Merge branch 'main' into release-candidate-v0.6.0

Signed-off-by: Dony Unardi <donyunardi@gmail.com>

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: teal.transform
 Title: Functions for Extracting and Merging Data in the 'teal' Framework
 Version: 0.6.0
-Date: 2025-02-04
+Date: 2025-02-06
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "aut"),
@@ -40,6 +40,7 @@ Imports:
 Suggests:
     knitr (>= 1.42),
     rmarkdown (>= 2.23),
+    roxy.shinylive (>= 1.0.0),
     testthat (>= 3.1.5),
     withr (>= 2.0.0)
 VignetteBuilder:

NEWS.md

@@ -5,6 +5,8 @@
 * Added utility functions `first_choice`, `last_choice`, `first_choices`, and `last_choices` to increase the repertoire of specifying choices in delayed data, previously only served by `all_choices`.
 * Allowed `value_choices` to use `delayed_variable_choices` objects for `var_choices`.
 It is now possible to define a `data_extract_spec` without naming any variables.
+* Replace the example data generated using `scda` with `random.cdisc.data`.
+* Change log level from trace to debug for several functions.
 
 # teal.transform 0.5.0
 

vignettes/data-extract-merge.Rmd → vignettes/combining-data-extract-with-data-merge.Rmd

@@ -34,7 +34,7 @@ Let's see how to achieve this dynamic `select`, `filter`, and `merge` operations
 
 #### Step 1/5 - Preparing the Data
 
-```{r}
+```{r library}
 library(teal.transform)
 library(teal.data)
 library(shiny)
@@ -68,7 +68,7 @@ It is created by the `data_extract_spec()` function which takes in four argument
 3. `filter` helps specify the values of a variable we wish to filter during extraction. It can be generated using the function `filter_spec()`. In the case of `ADTTE`, we filter the variable `PARAMCD` by allowing users to choose from `CRSD`, `EFS`, `OS`, and `PFS`, with `OS` being the default filter.
 4. `reshape` is a boolean which helps to specify if the data needs to be reshaped from long to wide format. By default it is set to `FALSE`.
 
-```{r}
+```{r data_extract_spec}
 adsl_extract <- data_extract_spec(
   dataname = "ADSL",
   select = select_spec(
@@ -104,7 +104,7 @@ Here, we define the `merge_ui` function, which will be used to create the UI com
 
 Note that we take in the list of `data_extract` objects as input, and make use of the `data_extract_ui` function to create our UI.
 
-```{r}
+```{r merge_ui}
 merge_ui <- function(id, data_extracts) {
   ns <- NS(id)
   sidebarLayout(
@@ -140,7 +140,7 @@ This function takes as arguments the datasets (as a list of reactive `data.frame
 We make use of the `merge_expression_srv` function to get a reactive list containing merge expression and information needed to perform the transformation - see more in `merge_expression_srv` documentation.
 We print this expression in the UI  and also evaluate it to get the final `ANL` dataset which is also displayed as a table in the UI.
 
-```{r}
+```{r merge_srv}
 merge_srv <- function(id, datasets, data_extracts, join_keys) {
   moduleServer(id, function(input, output, session) {
     selector_list <- data_extract_multiple_srv(data_extracts, datasets, join_keys)
@@ -166,7 +166,7 @@ merge_srv <- function(id, datasets, data_extracts, join_keys) {
 Finally, we include `merge_ui` and `merge_srv` in the UI and server components of the `shinyApp`, respectively,
 using the `data_extract`s defined in the first code block and the `datasets` object:
 
-```{r eval=FALSE}
+```{r shinyapp, eval=FALSE}
 shinyApp(
   ui = fluidPage(merge_ui("data_merge", data_extracts)),
   server = function(input, output, session) {
@@ -175,4 +175,21 @@ shinyApp(
 )
 ```
 
-<img src="images/app-data-extract-merge.png" alt="Shiny app output for Data Extract and Merge" style="width: 100%;" />
+## Try it out in Shinylive
+
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
+code <- paste0(c(
+  knitr::knit_code$get("library"),
+  knitr::knit_code$get("data_extract_spec"),
+  knitr::knit_code$get("merge_ui"),
+  knitr::knit_code$get("merge_srv"),
+  knitr::knit_code$get("shinyapp")
+), collapse = "\n")
+
+url <- roxy.shinylive::create_shinylive_url(code)
+cat(sprintf("[Open in Shinylive](%s)\n\n", url))
+```
+
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+knitr::include_url(url, height = "800px")
+```

vignettes/data-extract.Rmd

@@ -31,7 +31,7 @@ Let's delve into how it fulfills both of these responsibilities.
 
 #### Step 1/4 - Preparing the Data
 
-```{r}
+```{r library}
 library(teal.transform)
 library(teal.data)
 library(shiny)
@@ -59,7 +59,7 @@ Consider the following example, where we create two UI elements, one to filter o
 and a second one to select a variable from `c("BMRKR1", "AGE")`.
 `data_extract_spec` object is handed over to the `shiny` app and gives instructions to generate UI components.
 
-```{r}
+```{r data_extract_spec}
 simple_des <- data_extract_spec(
   dataname = "ADSL",
   filter = filter_spec(vars = "SEX", choices = c("F", "M")),
@@ -74,7 +74,7 @@ utilizes `data_extract_ui` and `data_extract_srv` to handle `data_extract_spec`
 This module creates a UI component for a single `data_extract_spec` and prints a list of values returned from the `data_extract_srv` module.
 For more information about `data_extract_ui` and `data_extract_srv`, please refer to the package documentation.
 
-```{r}
+```{r extract_ui_srv}
 extract_ui <- function(id, data_extract) {
   ns <- NS(id)
   sidebarLayout(
@@ -106,7 +106,7 @@ extract_srv <- function(id, datasets, data_extract, join_keys) {
 
 Finally, we include `extract_ui` in the UI of the `shinyApp`, and utilize `extract_srv` in the server function of the `shinyApp`:
 
-```{r eval=FALSE}
+```{r shinyapp, eval=FALSE}
 shinyApp(
   ui = fluidPage(extract_ui("data_extract", simple_des)),
   server = function(input, output, session) {
@@ -115,4 +115,20 @@ shinyApp(
 )
 ```
 
