Merge branch 'main' into shajoezhu-patch-1

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: teal.modules.clinical
 Title: 'teal' Modules for Standard Clinical Outputs
-Version: 0.9.1.9031
-Date: 2024-11-08
+Version: 0.9.1.9032
+Date: 2024-11-26
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),
     person("Jana", "Stoilova", , "[email protected]", role = "aut"),

NEWS.md

@@ -1,4 +1,4 @@
-# teal.modules.clinical 0.9.1.9031
+# teal.modules.clinical 0.9.1.9032
 
 ### Enhancements
 * Added `teal.logger` functionality for logging changes in shiny inputs in all modules.

R/tm_a_gee.R

@@ -531,7 +531,7 @@ srv_gee <- function(id,
         cor_struct = input$cor_struct,
         basic_table_args = basic_table_args
       )
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     output$gee_title <- renderText({

R/tm_a_mmrm.R

@@ -1244,7 +1244,7 @@ srv_mmrm <- function(id,
         weights_emmeans = input$weights_emmeans,
         parallel = input$parallel
       )
-      teal.code::eval_code(qenv, as.expression(my_calls))
+      teal.code::eval_code(qenv, as.expression(unlist(my_calls)))
     })
 
     output$mmrm_title <- renderText({

R/tm_g_forest_rsp.R

@@ -758,7 +758,7 @@ srv_g_forest_rsp <- function(id,
         ggplot2_args = ggplot2_args
       )
 
-      teal.code::eval_code(anl_q(), as.expression(my_calls))
+      teal.code::eval_code(anl_q(), as.expression(unlist(my_calls)))
     })
 
     plot_r <- reactive(all_q()[["p"]])

R/tm_g_forest_tte.R

@@ -687,7 +687,7 @@ srv_g_forest_tte <- function(id,
         font_size = input$font_size,
         ggplot2_args = ggplot2_args
       )
-      teal.code::eval_code(anl_q(), as.expression(my_calls))
+      teal.code::eval_code(anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_g_ipp.R

@@ -607,7 +607,7 @@ srv_g_ipp <- function(id,
         ggplot2_args = ggplot2_args,
         add_avalu = input$add_avalu
       )
-      teal.code::eval_code(anl_q(), as.expression(my_calls))
+      teal.code::eval_code(anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_g_km.R

@@ -806,7 +806,7 @@ srv_g_km <- function(id,
         ci_ribbon = input$show_ci_ribbon,
         title = title
       )
-      teal.code::eval_code(anl_q(), as.expression(my_calls))
+      teal.code::eval_code(anl_q(), as.expression(unlist(my_calls)))
     })
 
     plot_r <- reactive(all_q()[["plot"]])

R/tm_g_lineplot.R

@@ -628,7 +628,7 @@ srv_g_lineplot <- function(id,
         table_font_size = input$table_font_size,
         ggplot2_args = ggplot2_args
       )
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     plot_r <- reactive(all_q()[["plot"]])

R/tm_g_pp_therapy.R

@@ -666,7 +666,7 @@ srv_g_therapy <- function(id,
           )
         )
       ) %>%
-        teal.code::eval_code(as.expression(my_calls))
+        teal.code::eval_code(as.expression(unlist(my_calls)))
     })
 
     output$title <- renderText({

R/tm_g_pp_vitals.R

@@ -550,7 +550,7 @@ srv_g_vitals <- function(id,
           )
         )
       ) %>%
-        teal.code::eval_code(as.expression(my_calls))
+        teal.code::eval_code(as.expression(unlist(my_calls)))
     })
 
     plot_r <- reactive(all_q()[["result_plot"]])

R/tm_t_abnormality.R

@@ -641,7 +641,7 @@ srv_t_abnormality <- function(id,
         tbl_title = tbl_title
       )
 
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_abnormality_by_worst_grade.R

@@ -661,7 +661,7 @@ srv_t_abnormality_by_worst_grade <- function(id, # nolint: object_length.
         basic_table_args = basic_table_args
       )
 
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_ancova.R

@@ -937,7 +937,7 @@ srv_ancova <- function(id,
         conf_level = as.numeric(input$conf_level),
         basic_table_args = basic_table_args
       )
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Output to render.

R/tm_t_binary_outcome.R

@@ -992,7 +992,7 @@ srv_t_binary_outcome <- function(id,
         basic_table_args = basic_table_args
       )
 
-      teal.code::eval_code(qenv, as.expression(my_calls))
+      teal.code::eval_code(qenv, as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_events.R

@@ -805,7 +805,7 @@ srv_t_events_byterm <- function(id,
         basic_table_args = basic_table_args
       )
 
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_events_by_grade.R

@@ -1199,7 +1199,7 @@ srv_t_events_by_grade <- function(id,
           basic_table_args = basic_table_args
         )
       }
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_events_patyear.R

@@ -624,7 +624,7 @@ srv_events_patyear <- function(id,
         drop_arm_levels = input$drop_arm_levels,
         basic_table_args = basic_table_args
       )
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_events_summary.R

@@ -985,7 +985,7 @@ srv_t_events_summary <- function(id,
       all_basic_table_args <- teal.widgets::resolve_basic_table_args(user_table = basic_table_args)
       teal.code::eval_code(
         merged$anl_q(),
-        as.expression(my_calls)
+        as.expression(unlist(my_calls))
       ) %>%
         teal.code::eval_code(
           substitute(

R/tm_t_exposure.R

@@ -627,7 +627,7 @@ srv_t_exposure <- function(id,
         avalu_var = input_avalu_var,
         basic_table_args = basic_table_args
       )
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_mult_events.R

@@ -589,7 +589,7 @@ srv_t_mult_events_byterm <- function(id,
         drop_arm_levels = input$drop_arm_levels,
         basic_table_args = basic_table_args
       )
-      teal.code::eval_code(anl_q, as.expression(my_calls))
+      teal.code::eval_code(anl_q, as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_pp_basic_info.R

@@ -262,7 +262,7 @@ srv_t_basic_info <- function(id,
           )
         )
       ) %>%
-        teal.code::eval_code(as.expression(my_calls))
+        teal.code::eval_code(as.expression(unlist(my_calls)))
     })
 
     output$title <- renderText({

R/tm_t_pp_medical_history.R

@@ -332,7 +332,7 @@ srv_t_medical_history <- function(id,
           )
         )
       ) %>%
-        teal.code::eval_code(as.expression(my_calls))
+        teal.code::eval_code(as.expression(unlist(my_calls)))
     })
 
     table_r <- reactive(all_q()[["result"]])

R/tm_t_pp_prior_medication.R

@@ -325,7 +325,7 @@ srv_t_prior_medication <- function(id,
             )
           )
         ) %>%
-        teal.code::eval_code(as.expression(my_calls))
+        teal.code::eval_code(as.expression(unlist(my_calls)))
     })
 
     table_r <- reactive(all_q()[["result"]])

R/tm_t_shift_by_arm.R

@@ -560,7 +560,7 @@ srv_shift_by_arm <- function(id,
         basic_table_args = basic_table_args
       )
 
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_shift_by_arm_by_worst.R

@@ -594,7 +594,7 @@ srv_shift_by_arm_by_worst <- function(id,
         basic_table_args = basic_table_args
       )
 
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_shift_by_grade.R

@@ -862,7 +862,7 @@ srv_t_shift_by_grade <- function(id,
         basic_table_args = basic_table_args
       )
 
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_smq.R

@@ -639,7 +639,7 @@ srv_t_smq <- function(id,
         basic_table_args = basic_table_args
       )
 
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_summary.R

@@ -569,7 +569,7 @@ srv_summary <- function(id,
         basic_table_args = basic_table_args
       )
 
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_summary_by.R

@@ -712,7 +712,7 @@ srv_summary_by <- function(id,
         basic_table_args = basic_table_args
       )
 
-      teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
+      teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
     # Outputs to render.

R/tm_t_tte.R

@@ -944,7 +944,7 @@ srv_t_tte <- function(id,
         basic_table_args = basic_table_args
       )
 
-      anl_q() %>% teal.code::eval_code(as.expression(my_calls))
+      anl_q() %>% teal.code::eval_code(as.expression(unlist(my_calls)))
     })
 
     table_r <- reactive(all_q()[["table"]])