tdata to teal_data (#855)

--------- Signed-off-by: Aleksander Chlebowski <[email protected]> Signed-off-by: Vedha Viyash <[email protected]> Co-authored-by: go_gonzo <[email protected]> Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: unknown <[email protected]> Co-authored-by: Vedha Viyash <[email protected]> Co-authored-by: André Veríssimo <[email protected]> Co-authored-by: vedhav <[email protected]>
insightsengineering · Dec 8, 2023 · 029c1cc · 029c1cc
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,7 +26,7 @@ BugReports:
     https://github.com/insightsengineering/teal.modules.clinical/issues
 Depends:
     R (>= 4.0),
-    teal (>= 0.14.0.9019),
+    teal (>= 0.14.0.9027),
     tern (>= 0.9.2.9017)
 Imports:
     assertthat,
@@ -53,11 +53,11 @@ Imports:
     shinyWidgets,
     stats,
     styler,
-    teal.code (>= 0.4.0),
-    teal.data (>= 0.3.0.9010),
+    teal.code(>= 0.4.1.9009),
+    teal.data (>= 0.3.0.9018),
     teal.logger (>= 0.1.1),
     teal.reporter (>= 0.2.1),
-    teal.transform (>= 0.4.0.9007),
+    teal.transform (>= 0.4.0.9011),
     teal.widgets (>= 0.4.0),
     tern.gee (>= 0.1.0),
     tern.mmrm (>= 0.2.1),

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,19 @@
 # teal.modules.clinical 0.8.16.9018
 
+### Breaking Changes
++ Adapted all modules to use `teal_data` objects.
+
+### Enhancements
+* Updated the documentation and vignettes to demonstrate method to pass `teal_data` object to `teal::init()`.
+* Added parameter `sort_freq_col` to `tm_t_events` to allow the user to select column to use when sorting by decreasing frequency.
+* Added parameter `incl_overall_sum` to `tm_t_events` to allow the user to choose whether overall summary rows are included at the top of the table.
+* Updated the documentation and vignettes to demonstrate method to pass `teal_data` object to `teal::init()`.
+
+### Bug fixes
+* Fixed bug in `tm_g_lineplot` forcing module to initialize with a table.
+
+# teal.modules.clinical 0.8.16.9010
+
 ### Enhancements
 * Added more informative error message when grade mapping error occurs in `tm_t_abnormality_by_worst_grade`.
 * Fixed label indentation in `tm_t_abnormality_by_worst_grade`.
@@ -14,13 +28,9 @@
 * Updated `tm_t_pp_basic_info`, `tm_g_pp_therapy`, `tm_g_pp_adverse_events`, and `tm_t_pp_laboratory` to use `rlistings` to print data neatly in reports.
 * Updated `tm_g_lineplot` to allow user to remove interval from plot.
 * Updated the documentation and vignettes to demonstrate method to pass `teal_data` object to `teal::init()`.
-* Added parameter `sort_freq_col` to `tm_t_events` to allow the user to select column to use when sorting by decreasing frequency.
-* Added parameter `incl_overall_sum` to `tm_t_events` to allow the user to choose whether overall summary rows are included at the top of the table.
-* Updated the documentation and vignettes to demonstrate method to pass `teal_data` object to `teal::init()`.
 
 ### Bug fixes
 * Fixed bug in `tm_t_coxreg` preventing table from being displayed when no covariates are selected.
-* Fixed bug in `tm_g_lineplot` forcing module to initialize with a table.
 
 ### Miscellaneous
 * Updated `control_incidence_rate` parameter names in `tm_t_events_patyear` from `time_unit_input` and `time_unit_output` to `input_time_unit` and `num_pt_year`, respectively, after parameter names were changed in `tern`.

diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R
@@ -139,7 +139,7 @@ template_a_gee <- function(output_table,
 #'         as.factor() %>%
 #'         as.numeric() %>%
 #'         as.factor(),
-#'       AVALBIN = AVAL < 50 #' Just as an example to get a binary endpoint.
+#'       AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
 #'     ) %>%
 #'     droplevels()
 #' })
@@ -369,7 +369,8 @@ srv_gee <- function(id,
                     basic_table_args) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
-  checkmate::assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   shiny::moduleServer(id, function(input, output, session) {
     ## split_covariates ----
@@ -401,7 +402,7 @@ srv_gee <- function(id,
       input,
       output,
       id_arm_var = extract_input("arm_var", parentname),
-      data = data[[parentname]],
+      data = shiny::reactive(data()[[parentname]]),
       arm_ref_comp = arm_ref_comp,
       module = "tm_a_gee"
     )
@@ -446,19 +447,17 @@ srv_gee <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list,
-      merge_function = "dplyr::inner_join",
-      join_keys = teal.data::join_keys(data)
+      merge_function = "dplyr::inner_join"
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var),
-      anl_name = "ANL_ADSL",
-      join_keys = teal.data::join_keys(data)
+      anl_name = "ANL_ADSL"
     )
 