-<img src="images/app-data-extract.png" alt="Shiny app output for Data Extract" style="width: 100%;" />
+## Try it out in Shinylive
+
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
+code <- paste0(c(
+  knitr::knit_code$get("library"),
+  knitr::knit_code$get("data_extract_spec"),
+  knitr::knit_code$get("extract_ui_srv"),
+  knitr::knit_code$get("shinyapp")
+), collapse = "\n")
+
+url <- roxy.shinylive::create_shinylive_url(code)
+cat(sprintf("[Open in Shinylive](%s)\n\n", url))
+```
+
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+knitr::include_url(url, height = "800px")
+```

vignettes/data-merge.Rmd

@@ -35,7 +35,7 @@ a list of reactive or non-reactive `data.frame` objects, and a list of join keys
 
 #### Step 1/5 - Preparing the Data
 
-```{r}
+```{r library}
 library(teal.transform)
 library(teal.data)
 library(shiny)
@@ -61,7 +61,7 @@ join_keys <- join_keys(
 
 #### Step 2/5 - Creating the Data Extracts
 
-```{r}
+```{r data_extract_spec}
 adsl_extract <- data_extract_spec(
   dataname = "ADSL",
   select = select_spec(
@@ -88,7 +88,7 @@ data_extracts <- list(adsl_extract = adsl_extract, adtte_extract = adtte_extract
 
 #### Step 3/5 - Creating the UI
 
-```{r}
+```{r merge_ui}
 merge_ui <- function(id, data_extracts) {
   ns <- NS(id)
   sidebarLayout(
@@ -118,7 +118,7 @@ merge_ui <- function(id, data_extracts) {
 
 #### Step 4/5 - Creating the Server Logic
 
-```{r}
+```{r merge_srv}
 merge_srv <- function(id, datasets, data_extracts, join_keys) {
   moduleServer(id, function(input, output, session) {
     merged_data <- merge_expression_module(
@@ -140,7 +140,7 @@ merge_srv <- function(id, datasets, data_extracts, join_keys) {
 
 #### Step 5/5 - Creating the `shiny` App
 
-```{r eval=FALSE}
+```{r shinyapp, eval=FALSE}
 shinyApp(
   ui = fluidPage(merge_ui("data_merge", data_extracts)),
   server = function(input, output, session) {
@@ -149,8 +149,22 @@ shinyApp(
 )
 ```
 
-<img src="images/app-data-merge-1.png" alt="Shiny app output for Data Extract" style="width: 100%;" />
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
+code <- paste0(c(
+  knitr::knit_code$get("library"),
+  knitr::knit_code$get("data_extract_spec"),
+  knitr::knit_code$get("merge_ui"),
+  knitr::knit_code$get("merge_srv"),
+  knitr::knit_code$get("shinyapp")
+), collapse = "\n")
+
+url <- roxy.shinylive::create_shinylive_url(code)
+cat(sprintf("[Open in Shinylive](%s)\n\n", url))
+```
 
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+knitr::include_url(url, height = "800px")
+```
 
 <hr>
 
@@ -163,7 +177,7 @@ The `reactive_selector_list` is then passed to `merge_expression_srv`:
 
 #### Modifying the Server Logic
 
-```{r}
+```{r merge_srv2}
 merge_srv <- function(id, datasets, data_extracts, join_keys) {
   moduleServer(id, function(input, output, session) {
     selector_list <- data_extract_multiple_srv(data_extracts, datasets, join_keys)
@@ -194,7 +208,7 @@ merge_srv <- function(id, datasets, data_extracts, join_keys) {
 
 #### Updating the `shiny` app
 
-```{r eval=FALSE}
+```{r shinyapp2, eval=FALSE}
 shinyApp(
   ui = fluidPage(merge_ui("data_merge", data_extracts)),
   server = function(input, output, session) {
@@ -203,7 +217,22 @@ shinyApp(
 )
 ```
 
-<img src="images/app-data-merge-2.png" alt="Shiny app output for Data Extract" style="width: 100%;" />
+```{r shinylive_url2, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
+code <- paste0(c(
+  knitr::knit_code$get("library"),
+  knitr::knit_code$get("data_extract_spec"),
+  knitr::knit_code$get("merge_ui"),
+  knitr::knit_code$get("merge_srv2"),
+  knitr::knit_code$get("shinyapp2")
+), collapse = "\n")
+
+url <- roxy.shinylive::create_shinylive_url(code)
+cat(sprintf("[Open in Shinylive](%s)\n\n", url))
+```
+
+```{r shinylive_iframe2, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+knitr::include_url(url, height = "800px")
+```
 
 `merge_expression_module` is replaced here with three parts: