📑 Reporter Refactor: Adds support for new teal_report and teal_card class (#1392)

Closes #1376

---------

Signed-off-by: Marcin <[email protected]>
Signed-off-by: André Veríssimo <[email protected]>
Co-authored-by: André Veríssimo <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <[email protected]>

Author: 4 people

DESCRIPTION

@@ -32,8 +32,8 @@ URL: https://insightsengineering.github.io/teal.modules.clinical/,
 BugReports:
     https://github.com/insightsengineering/teal.modules.clinical/issues
 Depends:
-    R (>= 4.4.0),
-    teal (>= 1.0.0),
+    R (>= 4.4),
+    teal (>= 1.0.0.9003),
     teal.transform (>= 0.7.0),
     tern (>= 0.9.9)
 Imports:
@@ -60,7 +60,7 @@ Imports:
     teal.code (>= 0.7.0),
     teal.data (>= 0.8.0),
     teal.logger (>= 0.4.0),
-    teal.reporter (>= 0.5.0),
+    teal.reporter (>= 0.5.0.9001),
     teal.widgets (>= 0.5.0),
     tern.gee (>= 0.1.5),
     tern.mmrm (>= 0.3.3),
@@ -82,6 +82,9 @@ Suggests:
 VignetteBuilder:
     knitr,
     rmarkdown
+Remotes:
+    insightsengineering/teal.reporter,
+    insightsengineering/teal
 Config/Needs/verdepcheck: insightsengineering/teal,
     insightsengineering/teal.slice, insightsengineering/teal.transform,
     insightsengineering/tern, tidymodels/broom, mllg/checkmate,

R/tm_a_gee.R

@@ -159,6 +159,8 @@ template_a_gee <- function(output_table,
 #' To learn more please refer to the vignette
 #' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
+#' @inheritSection teal::example_module Reporting
+#'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
 #' interactive <- function() TRUE
@@ -299,10 +301,6 @@ ui_gee <- function(id, ...) {
       teal.widgets::table_with_settings_ui(ns("table"))
     ),
     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"), tags$br(),
       teal.transform::datanames_input(a[c("arm_var", "paramcd", "id_var", "visit_var", "cov_var", "aval_var")]),
       teal.transform::data_extract_ui(
@@ -402,8 +400,6 @@ ui_gee <- function(id, ...) {
 
 srv_gee <- function(id,
                     data,
-                    filter_panel_api,
-                    reporter,
                     dataname,
                     parentname,
                     arm_var,
@@ -419,8 +415,6 @@ srv_gee <- function(id,
                     plot_width,
                     basic_table_args,
                     decorators) {
-  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")
 
@@ -510,7 +504,14 @@ srv_gee <- function(id,
     )
 
     anl_q <- reactive({
-      data() %>%
+      obj <- data()
+      teal.reporter::teal_card(obj) <-
+        c(
+          teal.reporter::teal_card("# Generalized Estimating Equations (GEE) Analysis Table"),
+          teal.reporter::teal_card(obj),
+          teal.reporter::teal_card("## Module's code")
+        )
+      obj %>%
         teal.code::eval_code(as.expression(anl_inputs()$expr)) %>%
         teal.code::eval_code(as.expression(adsl_inputs()$expr))
     })
@@ -564,7 +565,16 @@ srv_gee <- function(id,
         cor_struct = input$cor_struct,
         basic_table_args = basic_table_args
       )
-      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
+
+      table_type <- switch(input$output_table,
+        "t_gee_cov" = "Residual Covariance Matrix Estimate",
+        "t_gee_coef" = "Model Coefficients",
+        "t_gee_lsmeans" = "LS Means Estimates"
+      )
+
+      obj <- merged$anl_q()
+      teal.reporter::teal_card(obj) <- c(teal.reporter::teal_card(obj), paste("## ", table_type, "Table"))
+      teal.code::eval_code(obj, as.expression(unlist(my_calls)))
     })
 
     output$gee_title <- renderText({
@@ -602,30 +612,6 @@ srv_gee <- function(id,
       title = label
     )
 
