198 Include user's card labels when generating the report (#835)

This PR allows end user to use their Card Name (label) to be passed to the Card Content. There are no more hardcoded titles. The hardcoded titles will be only used if Card Name (label0) is empty. A follow-up after insightsengineering/teal.reporter#219 --------- Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com> Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com> Co-authored-by: unknown <kirar.kartikeya1@gmail.com>
insightsengineering · Oct 13, 2023 · e5e8dae · e5e8dae
1 parent 672f9f9
commit e5e8dae
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Showing 38 changed files with 317 additions and 318 deletions.
diff --git a/.lintr b/.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
   )
diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R
@@ -547,14 +547,15 @@ 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$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "Generalized Estimating Equations (GEE) Analysis Table",
+          label = label,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         table_type <- switch(input$output_table,
           "t_gee_cov" = "Residual Covariance Matrix Estimate",
           "t_gee_coef" = "Model Coefficients",

diff --git a/R/tm_a_mmrm.R b/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 <- 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"
           ),
-          "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())

diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R
@@ -538,13 +538,13 @@ 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$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "Barchart Plot",
+          label = label,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

diff --git a/R/tm_g_ci.R b/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 <- teal::report_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 == "") {

diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R
@@ -718,13 +718,13 @@ 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$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "Forest Response Plot",
+          label = label,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R
@@ -652,13 +652,13 @@ 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$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "Forest Survival Plot",
+          label = label,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

diff --git a/R/tm_g_ipp.R b/R/tm_g_ipp.R
@@ -611,13 +611,13 @@ 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$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "Individual Patient Plot",
+          label = label,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

diff --git a/R/tm_g_km.R b/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 <- teal::report_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 == "") {

diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R
@@ -648,13 +648,13 @@ 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$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "Line Plot",
+          label = label,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R
@@ -575,13 +575,13 @@ 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$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "Patient Profile Adverse Events Plot",
+          label = label,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Table", "header3")
         card$append_table(teal.code::dev_suppress(all_q()[["table"]]))
         card$append_text("Plot", "header3")

diff --git a/R/tm_g_pp_patient_timeline.R b/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 +896,13 @@ 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$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "Patient Profile Timeline Plot",
+          label = label,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R
@@ -696,13 +696,13 @@ 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$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "Patient Profile Therapy",
+          label = label,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Table", "header3")
         card$append_table(teal.code::dev_suppress(all_q()[["therapy_table"]]))
         card$append_text("Plot", "header3")

diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R
@@ -528,13 +528,13 @@ 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$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "Patient Profile Vitals Plot",
+          label = label,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

diff --git a/R/tm_t_abnormality.R b/R/tm_t_abnormality.R
@@ -647,13 +647,13 @@ 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$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "Abnormality Summary Table",
+          label = label,
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Table", "header3")
         card$append_table(table_r())
         if (!comment == "") {

diff --git a/R/tm_t_abnormality_by_worst_grade.R b/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 <- teal::report_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 == "") {

diff --git a/R/tm_t_ancova.R b/R/tm_t_ancova.R
@@ -945,14 +945,14 @@ srv_ancova <- function(id,
 
     ### REPORTER
     if (with_reporter) {
-      card_fun <- function(comment) {
-        card <- teal::TealReportCard$new()
-        card$set_name("ANCOVA")
-        card$append_text("ANCOVA", "header2")
-        card$append_text("Analysis of Covariance", "header3")
-        if (with_filter) {
-          card$append_fs(filter_panel_api$get_filter_state())
-        }
+      card_fun <- function(comment, label) {
+        card <- teal::report_card_template(
+          title = "ANCOVA",
+          label = label,
+          description = "Analysis of Covariance",
+          with_filter = with_filter,
+          filter_panel_api = filter_panel_api
+        )
         card$append_text("Table", "header3")
         card$append_table(table_r())
         if (!comment == "") {