643 AEL02 [Spec Added]

.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
   )

DESCRIPTION

@@ -64,6 +64,9 @@ Collate:
     'utils.R'
     'chevron_tlg-S4class.R'
     'ael01_nollt.R'
+    'ael02.R'
+    'ael03.R'
+    'ael04.R'
     'aet01.R'
     'aet01_aesi.R'
     'aet02.R'
@@ -76,12 +79,17 @@ Collate:
     'cfbt01.R'
     'checks.R'
     'chevron_tlg-S4methods.R'
+    'cml02a_gl.R'
     'cmt01a.R'
     'cmt02_pt.R'
     'coxt01.R'
     'coxt02.R'
     'data.R'
+    'dml01.R'
+    'dml02.R'
     'dmt01.R'
+    'dsl01.R'
+    'dsl02.R'
     'dst01.R'
     'dtht01.R'
     'egt01.R'
@@ -103,6 +111,7 @@ Collate:
     'mht01.R'
     'mng01.R'
     'package.R'
+    'pdl01.R'
     'pdt01.R'
     'pdt02.R'
     'reexports.R'

NAMESPACE

@@ -9,12 +9,25 @@ S3method(droplevels,character)
 S3method(lvls,character)
 S3method(lvls,default)
 S3method(lvls,factor)
+S3method(report_null,"NULL")
+S3method(report_null,ElementaryTable)
+S3method(report_null,TableTree)
+S3method(report_null,listing_df)
 export("main<-")
 export("postprocess<-")
 export("preprocess<-")
 export(ael01_nollt)
 export(ael01_nollt_main)
 export(ael01_nollt_pre)
+export(ael02)
+export(ael02_main)
+export(ael02_pre)
+export(ael03)
+export(ael03_main)
+export(ael03_pre)
+export(ael04)
+export(ael04_main)
+export(ael04_pre)
 export(aet01)
 export(aet01_aesi)
 export(aet01_aesi_main)
@@ -58,6 +71,9 @@ export(cfbt01_pre)
 export(chevron_g)
 export(chevron_l)
 export(chevron_t)
+export(cml02a_gl)
+export(cml02a_gl_main)
+export(cml02a_gl_pre)
 export(cmt01_label)
 export(cmt01a)
 export(cmt01a_main)
@@ -74,10 +90,24 @@ export(coxt01_post)
 export(coxt01_pre)
 export(coxt02)
 export(coxt02_main)
+export(create_id_listings)
+export(dml01)
+export(dml01_main)
+export(dml01_pre)
+export(dml02)
+export(dml02_main)
+export(dml02_pre)
 export(dmt01)
 export(dmt01_main)
 export(dmt01_post)
 export(dmt01_pre)
+export(dose_change_rule)
+export(dsl01)
+export(dsl01_main)
+export(dsl01_pre)
+export(dsl02)
+export(dsl02_main)
+export(dsl02_pre)
 export(dst01)
 export(dst01_main)
 export(dst01_post)
@@ -108,6 +138,7 @@ export(ext01)
 export(ext01_main)
 export(ext01_post)
 export(ext01_pre)
+export(format_date)
 export(fstg01)
 export(fstg01_main)
 export(fstg01_pre)
@@ -162,6 +193,10 @@ export(mng01_pre)
 export(nocoding)
 export(null_listing)
 export(null_report)
+export(outcome_rule)
+export(pdl01)
+export(pdl01_main)
+export(pdl01_pre)
 export(pdt01)
 export(pdt01_main)
 export(pdt01_post)
@@ -213,6 +248,7 @@ export(vst02_2_main)
 export(vst02_post)
 export(vst02_pre)
 export(with_label)
+export(yes_no_rule)
 exportClasses(chevron_g)
 exportClasses(chevron_l)
 exportClasses(chevron_t)

NEWS.md

@@ -15,6 +15,7 @@ variables do not exist in analysis dataset.
 and `legend_pos` arguments. The `table` arguments now controls the behavior of the table. The arguments `show_n` and
 `show_table` are now defunct.
 * Add `RMPT06` template.
+* Add `AEL02`, `AEL03` and `AEL04`, `CML02A_GL`, `DSL01`, `DSL02`, `DML01`, `DML02` and `PDL01` listing templates.  
 * The `stats` and `precision` arguments now control the statistical analysis and numbers of digits presented in `DMT01`.
 * `FSTG01` and `FSTG02` template removes the `max_colwidth` argument. Default font size of the plot is set to 7.
 * Introduce `set_section_div` function to add empty line separator between specified row splits.