-    ### REPORTER
-    if (with_reporter) {
-      card_fun <- function(comment, label) {
-        card <- teal::report_card_template(
-          title = "Generalized Estimating Equations (GEE) Analysis Table",
-          label = label,
-          with_filter = with_filter,
-          filter_panel_api = filter_panel_api
-        )
-        table_type <- switch(input$output_table,
-          "t_gee_cov" = "Residual Covariance Matrix Estimate",
-          "t_gee_coef" = "Model Coefficients",
-          "t_gee_lsmeans" = "LS Means Estimates"
-        )
-        card$append_text(paste(table_type, "Table"), "header3")
-        card$append_table(table_r())
-        if (!comment == "") {
-          card$append_text("Comment", "header3")
-          card$append_text(comment)
-        }
-        card$append_src(source_code_r())
-        card
-      }
-      teal.reporter::add_card_button_srv("add_reporter", reporter = reporter, card_fun = card_fun)
-    }
+    decorated_table_q
   })
 }

R/tm_a_mmrm.R

@@ -493,6 +493,8 @@ template_mmrm_plots <- function(fit_name,
 #' To learn more please refer to the vignette
 #' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
+#' @inheritSection teal::example_module Reporting
+#'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
 #' interactive <- function() TRUE
@@ -520,7 +522,7 @@ template_mmrm_plots <- function(fit_name,
 #'       AVISITN = rank(AVISITN) %>%
 #'         as.factor() %>%
 #'         as.numeric() %>%
-#'         as.factor() #' making consecutive numeric factor
+#'         as.factor() # making consecutive numeric factor
 #'     )
 #' })
 #' join_keys(data) <- default_cdisc_join_keys[names(data)]
@@ -677,10 +679,6 @@ ui_mmrm <- function(id, ...) {
         teal.widgets::plot_with_settings_ui(id = ns("mmrm_plot"))
       ),
       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"), tags$br(),
         teal.transform::datanames_input(a[c("arm_var", "paramcd", "id_var", "visit_var", "cov_var", "aval_var")]),
         bslib::accordion(
@@ -901,8 +899,6 @@ ui_mmrm <- function(id, ...) {
 #' @keywords internal
 srv_mmrm <- function(id,
                      data,
-                     reporter,
-                     filter_panel_api,
                      dataname,
                      parentname,
                      arm_var,
@@ -920,8 +916,6 @@ srv_mmrm <- function(id,
                      basic_table_args,
                      ggplot2_args,
                      decorators) {
-  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")
 
@@ -1040,7 +1034,14 @@ srv_mmrm <- function(id,
     })
 
     anl_q <- reactive({
-      data_with_tern_options_r() %>%
+      obj <- data_with_tern_options_r()
+      teal.reporter::teal_card(obj) <-
+        c(
+          teal.reporter::teal_card("# Mixed Model Repeated Measurements (MMRM) Analysis"),
+          teal.reporter::teal_card(obj),
+          teal.reporter::teal_card("## Module's code")
+        )
+      obj %>%
         teal.code::eval_code(code = as.expression(anl_inputs()$expr)) %>%
         teal.code::eval_code(code = as.expression(adsl_merge_inputs()$expr))
     })
@@ -1412,7 +1413,9 @@ srv_mmrm <- function(id,
         basic_table_args = basic_table_args
       )
 
-      teal.code::eval_code(qenv, as.expression(mmrm_table))
+      obj <- qenv
+      teal.reporter::teal_card(obj) <- c(teal.reporter::teal_card(obj), "## Table")
+      teal.code::eval_code(obj, as.expression(mmrm_table))
     })
 
     # Endpoint:
@@ -1482,7 +1485,9 @@ srv_mmrm <- function(id,
         diagnostic_plot = diagnostic_args,
         ggplot2_args = ggplot2_args
       )
-      teal.code::eval_code(qenv, as.expression(mmrm_plot_expr))
+      obj <- qenv
+      teal.reporter::teal_card(obj) <- c(teal.reporter::teal_card(obj), "## Plot")
+      teal.code::eval_code(obj, as.expression(mmrm_plot_expr))
     })
 
     decorated_tables_q <- lapply(
@@ -1568,36 +1573,8 @@ srv_mmrm <- function(id,
       title = label
     )
 
