update args in lyt and main (#412)

Close #388 iterate through templates and update the scope of arguments in main and lyt to adapt new reformat

R/aet02.R

@@ -21,6 +21,8 @@
 aet02_1_main <- function(adam_db,
                          arm_var = "ACTARM",
                          lbl_overall = NULL,
+                         lbl_aebodsys = "MedDRA System Organ Class",
+                         lbl_aedecod = "MedDRA Preferred Term",
                          deco = std_deco("AET02")) {
   dbsel <- get_db_data(adam_db, "adsl", "adae")
 
@@ -29,6 +31,8 @@ aet02_1_main <- function(adam_db,
   lyt <- aet02_1_lyt(
     arm_var = arm_var,
     lbl_overall = lbl_overall,
+    lbl_aebodsys = lbl_aebodsys,
+    lbl_aedecod = lbl_aedecod,
     deco = deco
   )
 
@@ -47,8 +51,8 @@ aet02_1_main <- function(adam_db,
 #'
 aet02_1_lyt <- function(arm_var,
                         lbl_overall,
-                        lbl_aebodsys = "MedDRA System Organ Class",
-                        lbl_aedecod = "MedDRA Preferred Term",
+                        lbl_aebodsys,
+                        lbl_aedecod,
                         deco) {
   basic_table_deco(deco) %>%
     split_cols_by(var = arm_var) %>%
@@ -194,6 +198,9 @@ aet02_1 <- chevron_t(
 aet02_2_main <- function(adam_db,
                          arm_var = "ACTARM",
                          lbl_overall = NULL,
+                         lbl_aebodsys = "MedDRA System Organ Class",
+                         lbl_aedecod = "MedDRA Preferred Term",
+                         lbl_aehlt = "MedDRA High-Level Term",
                          deco = std_deco("AET02")) {
   dbsel <- get_db_data(adam_db, "adsl", "adae")
 
@@ -202,6 +209,9 @@ aet02_2_main <- function(adam_db,
   lyt <- aet02_2_lyt(
     arm_var = arm_var,
     lbl_overall = lbl_overall,
+    lbl_aebodsys = lbl_aebodsys,
+    lbl_aedecod = lbl_aedecod,
+    lbl_aehlt = lbl_aehlt,
     deco = deco
   )
 
@@ -222,9 +232,9 @@ aet02_2_main <- function(adam_db,
 #'
 aet02_2_lyt <- function(arm_var,
                         lbl_overall = NULL,
-                        lbl_aebodsys = "MedDRA System Organ Class",
-                        lbl_aehlt = "MedDRA High-Level Term",
-                        lbl_aedecod = "MedDRA Preferred Term",
+                        lbl_aebodsys,
+                        lbl_aedecod,
+                        lbl_aehlt,
                         deco) {
   basic_table_deco(deco) %>%
     split_cols_by(var = arm_var) %>%
@@ -369,12 +379,14 @@ aet02_2 <- chevron_t(
 aet02_3_main <- function(adam_db,
                          arm_var = "ACTARM",
                          lbl_overall = NULL,
+                         lbl_aedecod = "MedDRA Preferred Term",
                          deco = std_deco("AET02")) {
   assert_colnames(adam_db$adae, c("AEDECOD"))
 
   lyt <- aet02_3_lyt(
     arm_var = arm_var,
     lbl_overall = lbl_overall,
+    lbl_aedecod = lbl_aedecod,
     deco = deco
   )
 
@@ -396,7 +408,7 @@ aet02_3_main <- function(adam_db,
 #'
 aet02_3_lyt <- function(arm_var,
                         lbl_overall,
-                        lbl_aedecod = "MedDRA Preferred Term",
+                        lbl_aedecod,
                         deco) {
   lyt_top <- basic_table_deco(deco) %>%
     split_cols_by(var = arm_var) %>%