R/ael01_nollt.R

@@ -3,9 +3,7 @@
 #' @describeIn ael01_nollt Main TLG function
 #'
 #' @inheritParams gen_args
-#' @param dataset (`character`) the name of a table in the `adam_db` object.
-#' @param default_formatting (`list`) the default format of the listing columns. See [`rlistings::as_listing`].
-#' @param col_formatting (`list`) the format of specific listing columns. See [`rlistings::as_listing`].
+#' @param dataset (`string`) the name of a table in the `adam_db` object.
 #'
 #' @details
 #'  * Removes duplicate rows.
@@ -22,25 +20,18 @@ ael01_nollt_main <- function(adam_db,
                              dataset = "adae",
                              key_cols = c("AEBODSYS", "AEDECOD"),
                              disp_cols = "AETERM",
-                             default_formatting = list(
-                               all = fmt_config(align = "left"),
-                               numeric = fmt_config(align = "center")
-                             ),
-                             col_formatting = NULL,
-                             unique_rows = TRUE,
                              ...) {
   assert_all_tablenames(adam_db, dataset)
   assert_valid_variable(adam_db[[dataset]], c(key_cols, disp_cols), label = paste0("adam_db$", dataset))
-  assert_list(default_formatting, types = "fmt_config", names = "unique")
-  assert_list(col_formatting, null.ok = TRUE, types = "fmt_config", names = "unique")
-  assert_flag(unique_rows)
-  as_listing(
-    adam_db[[dataset]],
+
+  execute_with_args(
+    as_listing,
+    df = adam_db[[dataset]],
     key_cols = key_cols,
     disp_cols = disp_cols,
-    default_formatting = default_formatting,
-    col_formatting = col_formatting,
-    unique_rows = unique_rows
+    ...,
+    default_formatting = listing_format_chevron(),
+    unique_rows = TRUE
   )
 }
 
@@ -58,8 +49,7 @@ ael01_nollt_pre <- function(adam_db,
   adam_db[[dataset]] <- adam_db[[dataset]] %>%
     mutate(
       across(all_of(c(key_cols, disp_cols)), ~ reformat(.x, nocoding))
-    ) %>%
-    arrange(pick(all_of(c(key_cols, disp_cols))))
+    )
 
   adam_db
 }

R/ael02.R

@@ -0,0 +1,83 @@
+# ael02_main ----
+
+#' @describeIn ael02 Main TLG function
+#'
+#' @inheritParams gen_args
+#' @param dataset (`string`) the name of a table in the `adam_db` object.
+#'
+#' @export
+#'
+ael02_main <- function(adam_db,
+                       dataset = "adae",
+                       arm_var = "ACTARM",
+                       key_cols = c("ID", "ASR", arm_var),
+                       disp_cols = c(
+                         "AEDECOD", "TRTSDTM", "ASTDY", "ADURN", "AESER",
+                         "ASEV", "AREL", "AEOUT", "AECONTRT", "AEACN"
+                       ),
+                       ...) {
+  assert_all_tablenames(adam_db, dataset)
+  assert_valid_variable(adam_db[[dataset]], c(arm_var, key_cols, disp_cols), label = paste0("adam_db$", dataset))
+
+  execute_with_args(
+    as_listing,
+    df = adam_db[[dataset]],
+    key_cols = key_cols,
+    disp_cols = disp_cols,
+    ...,
+    default_formatting = listing_format_chevron(),
+    unique_rows = TRUE
+  )
+}
+
+#' @describeIn ael02 Preprocessing
+#'
+#' @inheritParams ael02_main
+#'
+#' @export
+#'
+ael02_pre <- function(adam_db,
+                      dataset = "adae",
+                      arm_var = "ACTARM",
+                      ...) {
+  adam_db[[dataset]] <- adam_db[[dataset]] %>%
+    filter(.data$ANL01FL == "Y") %>%
+    mutate(
+      across(
+        all_of(c(arm_var, "AEDECOD", "ASEV", "AEOUT", "AEACN")),
+        ~ reformat(.x, missing_rule)
+      )
+    ) %>%
+    mutate(
+      !!arm_var := with_label(.data[[arm_var]], "Treatment"),
+      ID = create_id_listings(.data$SITEID, .data$SUBJID),
+      ASR = with_label(paste(.data$AGE, .data$SEX, .data$RACE, sep = "/"), "Age/Sex/Race"),
+      TRTSDTM = with_label(
+        .data$TRTSDTM,
+        "Date of\nFirst Study\nDrug\nAdministration"
+      ),
+      AEDECOD = with_label(reformat(.data$AEDECOD, nocoding), "Adverse\nEvent MedDRA\nPreferred Term"),
+      ASTDY = with_label(.data$ASTDY, "Study\nDay of\nOnset"),
+      ADURN = with_label(.data$ADURN, "AE\nDuration\nin Days"),
+      AESER = with_label(reformat(.data$AESER, yes_no_rule), "Serious"),
+      ASEV = with_label(.data$ASEV, "Most\nExtreme\nIntensity"),
+      AREL = with_label(reformat(.data$AREL, yes_no_rule), "Caused by\nStudy\nDrug"),
+      AEOUT = with_label(as.numeric(reformat(.data$AEOUT, outcome_rule)), "Outcome\n(1)"),
+      AECONTRT = with_label(reformat(.data$AECONTRT, yes_no_rule), "Treatment\nfor AE"),
+      AEACN = with_label(as.numeric(reformat(.data$AEACN, dose_change_rule)), "Action\nTaken\n(2)")
+    )
+
+  adam_db
+}
+
+#' `AEL02` Listing 1 (Default) Listing of Adverse Events.
+#'
+#' @include chevron_tlg-S4class.R
+#' @export
+#'
+#' @examples
+#' res <- run(ael02, syn_data)
+ael02 <- chevron_l(
+  main = ael02_main,
+  preprocess = ael02_pre
+)

