📑 Reporter Refactor: Adds support for new teal_report and teal_card class

DESCRIPTION

@@ -49,7 +49,9 @@ Suggests:
     testthat (>= 3.2.3),
     withr (>= 3.0.0)
 Remotes:
-    insightsengineering/osprey
+    insightsengineering/osprey,
+    insightsengineering/teal@teal_reportable,
+    insightsengineering/teal.reporter@teal_reportable,
 Config/Needs/verdepcheck: insightsengineering/osprey, rstudio/shiny,
     insightsengineering/teal, insightsengineering/teal.slice,
     insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr,

R/tm_g_ae_oview.R

@@ -12,6 +12,7 @@
 #'   sub-groups (e.g. Serious events, Related events, etc.)
 #'
 #' @inherit argument_convention return
+#' @inheritSection teal::example_module Reporting
 #'
 #' @export
 #'
@@ -129,10 +130,6 @@ ui_g_ae_oview <- function(id, ...) {
       plot_decorate_output(id = ns(NULL))
     ),
     encoding = tags$div(
-      ### Reporter
-      teal.reporter::add_card_button_ui(ns("add_reporter"), label = "Add Report Card"),
-      tags$br(), tags$br(),
-      ###
       teal.widgets::optionalSelectInput(
         ns("arm_var"),
         "Arm Variable",
@@ -198,14 +195,10 @@ ui_g_ae_oview <- function(id, ...) {
 
 srv_g_ae_oview <- function(id,
                            data,
-                           filter_panel_api,
-                           reporter,
                            dataname,
                            label,
                            plot_height,
                            plot_width) {
-  with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
-  with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
 
@@ -286,7 +279,16 @@ srv_g_ae_oview <- function(id,
     output_q <- shiny::debounce(
       millis = 200,
       r = reactive({
-        ANL <- data()[[dataname]]
+        obj <- data()
+        teal.reporter::teal_card(obj) <-
+          c(
+            teal.reporter::teal_card("# AE Overview"),
+            teal.reporter::teal_card(obj),
+            teal.reporter::teal_card("## Module's code")
+          )
+        obj <- teal.code::eval_code(obj, expression(library("dplyr")))
+
+        ANL <- obj[[dataname]]
 
         teal::validate_has_data(ANL, min_nrow = 10, msg = sprintf("%s has not enough data", dataname))
 
@@ -297,7 +299,7 @@ srv_g_ae_oview <- function(id,
           "Treatment or Control not found in Arm Variable. Perhaps they have been filtered out?"
         ))
 
-        q1 <- teal.code::eval_code(data(), "library(dplyr)") %>%
+        q1 <- obj %>%
           teal.code::eval_code(
             code = as.expression(c(
               bquote(anl_labels <- formatters::var_labels(.(as.name(dataname)), fill = FALSE)),
@@ -309,6 +311,8 @@ srv_g_ae_oview <- function(id,
             ))
           )
 
+        teal.reporter::teal_card(q1) <- c(teal.reporter::teal_card(q1), "## Plot")
+
         teal.code::eval_code(
           q1,
           code = as.expression(c(
@@ -339,25 +343,6 @@ srv_g_ae_oview <- function(id,
       verbatim_content = reactive(teal.code::get_code(output_q())),
       title = paste("R code for", label)
     )
-    ### REPORTER
-    if (with_reporter) {
-      card_fun <- function(comment, label) {
-        card <- teal::report_card_template(
-          title = "AE Overview",
-          label = label,
-          with_filter = with_filter,
-          filter_panel_api = filter_panel_api
-        )
-        card$append_text("Plot", "header3")
-        card$append_plot(plot_r(), dim = pws$dim())
-        if (!comment == "") {
-          card$append_text("Comment", "header3")
-          card$append_text(comment)
-        }
-        card$append_src(teal.code::get_code(output_q()))
-        card
-      }
-      teal.reporter::add_card_button_srv("add_reporter", reporter = reporter, card_fun = card_fun)
-    }
+    output_q
   })
 }

R/tm_g_ae_sub.R

@@ -13,6 +13,7 @@
 #' @author Molly He (hey59) \email{[email protected]}
 #'
 #' @inherit argument_convention return
+#' @inheritSection teal::example_module Reporting
 #'
 #' @export
 #'
@@ -104,10 +105,6 @@ ui_g_ae_sub <- function(id, ...) {
       plot_decorate_output(id = ns(NULL))
     ),
     encoding = tags$div(
-      ### Reporter
-      teal.reporter::add_card_button_ui(ns("add_reporter"), label = "Add Report Card"),
-      tags$br(), tags$br(),
-      ###
       tags$label("Encodings", class = "text-primary"),
       helpText("Analysis data:", tags$code("ADAE")),
       teal.widgets::optionalSelectInput(
@@ -175,14 +172,10 @@ ui_g_ae_sub <- function(id, ...) {
 
 srv_g_ae_sub <- function(id,
                          data,
-                         filter_panel_api,
-                         reporter,
                          dataname,
                          label,
                          plot_height,
                          plot_width) {
-  with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
-  with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
@@ -317,8 +310,16 @@ srv_g_ae_sub <- function(id,
     output_q <- shiny::debounce(
       millis = 200,
       r = reactive({
-        ANL <- data()[[dataname]]
-        ADSL <- data()[["ADSL"]]
+        obj <- data()
+        teal.reporter::teal_card(obj) <-
+          c(
+            teal.reporter::teal_card("# AE by Subgroups"),
+            teal.reporter::teal_card(obj),
+            teal.reporter::teal_card("## Module's code")
+          )
+
+        ANL <- obj[[dataname]]
+        ADSL <- obj[["ADSL"]]
 
         teal::validate_has_data(ANL, min_nrow = 10, msg = sprintf("%s has not enough data", dataname))
 
