x, mph = NULL, distance = NULL)
+#' tags(x)
+#'
+#' ## setting tags providing a list (used to restore old tags here)
+#' x <- set_tags(x, !!!old_tags)
+#' tags(x)
 set_tags <- function(x, ..., tag_defaults = list(), allow_extra = TRUE) {
   # assert inputs
   checkmate::assertClass(x, "datatagr")

R/square_bracket.R

@@ -30,18 +30,15 @@
 #' @aliases sub_datatagr
 #'
 #' @examples
-#' if (require(outbreaks) && require(dplyr) && require(magrittr)) {
+#' if (require(dplyr) && require(magrittr)) {
 #'   ## create a datatagr
-#'   x <- measles_hagelloch_1861 %>%
+#'   x <- cars %>%
 #'     make_datatagr(
-#'       id = "case_ID",
-#'       date_onset = "date_of_prodrome",
-#'       age = "age",
-#'       gender = "gender"
+#'       mph = "speed",
+#'       distance = "dist"
 #'     ) %>%
-#'     mutate(result = if_else(is.na(date_of_death), "survived", "died")) %>%
-#'     set_tags(outcome = "result") %>%
-#'     rename(identifier = case_ID)
+#'     mutate(result = if_else(speed > 50, "fast", "slow")) %>%
+#'     set_tags(ticket = "result")
 #'   x
 #'
 #'   ## dangerous removal of a tagged column setting it to NULL issues a warning

R/tags.R

@@ -18,17 +18,14 @@
 #'
 #' @examples
 #'
-#' if (require(outbreaks)) {
-#'   ## make a datatagr
-#'   x <- make_datatagr(measles_hagelloch_1861, date_onset = "date_of_prodrome")
+#' ## make a datatagr
+#' x <- make_datatagr(cars, mph = "speed")
 #'
-#'   ## check non-null tags
-#'   tags(x)
-#'
-#'   ## get a list of all tags, including NULL ones
-#'   tags(x, TRUE)
-#' }
+#' ## check non-null tags
+#' tags(x)
 #'
+#' ## get a list of all tags, including NULL ones
+#' tags(x, TRUE)
 tags <- function(x, show_null = FALSE) {
   checkmate::assertClass(x, "datatagr")
   out <- attr(x, "tags")

R/tags_df.R

@@ -12,20 +12,13 @@
 #'
 #' @examples
 #'
-#' if (require(outbreaks) && require(magrittr)) {
-#'   ## create a tibble datatagr
-#'   x <- measles_hagelloch_1861 %>%
-#'     make_datatagr(
-#'       id = "case_ID",
-#'       date_onset = "date_of_prodrome",
-#'       age = "age",
-#'       gender = "gender"
-#'     )
-#'   x
+#' x <- make_datatagr(cars,
+#'   mph = "speed",
+#'   distance = "dist"
+#' )
 #'
-#'   ## get a data.frame of all tagged variables
-#'   tags_df(x)
-#' }
+#' ## get a data.frame of all tagged variables
+#' tags_df(x)
 tags_df <- function(x) {
   checkmate::assertClass(x, "datatagr")
   tags <- unlist(tags(x))