     anl_q <- shiny::reactive({
-      teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)) %>%
+      data() %>%
         teal.code::eval_code(as.expression(anl_inputs()$expr)) %>%
         teal.code::eval_code(as.expression(adsl_inputs()$expr))
     })
@@ -570,7 +569,7 @@ srv_gee <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
-        card$append_src(paste(teal.code::get_code(table_q()), collapse = "\n"))
+        card$append_src(teal.code::get_code(table_q()))
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)

diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R
@@ -824,7 +824,8 @@ srv_mmrm <- function(id,
                      ggplot2_args) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
-  checkmate::assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   shiny::moduleServer(id, function(input, output, session) {
     # Reactive responsible for sending a disable/enable signal
@@ -853,7 +854,7 @@ srv_mmrm <- function(id,
       input,
       output,
       id_arm_var = extract_input("arm_var", parentname), # From UI.
-      data = data[[parentname]],
+      data = shiny::reactive(data()[[parentname]]),
       arm_ref_comp = arm_ref_comp,
       module = "tm_mmrm"
     )
@@ -920,21 +921,19 @@ srv_mmrm <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list_without_cov,
-      join_keys = teal.data::join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_merge_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var),
-      join_keys = teal.data::join_keys(data),
       anl_name = "ANL_ADSL"
     )
 
     anl_q <- shiny::reactive({
-      qenv <- teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data))
-      qenv2 <- teal.code::eval_code(qenv, as.expression(anl_inputs()$expr))
-      teal.code::eval_code(qenv2, as.expression(adsl_merge_inputs()$expr))
+      data() %>%
+        teal.code::eval_code(code = as.expression(anl_inputs()$expr)) %>%
+        teal.code::eval_code(code = as.expression(adsl_merge_inputs()$expr))
     })
 
     # Initially hide the output title because there is no output yet.
@@ -1457,7 +1456,7 @@ srv_mmrm <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
-        card$append_src(paste(teal.code::get_code(all_q()), collapse = "\n"))
+        card$append_src(teal.code::get_code(all_q()))
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)

diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R
@@ -329,7 +329,8 @@ srv_g_barchart_simple <- function(id,
                                   ggplot2_args) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
-  checkmate::assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   shiny::moduleServer(id, function(input, output, session) {
     rule_dupl <- function(others) {
@@ -381,19 +382,17 @@ srv_g_barchart_simple <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::join_keys(data),
       selector_list = selector_list
     )
 
     anl_q <- shiny::reactive({
-      qenv <- teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data))
-      qenv <- teal.code::eval_code(qenv, as.expression(anl_inputs()$expr))
-      qenv
+      data() %>%
+        teal.code::eval_code(as.expression(anl_inputs()$expr))
     })
 
     count_q <- shiny::reactive({
-      qenv <- anl_q()
-      teal::validate_has_data(qenv[["ANL"]], 2)
+      anl_q <- anl_q()
+      teal::validate_has_data(anl_q[["ANL"]], 2)
       groupby_vars <- r_groupby_vars()
 
       # count
@@ -409,51 +408,46 @@ srv_g_barchart_simple <- function(id,
         count_str_to_col_exprs <- sapply(groupby_vars[-1], count_str_to_column_expr)
         count_exprs <- c(count_exprs, count_exprs2, count_str_to_col_exprs)
       }
-      qenv2 <- teal.code::eval_code(qenv, code = count_exprs)
+
+      data_list <- sapply(teal.data::datanames(data()), function(x) shiny::reactive(data()[[x]]),
+        simplify = FALSE
+      )
+
+      anl_q <- anl_q %>%
+        teal.code::eval_code(code = count_exprs)
 