@@ -347,29 +348,34 @@ srv_g_ae_sub <- function(id,
           bquote(group_labels <- setNames(.(group_labels), .(input$groups)))
         }
 
-        teal.code::eval_code(data(), code = group_labels_call) %>%
-          teal.code::eval_code(code = "") %>%
-          teal.code::eval_code(
-            code = as.expression(c(
-              bquote(
-                plot <- osprey::g_ae_sub(
-                  id = .(as.name(dataname))$USUBJID,
-                  arm = as.factor(.(as.name(dataname))[[.(input$arm_var)]]),
-                  arm_sl = as.character(ADSL[[.(input$arm_var)]]),
-                  trt = .(input$arm_trt),
-                  ref = .(input$arm_ref),
-                  subgroups = .(as.name(dataname))[.(input$groups)],
-                  subgroups_sl = ADSL[.(input$groups)],
-                  subgroups_levels = group_labels,
-                  conf_level = .(input$conf_level),
-                  diff_ci_method = .(input$ci),
-                  fontsize = .(font_size()),
-                  arm_n = .(input$arm_n),
-                  draw = TRUE
-                )
+        q1 <- teal.code::eval_code(obj, code = group_labels_call) %>%
+          teal.code::eval_code(code = "")
+
+        teal.reporter::teal_card(q1) <- c(teal.reporter::teal_card(q1), "## Plot")
+
+        teal.code::eval_code(
+          q1,
+          code = as.expression(c(
+            bquote(
+              plot <- osprey::g_ae_sub(
+                id = .(as.name(dataname))$USUBJID,
+                arm = as.factor(.(as.name(dataname))[[.(input$arm_var)]]),
+                arm_sl = as.character(ADSL[[.(input$arm_var)]]),
+                trt = .(input$arm_trt),
+                ref = .(input$arm_ref),
+                subgroups = .(as.name(dataname))[.(input$groups)],
+                subgroups_sl = ADSL[.(input$groups)],
+                subgroups_levels = group_labels,
+                conf_level = .(input$conf_level),
+                diff_ci_method = .(input$ci),
+                fontsize = .(font_size()),
+                arm_n = .(input$arm_n),
+                draw = TRUE
               )
-            ))
-          )
+            ),
+            quote(plot)
+          ))
+        )
       })
     )
 
@@ -380,26 +386,6 @@ srv_g_ae_sub <- function(id,
       verbatim_content = reactive(teal.code::get_code(output_q())),
       title = paste("R code for", label),
     )
-
-    ### REPORTER
-    if (with_reporter) {
-      card_fun <- function(comment, label) {
-        card <- teal::report_card_template(
-          title = "AE Subgroups",
-          label = label,
-          with_filter = with_filter,
-          filter_panel_api = filter_panel_api
-        )
-        card$append_text("Plot", "header3")
-        card$append_plot(plot_r(), dim = pws$dim())
-        if (!comment == "") {
-          card$append_text("Comment", "header3")
-          card$append_text(comment)
-        }
-        card$append_src(teal.code::get_code(output_q()))
-        card
-      }
-      teal.reporter::add_card_button_srv("add_reporter", reporter = reporter, card_fun = card_fun)
-    }
+    output_q
   })
 }

R/tm_g_butterfly.R

@@ -33,6 +33,7 @@
 #'   used directly as filter.
 #'
 #' @inherit argument_convention return
+#' @inheritSection teal::example_module Reporting
 #'
 #' @export
 #'
@@ -166,10 +167,6 @@ ui_g_butterfly <- function(id, ...) {
       teal.widgets::plot_with_settings_ui(id = ns("butterflyplot"))
     ),
     encoding = tags$div(
-      ### Reporter
-      teal.reporter::add_card_button_ui(ns("add_reporter"), label = "Add Report Card"),
-      tags$br(), tags$br(),
-      ###
       tags$label("Encodings", class = "text-primary"),
       helpText("Dataset is:", tags$code(a$dataname)),
       if (!is.null(a$filter_var)) {
@@ -264,9 +261,7 @@ ui_g_butterfly <- function(id, ...) {
   )
 }
 