R/ael03.R

@@ -0,0 +1,92 @@
+# ael03_main ----
+
+#' @describeIn ael03 Main TLG function
+#'
+#' @inheritParams gen_args
+#' @param dataset (`string`) the name of a table in the `adam_db` object.
+#'
+#' @export
+#'
+ael03_main <- function(adam_db,
+                       dataset = "adae",
+                       arm_var = "ACTARM",
+                       key_cols = c("ID", "ASR", arm_var),
+                       disp_cols = c(
+                         "AEDECOD", "TRTSDTM", "ASTDY", "ADURN", "ASEV",
+                         "AREL", "AEOUT", "AECONTRT", "AEACN", "SERREAS"
+                       ),
+                       ...) {
+  assert_all_tablenames(adam_db, dataset)
+  assert_valid_variable(adam_db[[dataset]], c(arm_var, key_cols, disp_cols), label = paste0("adam_db$", dataset))
+
+  execute_with_args(
+    as_listing,
+    df = adam_db[[dataset]],
+    key_cols = key_cols,
+    disp_cols = disp_cols,
+    ...,
+    default_formatting = listing_format_chevron(),
+    unique_rows = TRUE
+  )
+}
+
+#' @describeIn ael03 Preprocessing
+#'
+#' @inheritParams ael03_main
+#'
+#' @export
+#'
+ael03_pre <- function(adam_db,
+                      dataset = "adae",
+                      arm_var = "ACTARM",
+                      ...) {
+  adam_db[[dataset]] <- adam_db[[dataset]] %>%
+    filter(.data$ANL01FL == "Y") %>%
+    filter(.data$AESER == "Y") %>%
+    mutate(
+      across(
+        all_of(c(arm_var, "AEDECOD", "ASEV", "AEOUT", "AEACN")),
+        ~ reformat(.x, missing_rule)
+      )
+    ) %>%
+    mutate(
+      !!arm_var := with_label(.data[[arm_var]], "Treatment"),
+      ID = create_id_listings(.data$SITEID, .data$SUBJID),
+      AEDECOD = with_label(reformat(.data$AEDECOD, nocoding), "Adverse\nEvent MedDRA\nPreferred Term"),
+      ASR = with_label(paste(.data$AGE, .data$SEX, .data$RACE, sep = "/"), "Age/Sex/Race"),
+      # Datetime of First Exposure to Treatment
+      TRTSDTM = with_label(.data$TRTSDTM, "Date of\nFirst Study\nDrug\nAdministration"),
+      ASTDY = with_label(.data$ASTDY, "Study\nDay of\nOnset"),
+      ADURN = with_label(.data$AENDY - .data$ASTDY + 1, "AE\nDuration\nin Days"),
+      AESER = with_label(.data$AESER, "Serious"),
+      ASEV = with_label(.data$ASEV, "Most\nExtreme\nIntensity"),
+      AREL = with_label(reformat(.data$AREL, yes_no_rule), "Caused by\nStudy\nDrug"), # Analysis Causality
+      AEOUT = with_label(as.numeric(reformat(.data$AEOUT, outcome_rule)), "Outcome\n(1)"),
+      AECONTRT = with_label(reformat(.data$AECONTRT, yes_no_rule), "Treatment\nfor AE"),
+      AEACN = with_label(as.numeric(reformat(.data$AEACN, dose_change_rule)), "Action\nTaken\n(2)"),
+      # New derived column
+      SERREAS = with_label(case_when(
+        AESDTH == "Y" ~ "1",
+        AESLIFE == "Y" ~ "2",
+        AESHOSP == "Y" ~ "3",
+        AESDISAB == "Y" ~ "4",
+        AESCONG == "Y" ~ "5",
+        AESMIE == "Y" ~ "6",
+        TRUE ~ " "
+      ), "Reason\nClassified\nas Serious\n(3)"),
+    )
+
+  adam_db
+}
+
+#' `AEL03` Listing 1 (Default) Listing of Serious Adverse Events.
+#'
+#' @include chevron_tlg-S4class.R
+#' @export
+#'
+#' @examples
+#' res <- run(ael03, syn_data)
+ael03 <- chevron_l(
+  main = ael03_main,
+  preprocess = ael03_pre
+)