Replace TealData with teal_data in the docs

R/tm_g_ae_oview.R

@@ -16,77 +16,51 @@
 #' @export
 #'
 #' @examples
-#' library(nestcolor)
+#' data <- cdisc_data() |>
+#'   within(library(nestcolor)) |>
+#'   within({
+#'     ADSL <- rADSL
+#'     ADAE <- rADAE
+#'     add_event_flags <- function(dat) {
+#'       dat <- dat |>
+#'         mutate(
+#'           TMPFL_SER = AESER == "Y",
+#'           TMPFL_REL = AEREL == "Y",
+#'           TMPFL_GR5 = AETOXGR == "5",
+#'           AEREL1 = (AEREL == "Y" & ACTARM == "A: Drug X"),
+#'           AEREL2 = (AEREL == "Y" & ACTARM == "B: Placebo")
+#'         )
+#'       labels <- c(
+#'         "Serious AE", "Related AE", "Grade 5 AE",
+#'         "AE related to A: Drug X", "AE related to B: Placebo"
+#'       )
+#'       cols <- c("TMPFL_SER", "TMPFL_REL", "TMPFL_GR5", "AEREL1", "AEREL2")
+#'       for (i in seq_along(labels)) {
+#'         attr(dat[[cols[i]]], "label") <- labels[i]
+#'       }
+#'       dat
+#'     }
+#'     ADAE <- add_event_flags(ADAE)
+#'   })
 #'
-#' ADSL <- osprey::rADSL
-#' ADAE <- osprey::rADAE
+#' datanames(data) <- c("ADSL", "ADAE")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
 #'
-#' # Add additional dummy causality flags.
-#' add_event_flags <- function(dat) {
-#'   dat <- dat %>%
-#'     dplyr::mutate(
-#'       TMPFL_SER = AESER == "Y",
-#'       TMPFL_REL = AEREL == "Y",
-#'       TMPFL_GR5 = AETOXGR == "5",
-#'       AEREL1 = (AEREL == "Y" & ACTARM == "A: Drug X"),
-#'       AEREL2 = (AEREL == "Y" & ACTARM == "B: Placebo")
-#'     )
-#'   labels <- c(
-#'     "Serious AE", "Related AE", "Grade 5 AE",
-#'     "AE related to A: Drug X", "AE related to B: Placebo"
-#'   )
-#'   cols <- c("TMPFL_SER", "TMPFL_REL", "TMPFL_GR5", "AEREL1", "AEREL2")
-#'   for (i in seq_along(labels)) {
-#'     attr(dat[[cols[i]]], "label") <- labels[i]
-#'   }
-#'   dat
-#' }
-#' ADAE <- ADAE %>% add_event_flags()
+#' ADAE <- data[["ADAE"]]
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"),
-#'     cdisc_dataset("ADAE", ADAE,
-#'       code =
-#'         "ADAE <- osprey::rADAE
-#'            add_event_flags <- function(dat) {
-#'              dat <- dat %>%
-#'                dplyr::mutate(
-#'                  TMPFL_SER = AESER == 'Y',
-#'                  TMPFL_REL = AEREL == 'Y',
-#'                  TMPFL_GR5 = AETOXGR == '5',
-#'                  AEREL1 = (AEREL == 'Y' & ACTARM == 'A: Drug X'),
-#'                  AEREL2 = (AEREL == 'Y' & ACTARM == 'B: Placebo')
-#'                )
-#'              labels <- c(
-#'                'Serious AE',
-#'                'Related AE',
-#'                'Grade 5 AE',
-#'                'AE related to A: Drug X',
-#'                'AE related to B: Placebo'
-#'              )
-#'              cols <- c('TMPFL_SER', 'TMPFL_REL', 'TMPFL_GR5', 'AEREL1', 'AEREL2')
-#'              for (i in seq_along(labels)) {
-#'               attr(dat[[cols[i]]], 'label') <- labels[i]
-#'              }
-#'              dat
-#'            }
-#'            # Generating user-defined event flags.
-#'            ADAE <- ADAE %>% add_event_flags()"
-#'     ),
-#'     check = TRUE
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_g_ae_oview(
 #'       label = "AE Overview",
 #'       dataname = "ADAE",
-#'       arm_var = teal.transform::choices_selected(
+#'       arm_var = choices_selected(
 #'         selected = "ACTARM",
 #'         choices = c("ACTARM", "ACTARMCD")
 #'       ),
-#'       flag_var_anl = teal.transform::choices_selected(
+#'       flag_var_anl = choices_selected(
 #'         selected = "AEREL1",
-#'         choices = teal.transform::variable_choices(
+#'         choices = variable_choices(
 #'           ADAE,
 #'           c("TMPFL_SER", "TMPFL_REL", "TMPFL_GR5", "AEREL1", "AEREL2")
 #'         ),
@@ -98,6 +72,7 @@
 #' if (interactive()) {
 #'   shinyApp(app$ui, app$server)
 #' }
+#'
 tm_g_ae_oview <- function(label,
                           dataname,
                           arm_var,

R/tm_g_ae_sub.R

@@ -17,16 +17,18 @@
 #' @export
 #'
 #' @examples
-#' # Example using stream (ADaM) dataset
-#' ADSL <- osprey::rADSL
-#' ADAE <- osprey::rADAE
+# Example using stream (ADaM) dataset
+#' data <- cdisc_data() |>
+#'   within({
+#'     ADSL <- rADSL
+#'     ADAE <- rADAE
+#'   })
+#'
+#' datanames(data) <- c("ADSL", "ADAE")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"),
-#'     cdisc_dataset("ADAE", ADAE, code = "ADAE <- osprey::rADAE"),
-#'     check = TRUE
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_g_ae_sub(
 #'       label = "AE by Subgroup",
@@ -46,6 +48,7 @@
 #' if (interactive()) {
 #'   shinyApp(app$ui, app$server)
 #' }
+#'
 tm_g_ae_sub <- function(label,
                         dataname,
                         arm_var,

