webr-alone

book/_quarto.yml

@@ -47,6 +47,7 @@ webr:
   repos:
     - https://insightsengineering.r-universe.dev/
   show-startup-message: false
+  autoload-packages: false
 
 filters:
   - insightsengineering/pattern-strip

book/shinylive-alone.qmd

@@ -0,0 +1,46 @@
+<!--
+This shortcode will include chunk returning WebR instance.
+
+Global shinylive configuration is available in the `_quarto.yaml` file.
+-->
+
+::: {.callout-warning appearance="simple"}
+## Experimental use!
+:::
+
+Modify the code below and run it to see the results.
+
+<!--
+we have to put some code upfront
+- need to setup repos on r-universe - currently it's not possible to setup this elsewhere (e.g. shinylive config or chunk attribute)
+- currently shinylive is using [email protected] which is missing a feature of shimming `library()` calls - need to add this manually
+-->
+
+```{r shinylive-constructor, echo=FALSE, results='asis'}
+repo_url <- ifelse(identical(Sys.getenv("QUARTO_PROFILE"), "stable"), "https://insightsengineering.r-universe.dev", "https://pharmaverse.r-universe.dev")
+text <- unlist(c(
+  "```{shinylive-r}",
+  "#| standalone: true",
+  "#| viewerHeight: 800",
+  "#| components: [viewer, editor]",
+  "#| layout: vertical",
+  "",
+  "# -- WEBR HELPERS --",
+  sprintf("options(webr_pkg_repos = c(\"r-universe\" = \"%s\", getOption(\"webr_pkg_repos\")))", repo_url),
+  "if (packageVersion(\"webr\") < \"0.3.0\") {",
+  "  .e <- as.environment(\"webr_shims\")",
+  "  .e[[\"library\"]] <- function(pkg, ...) {",
+  "    package <- as.character(substitute(pkg))",
+  "    if (length(find.package(package, quiet = TRUE)) == 0) {",
+  "      webr::install(package)",
+  "    }",
+  "    base::library(package, character.only = TRUE, ...)",
+  "  }",
+  "}",
+  "",
+  "# -- APP CODE --",
+  knitr::knit_code$get(c("teal")),
+  "```"
+))
+cat(text, sep = "\n")
+```

book/tables/adverse-events/aet02.qmd

@@ -7,7 +7,7 @@ subtitle: Adverse Events
 
 {{< include ../../test-utils/envir_hook.qmd >}}
 
-::: panel-tabset
+:::: panel-tabset
 ## Data Setup
 
 ```{r setup, message = FALSE}
@@ -35,7 +35,7 @@ split_fun <- drop_split_levels
 
 ## Standard Table
 
-```{r variant1, test = list(result_v1 = "result")}
+```{r variant1, test = list(result_v1 = "result"), include = FALSE}
 lyt <- basic_table(show_colcounts = TRUE) %>%
   split_cols_by(var = "ACTARM") %>%
   add_overall_col(label = "All Patients") %>%
@@ -72,11 +72,14 @@ lyt <- basic_table(show_colcounts = TRUE) %>%
 result <- build_table(lyt, df = adae, alt_counts_df = adsl)
 ```
 
+`r webr_code_labels <- c("setup", "variant1")`
+{{< include ../../webr-alone.qmd >}}
+
 The variable `result` corresponds to the adverse events table.
 However, it includes many empty rows accounting for events which were not reported.
 The table can be post-processed to prune empty rows and to sort rows, for example by occurrence.
 
-```{r variant2, test = list(result_v2 = "result")}
+```{r variant2, test = list(result_v2 = "result"), include = FALSE}
 result <- result %>%
   prune_table() %>%
   sort_at_path(
@@ -91,9 +94,12 @@ result <- result %>%
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant1", "variant2")`
+{{< include ../../webr-alone.qmd >}}
+
 ## Table with <br/> Event Totals
 
-```{r variant3, test = list(result_v3 = "result")}
+```{r variant3, test = list(result_v3 = "result"), include = FALSE}
 lyt <- basic_table(show_colcounts = TRUE) %>%
   split_cols_by(var = "ACTARM") %>%
   add_overall_col(label = "All Patients") %>%
@@ -144,9 +150,12 @@ result <- build_table(lyt, df = adae, alt_counts_df = adsl) %>%
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant3")`
+{{< include ../../webr-alone.qmd >}}
+
 ## Table with <br/> High-Level Term
 