-    ### REPORTER
-    if (with_reporter) {
-      card_fun <- function(comment, label) {
-        card <- teal::report_card_template(
-          title = "Mixed Model Repeated Measurements (MMRM) Analysis",
-          label = label,
-          description = paste(
-            "Mixed Models procedure analyzes results from repeated measures designs",
-            "in which the outcome is continuous and measured at fixed time points"
-          ),
-          with_filter = with_filter,
-          filter_panel_api = filter_panel_api
-        )
-        if (!is.null(table_r())) {
-          card$append_text("Table", "header3")
-          card$append_table(table_r())
-        }
-        if (!is.null(plot_r())) {
-          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(source_code_r())
-        card
-      }
-      teal.reporter::add_card_button_srv("add_reporter", reporter = reporter, card_fun = card_fun)
-    }
-    ###
+    set_chunk_dims(pws, reactive({
+      decorated_objs_q[[obj_ix_r()]]()
+    }))
   })
 }

R/tm_g_barchart_simple.R

@@ -40,6 +40,8 @@
 #' To learn more please refer to the vignette
 #' `vignette("transform-module-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
+#' @inheritSection teal::example_module Reporting
+#'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
 #' interactive <- function() TRUE
@@ -248,10 +250,6 @@ ui_g_barchart_simple <- function(id, ...) {
         uiOutput(ns("table"), style = "overflow-y: scroll; max-height: 250px;")
       ),
       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"), tags$br(),
         teal.transform::datanames_input(args[c("x", "fill", "x_facet", "y_facet")]),
         if (!is.null(args$x)) {
@@ -367,8 +365,6 @@ ui_g_barchart_simple <- function(id, ...) {
 #' @keywords internal
 srv_g_barchart_simple <- function(id,
                                   data,
-                                  reporter,
-                                  filter_panel_api,
                                   x,
                                   fill,
                                   x_facet,
@@ -378,8 +374,6 @@ srv_g_barchart_simple <- function(id,
                                   plot_width,
                                   ggplot2_args,
                                   decorators) {
-  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")
 
@@ -438,8 +432,14 @@ srv_g_barchart_simple <- function(id,
     )
 
     anl_q <- reactive({
-      data() %>%
-        teal.code::eval_code(as.expression(anl_inputs()$expr))
+      obj <- data()
+      teal.reporter::teal_card(obj) <-
+        c(
+          teal.reporter::teal_card("# Barchart"),
+          teal.reporter::teal_card(obj),
+          teal.reporter::teal_card("## Module's code")
+        )
+      obj %>% teal.code::eval_code(as.expression(anl_inputs()$expr))
     })
 
     count_q <- reactive({
@@ -538,17 +538,17 @@ srv_g_barchart_simple <- function(id,
       )
 
       ANL <- count_q()[["ANL"]]
-
-      all_q <- count_q() %>%
+      obj <- count_q() %>%
         teal.code::eval_code(substitute(
           env = list(groupby_vars = paste(groupby_vars, collapse = ", ")),
           plot_title <- sprintf(
             "Number of patients (total N = %s) for each combination of (%s)",
             nrow(ANL),
             groupby_vars
           )
-        )) %>%
-        teal.code::eval_code(code = plot_call)
+        ))
+      teal.reporter::teal_card(obj) <- c(teal.reporter::teal_card(obj), "## Plot")
+      teal.code::eval_code(obj, code = plot_call)
     })
 
     decorated_all_q_code <- srv_decorate_teal_data(
@@ -602,27 +602,7 @@ srv_g_barchart_simple <- function(id,
       title = label
     )
 
-    ### REPORTER
-    if (with_reporter) {
-      card_fun <- function(comment, label) {
-        card <- teal::report_card_template(
-          title = "Barchart Plot",
-          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(source_code_r())
-        card
-      }
-      teal.reporter::add_card_button_srv("add_reporter", reporter = reporter, card_fun = card_fun)
-    }
-    ###
+    set_chunk_dims(pws, decorated_all_q_code)
   })
 }