included code vignettes and fixing notes

R/tm_g_barchart_simple.R

@@ -16,17 +16,21 @@
 #' @examples
 #' library(nestcolor)
 #'
-#' ADSL <- tmc_ex_adsl %>% dplyr::mutate(ITTFL = factor("Y") %>%
+#' ADSL <- tmc_ex_adsl %>%
+#'   dplyr::mutate(ITTFL = factor("Y") %>%
 #'   formatters::with_label("Intent-To-Treat Population Flag"))
-#' ADAE <- tmc_ex_adae %>% dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
+#' ADAE <- tmc_ex_adae %>%
+#'   dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
 #'
 #' app <- init(
 #'   data = cdisc_data(
 #'     ADSL = ADSL,
 #'     ADAE = ADAE,
-#'     code = "ADSL <- tmc_ex_adsl %>% dplyr::mutate(ITTFL = factor(\"Y\") %>%
+#'     code = "ADSL <- tmc_ex_adsl %>%
+#'               dplyr::mutate(ITTFL = factor(\"Y\") %>%
 #'               formatters::with_label(\"Intent-To-Treat Population Flag\"))
-#'             ADAE <- tmc_ex_adae %>% dplyr::filter(!((AETOXGR == 1) & (AESEV == \"MILD\") & (ARM == \"A: Drug X\")))"
+#'             ADAE <- tmc_ex_adae %>%
+#'               dplyr::filter(!((AETOXGR == 1) & (AESEV == \"MILD\") & (ARM == \"A: Drug X\")))"
 #'   ),
 #'   modules = modules(
 #'     tm_g_barchart_simple(

R/tm_g_pp_therapy.R

@@ -272,7 +272,7 @@ template_therapy <- function(dataname = "ANL",
 #' app <- init(
 #'   data = cdisc_data(
 #'     ADSL = ADSL,
-#'     ADCM = adcm,
+#'     ADCM = ADCM,
 #'     code = "
 #'       ADCM <- tmc_ex_adcm
 #'       ADSL <- tmc_ex_adsl %>% dplyr::filter(USUBJID %in% ADCM$USUBJID)

R/tm_t_logistic.R

@@ -250,7 +250,7 @@ template_logistic <- function(dataname,
 #'     code = "
 #'       ADSL <- tmc_ex_adsl
 #'       ADRS <- tmc_ex_adrs %>%
-#'         dplyr::filter(PARAMCD %in% c("BESRSPI", "INVET"))
+#'         dplyr::filter(PARAMCD %in% c(\"BESRSPI\", \"INVET\"))
 #'     "
 #'   ),
 #'   modules = modules(

vignettes/teal-modules-clinical.Rmd

@@ -52,21 +52,25 @@ A simple application including a bar chart module could look like this:
 library(teal.modules.clinical)
 library(nestcolor)
 
-adsl <- tmc_ex_adsl
-adae <- tmc_ex_adae
+ADSL <- tmc_ex_adsl
+ADAE <- tmc_ex_adae
 
 app <- teal::init(
   data = teal.data::cdisc_data(
-    ADSL = adsl,
-    ADAE = adae
+    ADSL = ADSL,
+    ADAE = ADAE,
+    code = "
+      ADSL <- tmc_ex_adsl
+      ADAE <- tmc_ex_adae
+    "
   ),
   modules = list(
     tm_g_barchart_simple(
       label = "ADAE Analysis", 
       x = teal.transform::data_extract_spec(
         dataname = "ADAE",
         select = teal.transform::select_spec(
-          choices = teal.transform::variable_choices(adae),
+          choices = teal.transform::variable_choices(ADAE),
           multiple = FALSE
         )
       )
@@ -90,8 +94,8 @@ library(nestcolor)
 ```
 The above lines load the libraries used in this example. We will use the example data provided in the `teal.modules.clinical` package:
 ```r
-adsl <- tmc_ex_adsl
-adae <- tmc_ex_adae
+ADSL <- tmc_ex_adsl
+ADAE <- tmc_ex_adae
 ```
 `nestcolor` is an optional package that can be loaded in to apply the standardized NEST color palette to all module plots.
 
@@ -103,15 +107,19 @@ argument indicates the modules included in the application. Here, we include onl
 ```r
 app <- teal::init(
   data = teal.data::cdisc_data(
-    ADSL = adsl,
-    ADAE = adae
+    ADSL = ADSL,
+    ADAE = ADAE,
+    code = "
+      ADSL <- tmc_ex_adsl
+      ADAE <- tmc_ex_adae
+    "
   ),
   modules = list(
     tm_g_barchart_simple(
       label = "ADAE Analysis", 
       x = teal.transform::data_extract_spec(
         dataname = "ADAE",
-        select = teal.transform::select_spec(choices = teal.transform::variable_choices(adae), multiple = FALSE)
+        select = teal.transform::select_spec(choices = teal.transform::variable_choices(ADAE), multiple = FALSE)
       )
     )
   )
@@ -126,9 +134,9 @@ if (interactive()) shiny::shinyApp(app$ui, app$server)
 Some of `teal.modules.clinical` modules allow specifying arguments using `teal.transform::choices_selected` such as
 `tm_t_summary` module in this example:
 ```r
-adsl <- tmc_ex_adsl
+ADSL <- tmc_ex_adsl
 app <- teal::init(
-  data = teal.data::cdisc_data(ADSL = adsl),
+  data = teal.data::cdisc_data(ADSL = ADSL, code = "ADSL <- tmc_ex_adsl"),
   modules = list(
     tm_t_summary(
       label = "Demographic Table",