insightsengineering · pawelru · Oct 4, 2024 · Sep 30, 2024 · Sep 30, 2024 · Sep 30, 2024
diff --git a/.gitignore b/.gitignore
@@ -29,3 +29,5 @@ vignettes/*.R
 coverage.*
 tests/testthat/_snaps/**/*.new.md
 tests/testthat/_snaps/**/*.new.svg
+/doc/
+/Meta/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -71,6 +71,7 @@ Suggests:
     lubridate (>= 1.7.9),
     nestcolor (>= 0.1.0),
     pkgload,
+    roxy.shinylive,
     rvest,
     shinytest2,
     styler,
@@ -90,12 +91,12 @@ Config/Needs/verdepcheck: insightsengineering/teal,
     insightsengineering/teal.widgets, insightsengineering/tern.gee,
     insightsengineering/tern.mmrm, shosaco/vistime, tidyverse/forcats,
     yihui/knitr, tidyverse/lubridate, insightsengineering/nestcolor,
-    r-lib/pkgload, tidyverse/rvest, rstudio/shinytest2, r-lib/styler,
+    r-lib/pkgload, insightsengineering/roxy.shinylive, tidyverse/rvest, rstudio/shinytest2, r-lib/styler,
     r-lib/testthat, r-lib/withr
 Config/Needs/website: insightsengineering/nesttemplate
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-Roxygen: list(markdown = TRUE)
+Roxygen: list(markdown = TRUE, packages = c("roxy.shinylive"))
 RoxygenNote: 7.3.2
diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R
@@ -135,8 +135,14 @@ template_a_gee <- function(output_table,
 #'
 #' @inherit module_arguments return seealso
 #'
+#' @examplesShinylive
+#' library(teal.modules.clinical)
+#' interactive <- function() TRUE
+#' {{ next_example }}
+#'
 #' @examples
 #' library(dplyr)
+#'
 #' data <- teal_data()
 #' data <- within(data, {
 #'   ADSL <- tmc_ex_adsl
@@ -152,9 +158,8 @@ template_a_gee <- function(output_table,
 #'     ) %>%
 #'     droplevels()
 #' })
-#' datanames <- c("ADSL", "ADQS")
-#' datanames(data) <- datanames
-#' join_keys(data) <- default_cdisc_join_keys[datanames]
+#' datanames(data) <- c("ADSL", "ADQS")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
 #'
 #' app <- init(
 #'   data = data,

diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R
@@ -462,8 +462,14 @@ template_mmrm_plots <- function(fit_name,
 #'
 #' @inherit module_arguments return seealso
 #'
+#' @examplesShinylive
+#' library(teal.modules.clinical)
+#' interactive <- function() TRUE
+#' {{ next_example }}
+#'
 #' @examples
 #' library(dplyr)
+#'
 #' arm_ref_comp <- list(
 #'   ARMCD = list(
 #'     ref = "ARM B",
@@ -485,10 +491,9 @@ template_mmrm_plots <- function(fit_name,
 #'         as.factor() #' making consecutive numeric factor
 #'     )
 #' })
+#' datanames(data) <- c("ADSL", "ADQS")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
 #'
-#' datanames <- c("ADSL", "ADQS")
-#' datanames(data) <- datanames
-#' join_keys(data) <- default_cdisc_join_keys[datanames]
 #' app <- init(
 #'   data = data,
 #'   modules = modules(

diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R
@@ -15,26 +15,31 @@
 #'
 #' @inherit module_arguments return seealso
 #'
+#' @examplesShinylive
+#' library(teal.modules.clinical)
+#' interactive <- function() TRUE
+#' {{ next_example }}
+#'
 #' @examples
 #' library(nestcolor)
 #' library(dplyr)
 #'
-#' ADSL <- tmc_ex_adsl %>%
-#'   mutate(ITTFL = factor("Y") %>%
-#'     with_label("Intent-To-Treat Population Flag"))
-#' ADAE <- tmc_ex_adae %>%
-#'   filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADSL <- tmc_ex_adsl %>%
+#'     mutate(ITTFL = factor("Y") %>%
+#'       with_label("Intent-To-Treat Population Flag"))
+#'   ADAE <- tmc_ex_adae %>%
+#'     filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
+#' })
+#' datanames(data) <- c("ADSL", "ADAE")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#'
+#' ADSL <- data[["ADSL"]]
+#' ADAE <- data[["ADAE"]]
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     ADSL = ADSL,
-#'     ADAE = ADAE,
-#'     code = "ADSL <- tmc_ex_adsl %>%
-#'               mutate(ITTFL = factor(\"Y\") %>%
-#'               with_label(\"Intent-To-Treat Population Flag\"))
-#'             ADAE <- tmc_ex_adae %>%
-#'               filter(!((AETOXGR == 1) & (AESEV == \"MILD\") & (ARM == \"A: Drug X\")))"
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_g_barchart_simple(
 #'       label = "ADAE Analysis",