-```{r variant4, test = list(result_v4 = "result")}
+```{r variant4, test = list(result_v4 = "result"), include = FALSE}
 lyt <- basic_table(show_colcounts = TRUE) %>%
   split_cols_by(var = "ACTARM") %>%
   analyze_num_patients(
@@ -211,9 +220,12 @@ result <- build_table(lyt, df = adae, alt_counts_df = adsl) %>%
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant4")`
+{{< include ../../webr-alone.qmd >}}
+
 ## Table with Preferred <br/> Terms Only
 
-```{r variant5, test = list(result_v5 = "result")}
+```{r variant5, test = list(result_v5 = "result"), include = FALSE}
 lyt <- basic_table(show_colcounts = TRUE) %>%
   split_cols_by(var = "ACTARM") %>%
   analyze_num_patients(
@@ -237,9 +249,12 @@ result <- build_table(lyt, df = adae, alt_counts_df = adsl) %>%
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant5")`
+{{< include ../../webr-alone.qmd >}}
+
 ## Table with Fill-In of <br/> Treatment Groups
 
-```{r variant6, test = list(result_v6 = "result")}
+```{r variant6, test = list(result_v6 = "result"), include = FALSE}
 adae_5 <- adae %>% dplyr::filter(ACTARM != "C: Combination")
 
 lyt <- basic_table(show_colcounts = TRUE) %>%
@@ -285,9 +300,12 @@ result <- build_table(lyt, df = adae_5, alt_counts_df = adsl) %>%
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant6")`
+{{< include ../../webr-alone.qmd >}}
+
 ## Table of AEs with an Incidence Rate <br/> $\geq$ 5% in Any Treatment Group (subsetting <br/> preferred terms based on frequency)
 
-```{r variant7, test = list(result_v7 = "result")}
+```{r variant7, test = list(result_v7 = "result"), include = FALSE}
 lyt <- basic_table(show_colcounts = TRUE) %>%
   split_cols_by(var = "ACTARM") %>%
   split_rows_by(
@@ -333,9 +351,12 @@ result <- prune_table(result, keep_rows(row_condition))
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant7")`
+{{< include ../../webr-alone.qmd >}}
+
 ## Table of AEs with an Incidence Rate $\geq$ 5% in <br/> Any Treatment Group (subsetting preferred terms <br/> based on frequency with high-level terms)
 
-```{r variant8, test = list(result_v8 = "result")}
+```{r variant8, test = list(result_v8 = "result"), include = FALSE}
 lyt <- basic_table(show_colcounts = TRUE) %>%
   split_cols_by(var = "ACTARM") %>%
   split_rows_by(
@@ -397,9 +418,12 @@ result <- prune_table(result, keep_rows(row_condition))
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant8")`
+{{< include ../../webr-alone.qmd >}}
+
 ## Table of AEs with an Incidence Rate $\geq$ 10% <br/> in Any Treatment Group (subsetting <br/> preferred terms based on frequency)
 
-```{r variant9, test = list(result_v9 = "result")}
+```{r variant9, test = list(result_v9 = "result"), include = FALSE}
 lyt <- basic_table(show_colcounts = TRUE) %>%
   split_cols_by(var = "ACTARM") %>%
   split_rows_by(
@@ -445,9 +469,12 @@ result <- prune_table(result, keep_rows(row_condition))
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant9")`
+{{< include ../../webr-alone.qmd >}}
+
 ## Table of AEs with an Incidence Rate $\geq$ 3 <br/> Patients in Any Treatment Group (subsetting <br/> preferred terms based on number of patients)
 
-```{r variant10, test = list(result_v10 = "result")}
+```{r variant10, test = list(result_v10 = "result"), include = FALSE}
 lyt <- basic_table(show_colcounts = TRUE) %>%
   split_cols_by(var = "ACTARM") %>%
   split_rows_by(
@@ -493,9 +520,12 @@ result <- prune_table(result, keep_rows(row_condition))
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant10")`
+{{< include ../../webr-alone.qmd >}}
+
 ## Table of AEs with a Difference in Incidence Rate $\geq$ 5% <br/> Between Any Treatment (subsetting preferred terms based <br/> on difference in percentage between treatment groups)
 