R/aet03.R

@@ -21,6 +21,8 @@
 aet03_1_main <- function(adam_db,
                          arm_var = "ACTARM",
                          lbl_overall = NULL,
+                         lbl_aebodsys = "MedDRA System Organ Class",
+                         lbl_aedecod = "MedDRA Preferred Term",
                          deco = std_deco("AET03")) {
   dbsel <- get_db_data(adam_db, "adsl", "adae")
   assert_colnames(dbsel$adae, c("AEBODSYS", "AEDECOD", "ASEV"))
@@ -31,6 +33,8 @@ aet03_1_main <- function(adam_db,
   lyt <- aet03_1_lyt(
     arm_var = arm_var,
     lbl_overall = lbl_overall,
+    lbl_aebodsys = lbl_aebodsys,
+    lbl_aedecod = lbl_aedecod,
     intensity_grade = intensity_grade,
     deco = deco
   )
@@ -52,8 +56,8 @@ aet03_1_main <- function(adam_db,
 #'
 aet03_1_lyt <- function(arm_var,
                         lbl_overall,
-                        lbl_aebodsys = "MedDRA System Organ Class",
-                        lbl_aedecod = "MedDRA Preferred Term",
+                        lbl_aebodsys,
+                        lbl_aedecod,
                         intensity_grade,
                         deco) {
   all_grade_groups <- list("- Any Intensity -" = intensity_grade)

R/aet04.R

@@ -21,8 +21,10 @@
 #'
 aet04_1_main <- function(adam_db,
                          arm_var = "ACTARM",
-                         grade_groups = NULL,
                          lbl_overall = NULL,
+                         lbl_aebodsys = "MedDRA System Organ Class",
+                         lbl_aedecod = "MedDRA Preferred Term",
+                         grade_groups = NULL,
                          deco = std_deco("AET04")) {
   dbsel <- get_db_data(adam_db, "adsl", "adae")
   assert_colnames(dbsel$adae, c("AEBODSYS", "AEDECOD", "ATOXGR"))
@@ -43,6 +45,8 @@ aet04_1_main <- function(adam_db,
   lyt <- aet04_1_lyt(
     arm_var = arm_var,
     lbl_overall = lbl_overall,
+    lbl_aebodsys = lbl_aebodsys,
+    lbl_aedecod = lbl_aedecod,
     toxicity_grade = toxicity_grade,
     grade_groups = grade_groups,
     deco = deco
@@ -66,8 +70,8 @@ aet04_1_main <- function(adam_db,
 #'
 aet04_1_lyt <- function(arm_var,
                         lbl_overall,
-                        lbl_aebodsys = "MedDRA System Organ Class",
-                        lbl_aedecod = "MedDRA Preferred Term",
+                        lbl_aebodsys,
+                        lbl_aedecod,
                         toxicity_grade,
                         grade_groups,
                         deco) {

R/dst01.R

@@ -95,9 +95,9 @@ dst01_1_main <- function(adam_db,
 dst01_1_lyt <- function(arm_var,
                         status_var,
                         disc_reason_var,
-                        completed_lbl = "COMPLETED",
-                        ongoing_lbl = "ONGOING",
-                        discontinued_lbl = "DISCONTINUED",
+                        completed_lbl,
+                        ongoing_lbl,
+                        discontinued_lbl,
                         lbl_overall,
                         deco) {
   layout_table <- basic_table_deco(deco) %>%

R/egt02.R

@@ -47,10 +47,10 @@ egt02_1_main <- function(adam_db,
 #' @export
 #'
 egt02_1_lyt <- function(arm_var = "ACTARM",
-                        lbl_vs_assessment = "Assessment",
-                        lbl_vs_abnormality = "Abnormality",
-                        lbl_overall = NULL,
-                        deco = std_deco("EGT02")) {
+                        lbl_vs_assessment,
+                        lbl_vs_abnormality,
+                        lbl_overall,
+                        deco) {
   basic_table_deco(deco) %>%
     split_cols_by(var = arm_var) %>%
     add_colcounts() %>%

R/egt05_qtcat.R

@@ -71,7 +71,7 @@ egt05_qtcat_1_main <- function(adam_db,
 egt05_qtcat_1_lyt <- function(arm_var,
                               summaryvars,
                               summaryvars_lbls,
-                              lbl_overall = NULL,
+                              lbl_overall,
                               visitvar,
                               lbl_avisit,
                               lbl_param,

R/vst02.R

@@ -55,7 +55,7 @@ vst02_1_lyt <- function(arm_var,
                         lbl_vs_assessment,
                         lbl_vs_abnormality,
                         lbl_overall,
-                        deco = std_deco("VST02")) {
+                        deco) {
   basic_table_deco(deco) %>%
     split_cols_by(var = arm_var) %>%
     add_colcounts() %>%