       # add label and slice(1) as all patients in the same subgroup have same n_'s
-      qenv3 <- teal.code::eval_code(
-        qenv2,
-        as.expression(
-          c(
-            bquote(attr(counts[[.(get_n_name(groupby_vars))]], "label") <- "Count"),
-            bquote(
-              counts <- counts %>%
-                dplyr::group_by_at(.(as.vector(groupby_vars))) %>%
-                dplyr::slice(1) %>%
-                dplyr::ungroup() %>%
-                dplyr::select(.(as.vector(groupby_vars)), dplyr::starts_with("n_"))
+      anl_q <- anl_q %>%
+        teal.code::eval_code(
+          as.expression(
+            c(
+              bquote(attr(counts[[.(get_n_name(groupby_vars))]], "label") <- "Count"),
+              bquote(
+                counts <- counts %>%
+                  dplyr::group_by_at(.(as.vector(groupby_vars))) %>%
+                  dplyr::slice(1) %>%
+                  dplyr::ungroup() %>%
+                  dplyr::select(.(as.vector(groupby_vars)), dplyr::starts_with("n_"))
+              )
             )
           )
         )
-      )
 
       # dplyr::select loses labels
-      teal.code::eval_code(
-        qenv3,
-        teal.transform::get_anl_relabel_call(
-          columns_source = anl_inputs()$columns_source,
-          datasets = data,
-          anl_name = "counts"
+      anl_q %>%
+        teal.code::eval_code(
+          teal.transform::get_anl_relabel_call(
+            columns_source = anl_inputs()$columns_source,
+            datasets = data_list,
+            anl_name = "counts"
+          )
         )
-      )
     })
 
     all_q <- shiny::reactive({
       teal::validate_inputs(iv_r())
       groupby_vars <- as.list(r_groupby_vars()) # so $ access works below
 
-      ANL <- count_q()[["ANL"]] # nolint
-
-      qenv2 <- teal.code::eval_code(count_q(), 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
-        )
-      ))
-
       y_lab <- substitute(
         column_annotation_label(counts, y_name),
         list(y_name = get_n_name(groupby_vars))
@@ -487,11 +481,22 @@ srv_g_barchart_simple <- function(id,
         ggplot2_args = all_ggplot2_args
       )
 
-      qenv3 <- teal.code::eval_code(qenv2, code = plot_call)
+      ANL <- count_q()[["ANL"]] # nolint
+
+      all_q <- 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)
 
       # explicitly calling print on the plot inside the qenv evaluates
       # the ggplot call and therefore catches errors
-      teal.code::eval_code(qenv3, code = quote(print(plot)))
+      teal.code::eval_code(all_q, code = quote(print(plot)))
     })
 
     plot_r <- shiny::reactive(all_q()[["plot"]])
@@ -558,7 +563,7 @@ srv_g_barchart_simple <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
-        card$append_src(paste(teal.code::get_code(all_q()), collapse = "\n"))
+        card$append_src(teal.code::get_code(all_q()))
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)

diff --git a/R/tm_g_ci.R b/R/tm_g_ci.R
@@ -376,7 +376,8 @@ srv_g_ci <- function(id, # nolint
                      ggplot2_args) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
-  checkmate::assert_class(data, "tdata")
+  checkmate::assert_class(data, "reactive")
+  checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   shiny::moduleServer(id, function(input, output, session) {
     selector_list <- teal.transform::data_extract_multiple_srv(
@@ -407,12 +408,10 @@ srv_g_ci <- function(id, # nolint
       selector_list = selector_list
     )
 
-    anl_q <- shiny::reactive(
-      teal.code::eval_code(
-        object = teal.code::new_qenv(tdata2env(data), code = get_code_tdata(data)),
-        code = as.expression(anl_inputs()$expr)
-      )
-    )
+    anl_q <- shiny::reactive({
+      data() %>%
+        teal.code::eval_code(as.expression(anl_inputs()$expr))
+    })
 
     all_q <- shiny::reactive({
       teal::validate_inputs(iv_r())
@@ -429,10 +428,10 @@ srv_g_ci <- function(id, # nolint
         )
       )
 
-      x_label <- column_annotation_label(data[[attr(x, "dataname")]](), x)
-      y_label <- column_annotation_label(data[[attr(y, "dataname")]](), y)
+      x_label <- column_annotation_label(data()[[attr(x, "dataname")]], x)
+      y_label <- column_annotation_label(data()[[attr(y, "dataname")]], y)
       color_label <- if (length(color)) {
-        column_annotation_label(data[[attr(color, "dataname")]](), color)
+        column_annotation_label(data()[[attr(color, "dataname")]], color)
       } else {
         NULL
       }
@@ -501,7 +500,7 @@ srv_g_ci <- function(id, # nolint
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
-        card$append_src(paste(teal.code::get_code(all_q()), collapse = "\n"))
+        card$append_src(teal.code::get_code(all_q()))
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)