-```{r variant11, test = list(result_v11 = "result")}
+```{r variant11, test = list(result_v11 = "reresult"), include = FALSE}
 lyt <- basic_table(show_colcounts = TRUE) %>%
   split_cols_by(var = "ACTARM") %>%
   split_rows_by(
@@ -541,9 +571,12 @@ result <- prune_table(result, keep_rows(row_condition))
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant11")`
+{{< include ../../webr-alone.qmd >}}
+
 ## Table of AEs with an Incidence Rate $\geq$ 5% <br/> in B: Placebo (subsetting preferred terms based <br/> on frequency for a particular treatment group)
 
-```{r variant12, test = list(result_v12 = "result")}
+```{r variant12, test = list(result_v12 = "result"), include = FALSE}
 lyt <- basic_table(show_colcounts = TRUE) %>%
   split_cols_by(var = "ACTARM") %>%
   split_rows_by(
@@ -589,9 +622,12 @@ result <- prune_table(result, keep_rows(row_condition))
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant12")`
+{{< include ../../webr-alone.qmd >}}
+
 ## Table of AEs with a Difference in Incidence Rate $\geq$ 5% Between <br/> Arm A and Arm B or Arm C (displaying preferred terms with a <br/> difference of at least x% between selected treatment groups)
 
-```{r variant13, test = list(result_v13 = "result")}
+```{r variant13, test = list(result_v13 = "result"), include = FALSE}
 lyt <- basic_table(show_colcounts = TRUE) %>%
   split_cols_by(var = "ACTARM") %>%
   split_rows_by(
@@ -636,17 +672,22 @@ result <- prune_table(result, keep_rows(row_condition))
 result
 ```
 
+`r webr_code_labels <- c("setup", "variant13")`
+{{< include ../../webr-alone.qmd >}}
+
 {{< include ../../test-utils/save_results.qmd >}}
 
 ## `teal` App
 
-```{r teal, opts.label = c("skip_if_testing", "app")}
+```{r teal, opts.label = c("skip_if_testing", "app"), include = FALSE}
 library(teal.modules.clinical)
 
 ## Data reproducible code
 data <- teal_data()
 data <- within(data, {
   library(scda)
+  library(scda.2022)
+  library(tern)
   ADSL <- synthetic_cdisc_dataset("latest", "adsl")
   ADAE <- synthetic_cdisc_dataset("latest", "adae")
 
@@ -686,5 +727,7 @@ app <- init(
 shinyApp(app$ui, app$server)
 ```
 
+{{< include ../../shinylive-alone.qmd >}}
+
 {{< include ../../repro.qmd >}}
 :::

book/webr-alone.qmd

@@ -0,0 +1,33 @@
+<!--
+This shortcode will include chunk returning WebR instance.
+It requires pre-set `webr_code_labels` variable (character vector) containing labels of chunks to be included.
+
+Global WebR configuration is available in the `_quarto.yaml` file.
+-->
+
+::: {.callout-warning appearance="simple"}
+## Experimental use!
+:::
+
+Modify the code below and run it to see the results. Note that this includes also the "Data Setup" step from previous tab to make the code fully executable.
+
+```{r, echo=FALSE, results='asis'}
+if (!exists("webr_code_labels")) {
+  webr_code_labels <- character(0L)
+}
+if (!all(webr_code_labels %in% knitr::all_labels())) {
+  stop(sprintf(
+    "Not all of provided labels exist in the current document!\nNot found labels are: %s.",
+    paste0(setdiff(webr_code_labels, knitr::all_labels()), collapse = ", ")
+  ))
+}
+
+text <- unlist(c(
+  "```{webr-r}",
+  "#| editor-max-height: 500",
+  "#| autorun: true",
+  lapply(webr_code_labels, knitr::knit_code$get),
+  "```"
+))
+cat(text, sep = "\n")
+```