-srv_g_butterfly <- function(id, data, filter_panel_api, reporter, dataname, label, plot_height, plot_width) {
-  with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
-  with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
+srv_g_butterfly <- function(id, data, dataname, label, plot_height, plot_width) {
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
@@ -386,8 +381,17 @@ srv_g_butterfly <- function(id, data, filter_panel_api, reporter, dataname, labe
     output_q <- shiny::debounce(
       millis = 200,
       r = reactive({
-        ADSL <- data()[["ADSL"]]
-        ANL <- data()[[dataname]]
+        obj <- data()
+        teal.reporter::teal_card(obj) <-
+          c(
+            teal.reporter::teal_card("# Butterfly Plot"),
+            teal.reporter::teal_card(obj),
+            teal.reporter::teal_card("## Module's code")
+          )
+        obj <- teal.code::eval_code(obj, expression(library("dplyr")))
+
+        ADSL <- obj[["ADSL"]]
+        ANL <- obj[[dataname]]
 
         teal::validate_has_data(ADSL, min_nrow = 0, msg = sprintf("%s Data is empty", "ADSL"))
         teal::validate_has_data(ANL, min_nrow = 0, msg = sprintf("%s Data is empty", dataname))
@@ -422,13 +426,13 @@ srv_g_butterfly <- function(id, data, filter_panel_api, reporter, dataname, labe
         adsl_vars <- unique(c("USUBJID", "STUDYID", varlist_from_adsl))
         anl_vars <- unique(c("USUBJID", "STUDYID", varlist_from_anl))
 
-        q1 <- teal.code::eval_code(data(), "library(dplyr)") %>%
-          teal.code::eval_code(
-            code = bquote({
-              ADSL <- ADSL[, .(adsl_vars)] %>% as.data.frame()
-              ANL <- .(as.name(dataname))[, .(anl_vars)] %>% as.data.frame()
-            })
-          )
+        q1 <- teal.code::eval_code(
+          obj,
+          code = bquote({
+            ADSL <- ADSL[, .(adsl_vars)] %>% as.data.frame()
+            ANL <- .(as.name(dataname))[, .(anl_vars)] %>% as.data.frame()
+          })
+        )
 
         if (!("NULL" %in% filter_var) && !is.null(filter_var)) {
           q1 <- teal.code::eval_code(
@@ -461,6 +465,21 @@ srv_g_butterfly <- function(id, data, filter_panel_api, reporter, dataname, labe
           )
         }
 
+        teal.reporter::teal_card(q1) <- c(teal.reporter::teal_card(q1), "## Plot")
+
+        if (!is.null(input$filter_var) || !is.null(input$facet_var) || !is.null(input$sort_by_var)) {
+          teal.reporter::teal_card(q1) <- c(teal.reporter::teal_card(q1), "### Selected Options")
+        }
+        if (!is.null(input$filter_var)) {
+          teal.reporter::teal_card(q1) <- c(teal.reporter::teal_card(q1), paste0("Preset Data Filters: ", paste(input$filter_var, collapse = ", "), "."))
+        }
+        if (!is.null(input$facet_var)) {
+          teal.reporter::teal_card(q1) <- c(teal.reporter::teal_card(q1), paste0("Faceted by: ", paste(input$facet_var, collapse = ", "), "."))
+        }
+        if (!is.null(input$sort_by_var)) {
+          teal.reporter::teal_card(q1) <- c(teal.reporter::teal_card(q1), paste0("Sorted by: ", paste(input$sort_by_var, collapse = ", "), "."))
+        }
+
         if (!is.null(right_val) && !is.null(left_val)) {
           q1 <- teal.code::eval_code(
             q1,
@@ -511,38 +530,6 @@ srv_g_butterfly <- function(id, data, filter_panel_api, reporter, dataname, labe
       title = paste("R code for", label),
       verbatim_content = reactive(teal.code::get_code(output_q()))
     )
-
-    ### REPORTER
-    if (with_reporter) {
-      card_fun <- function(comment, label) {
-        card <- teal::report_card_template(
-          title = "Butterfly Plot",
-          label = label,
-          with_filter = with_filter,
-          filter_panel_api = filter_panel_api
-        )
-        if (!is.null(input$filter_var) || !is.null(input$facet_var) || !is.null(input$sort_by_var)) {
-          card$append_text("Selected Options", "header3")
-        }
-        if (!is.null(input$filter_var)) {
-          card$append_text(paste0("Preset Data Filters: ", paste(input$filter_var, collapse = ", "), "."))
-        }
-        if (!is.null(input$facet_var)) {
-          card$append_text(paste0("Faceted by: ", paste(input$facet_var, collapse = ", "), "."))
-        }
-        if (!is.null(input$sort_by_var)) {
-          card$append_text(paste0("Sorted by: ", paste(input$sort_by_var, collapse = ", "), "."))
-        }
-        card$append_text("Plot", "header3")
-        card$append_plot(plot_r(), dim = pws$dim())
-        if (!comment == "") {
-          card$append_text("Comment", "header3")
-          card$append_text(comment)
-        }
-        card$append_src(teal.code::get_code(output_q()))
-        card
-      }
-      teal.reporter::add_card_button_srv("add_reporter", reporter = reporter, card_fun = card_fun)
-    }
+    output_q
   })
 }