R/tm_g_butterfly.R

@@ -40,69 +40,60 @@
 #' @template author_liaoc10
 #'
 #' @examples
+# Example using stream (ADaM) dataset
+#' data <- cdisc_data() |>
+#'   within({
+#'     library(dplyr)
+#'     library(nestcolor)
+#'   }) |>
+#'   within({
+#'     set.seed(23)
+#'     ADSL <- rADSL
+#'     ADAE <- rADAE
+#'     ADSL <- mutate(ADSL, DOSE = paste(sample(1:3, n(), replace = TRUE), "UG"))
+#'     ADAE <- mutate(
+#'       ADAE,
+#'       flag1 = ifelse(AETOXGR == 1, 1, 0),
+#'       flag2 = ifelse(AETOXGR == 2, 1, 0),
+#'       flag3 = ifelse(AETOXGR == 3, 1, 0),
+#'       flag1_filt = rep("Y", n())
+#'     )
+#'   })
 #'
-#' # Example using stream (ADaM) dataset
-#' library(dplyr)
-#' library(nestcolor)
-#'
-#' set.seed(23)
-#' ADSL <- osprey::rADSL
-#' ADAE <- osprey::rADAE
-#' ADSL <- mutate(ADSL, DOSE = paste(sample(1:3, n(), replace = TRUE), "UG"))
-#' ADAE <- mutate(
-#'   ADAE,
-#'   flag1 = ifelse(AETOXGR == 1, 1, 0),
-#'   flag2 = ifelse(AETOXGR == 2, 1, 0),
-#'   flag3 = ifelse(AETOXGR == 3, 1, 0),
-#'   flag1_filt = rep("Y", n())
-#' )
+#' datanames(data) <- c("ADSL", "ADAE")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL,
-#'       code = "ADSL <- osprey::rADSL
-#'               set.seed(23)
-#'               ADSL <- mutate(ADSL, DOSE = paste(sample(1:3, n(), replace = TRUE), 'UG'))"
-#'     ),
-#'     cdisc_dataset("ADAE", ADAE,
-#'       code = "ADAE <- osprey::rADAE
-#'               ADAE <- mutate(ADAE,
-#'               flag1 = ifelse(AETOXGR == 1, 1, 0),
-#'               flag2 = ifelse(AETOXGR == 2, 1, 0),
-#'               flag3 = ifelse(AETOXGR == 3, 1, 0),
-#'               flag1_filt = rep('Y', n()))"
-#'     ),
-#'     check = TRUE
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_g_butterfly(
 #'       label = "Butterfly Plot",
 #'       dataname = "ADAE",
-#'       right_var = teal.transform::choices_selected(
+#'       right_var = choices_selected(
 #'         selected = "SEX",
 #'         choices = c("SEX", "ARM", "RACE")
 #'       ),
-#'       left_var = teal.transform::choices_selected(
+#'       left_var = choices_selected(
 #'         selected = "RACE",
 #'         choices = c("SEX", "ARM", "RACE")
 #'       ),
-#'       category_var = teal.transform::choices_selected(
+#'       category_var = choices_selected(
 #'         selected = "AEBODSYS",
 #'         choices = c("AEDECOD", "AEBODSYS")
 #'       ),
-#'       color_by_var = teal.transform::choices_selected(
+#'       color_by_var = choices_selected(
 #'         selected = "AETOXGR",
 #'         choices = c("AETOXGR", "None")
 #'       ),
-#'       count_by_var = teal.transform::choices_selected(
+#'       count_by_var = choices_selected(
 #'         selected = "# of patients",
 #'         choices = c("# of patients", "# of AEs")
 #'       ),
-#'       facet_var = teal.transform::choices_selected(
+#'       facet_var = choices_selected(
 #'         selected = NULL,
 #'         choices = c("RACE", "SEX", "ARM")
 #'       ),
-#'       sort_by_var = teal.transform::choices_selected(
+#'       sort_by_var = choices_selected(
 #'         selected = "count",
 #'         choices = c("count", "alphabetical")
 #'       ),

R/tm_g_events_term_id.R

@@ -18,29 +18,30 @@
 #' @author Molly He (hey59) \email{[email protected]}
 #'
 #' @examples
-#' library(nestcolor)
+#' data <- cdisc_data() |>
+#'   within(library(nestcolor)) |>
+#'   within({
+#'     ADSL <- rADSL
+#'     ADAE <- rADAE
+#'   })
 #'
-#' ADSL <- osprey::rADSL
-#' ADAE <- osprey::rADAE
+#' datanames(data) <- c("ADSL", "ADAE")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"),
-#'     cdisc_dataset("ADAE", ADAE, code = "ADAE <- osprey::rADAE"),
-#'     check = TRUE
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_g_events_term_id(
 #'       label = "Common AE",
 #'       dataname = "ADAE",
-#'       term_var = teal.transform::choices_selected(
+#'       term_var = choices_selected(
 #'         selected = "AEDECOD",
 #'         choices = c(
 #'           "AEDECOD", "AETERM",
 #'           "AEHLT", "AELLT", "AEBODSYS"
 #'         )
 #'       ),
-#'       arm_var = teal.transform::choices_selected(
+#'       arm_var = choices_selected(
 #'         selected = "ACTARMCD",
 #'         choices = c("ACTARM", "ACTARMCD")
 #'       ),