diff --git a/R/tm_g_ci.R b/R/tm_g_ci.R
@@ -189,21 +189,27 @@ template_g_ci <- function(dataname,
 #'
 #' @inherit module_arguments return seealso
 #'
+#' @examplesShinylive
+#' library(teal.modules.clinical)
+#' interactive <- function() TRUE
+#' {{ next_example }}
+#'
 #' @examples
 #' library(nestcolor)
 #'
-#' ADSL <- tmc_ex_adsl
-#' ADLB <- tmc_ex_adlb
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADSL <- tmc_ex_adsl
+#'   ADLB <- tmc_ex_adlb
+#' })
+#' datanames(data) <- c("ADSL", "ADLB")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#'
+#' ADSL <- data[["ADSL"]]
+#' ADLB <- data[["ADLB"]]
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     ADSL = ADSL,
-#'     ADLB = ADLB,
-#'     code = "
-#'       ADSL <- tmc_ex_adsl
-#'       ADLB <- tmc_ex_adlb
-#'     "
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_g_ci(
 #'       label = "Confidence Interval Plot",
@@ -253,10 +259,6 @@ template_g_ci <- function(dataname,
 #'         )
 #'       )
 #'     )
-#'   ),
-#'   header = "Example of Confidence Interval Plot",
-#'   footer = tags$p(
-#'     class = "text-muted", "Source: `teal.modules.clinical::tm_g_ci`"
 #'   )
 #' )
 #' if (interactive()) {

diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R
@@ -243,15 +243,28 @@ template_forest_rsp <- function(dataname = "ANL",
 #'
 #' @inherit module_arguments return seealso
 #'
+#' @examplesShinylive
+#' library(teal.modules.clinical)
+#' interactive <- function() TRUE
+#' {{ next_example }}
+#'
 #' @examples
 #' library(nestcolor)
 #' library(dplyr)
 #'
-#' ADSL <- tmc_ex_adsl
-#' ADRS <- tmc_ex_adrs %>%
-#'   mutate(AVALC = d_onco_rsp_label(AVALC) %>%
-#'     with_label("Character Result/Finding")) %>%
-#'   filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADSL <- tmc_ex_adsl
+#'   ADRS <- tmc_ex_adrs %>%
+#'     mutate(AVALC = d_onco_rsp_label(AVALC) %>%
+#'       with_label("Character Result/Finding")) %>%
+#'     filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
+#' })
+#' datanames(data) <- c("ADSL", "ADRS")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#'
+#' ADSL <- data[["ADSL"]]
+#' ADRS <- data[["ADRS"]]
 #'
 #' arm_ref_comp <- list(
 #'   ARM = list(
@@ -265,17 +278,7 @@ template_forest_rsp <- function(dataname = "ANL",
 #' )
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     ADSL = ADSL,
-#'     ADRS = ADRS,
-#'     code = "
-#'       ADSL <- tmc_ex_adsl
-#'       ADRS <- tmc_ex_adrs %>%
-#'         mutate(AVALC = d_onco_rsp_label(AVALC) %>%
-#'         with_label(\"Character Result/Finding\")) %>%
-#'         filter(PARAMCD != \"OVRINV\" | AVISIT == \"FOLLOW UP\")
-#'     "
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_g_forest_rsp(
 #'       label = "Forest Response",

diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R
@@ -243,12 +243,26 @@ template_forest_tte <- function(dataname = "ANL",
 #'
 #' @inherit module_arguments return seealso
 #'
+#' @examplesShinylive
+#' library(teal.modules.clinical)
+#' interactive <- function() TRUE
+#' {{ next_example }}
+#'
 #' @examples
 #' library(nestcolor)
+#' library(dplyr)
+#'
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADSL <- tmc_ex_adsl
+#'   ADTTE <- tmc_ex_adtte
+#'   ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label("Race")
+#' })
+#' datanames(data) <- c("ADSL", "ADTTE")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
 #'
-#' ADSL <- tmc_ex_adsl
-#' ADTTE <- tmc_ex_adtte
-#' ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label("Race")
+#' ADSL <- data[["ADSL"]]
+#' ADTTE <- data[["ADTTE"]]
 #'
 #' arm_ref_comp <- list(
 #'   ARM = list(
@@ -262,15 +276,7 @@ template_forest_tte <- function(dataname = "ANL",
 #' )
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     ADSL = ADSL,
-#'     ADTTE = ADTTE,
-#'     code = "
-#'       ADSL <- tmc_ex_adsl
-#'       ADTTE <- tmc_ex_adtte
-#'       ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label(\"Race\")
-#'     "
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_g_forest_tte(
 #'       label = "Forest Survival",

diff --git a/R/tm_g_ipp.R b/R/tm_g_ipp.R
@@ -179,28 +179,33 @@ template_g_ipp <- function(dataname = "ANL",
 #'
 #' @inherit module_arguments return seealso
 #'
+#' @examplesShinylive
+#' library(teal.modules.clinical)
+#' interactive <- function() TRUE
+#' {{ next_example }}
+#'
 #' @examples
 #' library(nestcolor)
 #' library(dplyr)
 #'
-#' ADSL <- tmc_ex_adsl %>%
-#'   slice(1:20) %>%
-#'   df_explicit_na()
-#' ADLB <- tmc_ex_adlb %>%
-#'   filter(USUBJID %in% ADSL$USUBJID) %>%
-#'   df_explicit_na() %>%
-#'   filter(AVISIT != "SCREENING")
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADSL <- tmc_ex_adsl %>%
+#'     slice(1:20) %>%
+#'     df_explicit_na()
+#'   ADLB <- tmc_ex_adlb %>%
+#'     filter(USUBJID %in% ADSL$USUBJID) %>%
+#'     df_explicit_na() %>%
+#'     filter(AVISIT != "SCREENING")
+#' })
+#' datanames(data) <- c("ADSL", "ADLB")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#'
+#' ADSL <- data[["ADSL"]]
+#' ADLB <- data[["ADLB"]]
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     ADSL = ADSL,
-#'     ADLB = ADLB,
-#'     code = "
-#'       ADSL <- tmc_ex_adsl %>% slice(1:20) %>% df_explicit_na()
-#'       ADLB <- tmc_ex_adlb %>% filter(USUBJID %in% ADSL$USUBJID) %>%
-#'         df_explicit_na() %>% filter(AVISIT != \"SCREENING\")
-#'     "
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_g_ipp(
 #'       label = "Individual Patient Plot",

diff --git a/R/tm_g_km.R b/R/tm_g_km.R
@@ -271,11 +271,24 @@ template_g_km <- function(dataname = "ANL",
 #'
 #' @inherit module_arguments return seealso
 #'
+#' @examplesShinylive
+#' library(teal.modules.clinical)
+#' interactive <- function() TRUE
+#' {{ next_example }}
+#'
 #' @examples
 #' library(nestcolor)
 #'
-#' ADSL <- tmc_ex_adsl
-#' ADTTE <- tmc_ex_adtte
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADSL <- tmc_ex_adsl
+#'   ADTTE <- tmc_ex_adtte
+#' })
+#' datanames(data) <- c("ADSL", "ADTTE")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#'
+#' ADSL <- data[["ADSL"]]
+#' ADTTE <- data[["ADTTE"]]
 #'
 #' arm_ref_comp <- list(
 #'   ACTARMCD = list(
@@ -289,14 +302,7 @@ template_g_km <- function(dataname = "ANL",
 #' )
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     ADSL = ADSL,
-#'     ADTTE = ADTTE,
-#'     code = "
-#'       ADSL <- tmc_ex_adsl
-#'       ADTTE <- tmc_ex_adtte
-#'     "
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_g_km(
 #'       label = "Kaplan-Meier Plot",