198 Include user's card labels when generating the report

.lintr

@@ -1,5 +1,6 @@
 linters: linters_with_defaults(
   line_length_linter = line_length_linter(120),
   cyclocomp_linter = NULL,
-  object_usage_linter = NULL
+  object_usage_linter = NULL,
+  indentation_linter = NULL
   )

R/tm_a_gee.R

@@ -547,14 +547,16 @@ srv_gee <- function(id,
       title = label
     )
 
+    ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Generalized Estimating Equations (GEE) Analysis Table")
-        card$append_text("Generalized Estimating Equations (GEE) Analysis Table", "header2")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Generalized Estimating Equations (GEE) Analysis Table",
+          label = label,
+          description = NULL,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         table_type <- switch(input$output_table,
           "t_gee_cov" = "Residual Covariance Matrix Estimate",
           "t_gee_coef" = "Model Coefficients",

R/tm_a_mmrm.R

@@ -239,11 +239,10 @@ template_mmrm_tables <- function(parentname,
     layout_list <- add_expr(
       layout_list,
       substitute(
-        expr =
-          rtables::add_overall_col(total_label) %>%
-            rtables::split_rows_by(visit_var) %>%
-            tern.mmrm::summarize_lsmeans(arms = FALSE) %>%
-            rtables::append_topleft(paste0("  ", paramcd)),
+        expr = rtables::add_overall_col(total_label) %>%
+          rtables::split_rows_by(visit_var) %>%
+          tern.mmrm::summarize_lsmeans(arms = FALSE) %>%
+          rtables::append_topleft(paste0("  ", paramcd)),
         env = list(
           total_label = total_label,
           visit_var = visit_var,
@@ -1432,20 +1431,17 @@ srv_mmrm <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("MMRM")
-        card$append_text("Mixed Model Repeated Measurements (MMRM) Analysis", "header2")
-        card$append_text(
-          paste(
+      card_fun <- function(comment, label) {
+        card <- 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"
           ),
-          "header3"
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
         )
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
         if (!is.null(table_r())) {
           card$append_text("Table", "header3")
           card$append_table(table_r())

R/tm_g_barchart_simple.R

@@ -538,13 +538,14 @@ srv_g_barchart_simple <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Barchart Plot")
-        card$append_text("Barchart Plot", "header2")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Barchart Plot",
+          label = label,
+          description = NULL,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

R/tm_g_ci.R

@@ -483,14 +483,14 @@ srv_g_ci <- function(id, # nolint
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("CI Plot")
-        card$append_text("CI Plot", "header2")
-        card$append_text("Confidence Interval Plot", "header3")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "CI Plot",
+          label = label,
+          description = "Confidence Interval Plot",
+          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 == "") {

R/tm_g_forest_rsp.R

@@ -718,13 +718,14 @@ srv_g_forest_rsp <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Forest Response Plot")
-        card$append_text("Forest Response Plot", "header2")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Forest Response Plot",
+          label = label,
+          description = NULL,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

R/tm_g_forest_tte.R

@@ -652,13 +652,14 @@ srv_g_forest_tte <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Forest Survival Plot")
-        card$append_text("Forest Survival Plot", "header2")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Forest Survival Plot",
+          label = label,
+          description = NULL,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

R/tm_g_ipp.R

@@ -611,13 +611,14 @@ srv_g_ipp <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Individual Patient Plot")
-        card$append_text("Individual Patient Plot", "header2")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Individual Patient Plot",
+          label = label,
+          description = NULL,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

R/tm_g_km.R

@@ -773,14 +773,14 @@ srv_g_km <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Kaplan Meier Plot")
-        card$append_text("Kaplan Meier Plot", "header2")
-        card$append_text("Non-parametric method used to estimate the survival function from lifetime data", "header3")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Kaplan Meier Plot",
+          label = label,
+          description = "Non-parametric method used to estimate the survival function from lifetime data",
+          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 == "") {

R/tm_g_lineplot.R

@@ -648,13 +648,14 @@ srv_g_lineplot <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Line Plot")
-        card$append_text("Line Plot", "header2")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Line Plot",
+          label = label,
+          description = NULL,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

R/tm_g_pp_adverse_events.R

@@ -575,13 +575,14 @@ srv_g_adverse_events <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Patient Profile Adverse Events")
-        card$append_text("Patient Profile Adverse Events", "header2")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Patient Profile Adverse Events Plot",
+          label = label,
+          description = NULL,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Table", "header3")
         card$append_table(teal.code::dev_suppress(all_q()[["table"]]))
         card$append_text("Plot", "header3")

R/tm_g_pp_patient_timeline.R

@@ -831,8 +831,10 @@ srv_g_patient_timeline <- function(id,
       shiny::validate(
         shiny::need(
           !input$relday_x_axis ||
-            (sum(stats::complete.cases(p_time_data_pat[, c(aerelday_start_name, aerelday_end_name)])) > 0 ||
-              sum(stats::complete.cases(p_time_data_pat[, c(dsrelday_start_name, dsrelday_end_name)])) > 0),
+            (
+              sum(stats::complete.cases(p_time_data_pat[, c(aerelday_start_name, aerelday_end_name)])) > 0 ||
+                sum(stats::complete.cases(p_time_data_pat[, c(dsrelday_start_name, dsrelday_end_name)])) > 0
+            ),
           "Selected patient is not in dataset (either due to filtering or missing values). Consider relaxing filters."
         )
       )
@@ -894,13 +896,14 @@ srv_g_patient_timeline <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Patient Profile Timeline Plot")
-        card$append_text("Patient Profile Timeline Plot", "header2")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Patient Profile Timeline Plot",
+          label = label,
+          description = NULL,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

R/tm_g_pp_therapy.R

@@ -696,13 +696,14 @@ srv_g_therapy <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Patient Profile Therapy")
-        card$append_text("Patient Profile Therapy", "header2")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Patient Profile Therapy",
+          label = label,
+          description = NULL,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Table", "header3")
         card$append_table(teal.code::dev_suppress(all_q()[["therapy_table"]]))
         card$append_text("Plot", "header3")

R/tm_g_pp_vitals.R

@@ -528,13 +528,14 @@ srv_g_vitals <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Patient Profile Vitals Plot")
-        card$append_text("Patient Profile Vitals Plot", "header2")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Patient Profile Vitals Plot",
+          label = label,
+          description = NULL,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

R/tm_t_abnormality.R

@@ -647,13 +647,14 @@ srv_t_abnormality <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Abnormality Summary Table")
-        card$append_text("Abnormality Summary Table", "header2")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Abnormality Summary Table",
+          label = label,
+          description = NULL,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Table", "header3")
         card$append_table(table_r())
         if (!comment == "") {

R/tm_t_abnormality_by_worst_grade.R

@@ -664,14 +664,14 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("Laboratory Test Results Table")
-        card$append_text("Laboratory Test Results Table", "header2")
-        card$append_text("Laboratory test results with highest grade post-baseline Table", "header3")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- card_template(
+          title = "Laboratory Test Results Table",
+          label = label,
+          description = "Laboratory test results with highest grade post-baseline Table",
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Table", "header3")
         card$append_table(table_r())
         if (!comment == "") {