643 AEL02 [Spec Added]

DESCRIPTION

@@ -63,6 +63,9 @@ Collate:
     'utils.R'
     'chevron_tlg-S4class.R'
     'ael01_nollt.R'
+    'ael02.R'
+    'ael03.R'
+    'ael04.R'
     'aet01.R'
     'aet01_aesi.R'
     'aet02.R'

NAMESPACE

@@ -15,6 +15,15 @@ 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)

NEWS.md

@@ -14,6 +14,7 @@ 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` listing templates.
 
 # chevron 0.2.2
 

R/ael01_nollt.R

@@ -3,7 +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 dataset (`string`) 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`].
 #'

R/ael02.R

@@ -0,0 +1,124 @@
+# ael02_main ----
+
+#' @describeIn ael02 Main TLG function
+#'
+#' @inheritParams gen_args
+#' @param dataset (`string`) 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`].
+#'
+#' @export
+#'
+ael02_main <- function(adam_db,
+                       dataset = "adae",
+                       key_cols = c("CPID", "ASR", "TRT01A"),
+                       disp_cols = names(adam_db[[dataset]]),
+                       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$", dataset))
+  assert_list(default_formatting, types = "fmt_config", names = "unique")
+  assert_list(col_formatting, null.ok = TRUE, types = "fmt_config", names = "unique")
+  assert_flag(unique_rows)
+
+  as_listing(
+    adam_db[[dataset]],
+    key_cols = key_cols,
+    disp_cols = disp_cols,
+    default_formatting = default_formatting,
+    col_formatting = col_formatting,
+    unique_rows = unique_rows
+  )
+}
+
+#' @describeIn ael02 Preprocessing
+#'
+#' @inheritParams ael02_main
+#'
+#' @export
+#'
+ael02_pre <- function(adam_db,
+                      dataset = "adae",
+                      ...) {
+  adam_db[[dataset]] <- adam_db[[dataset]] %>%
+    filter(.data$ANL01FL == "Y") %>%
+    mutate(
+      across(
+        all_of(c("TRT01A", "AEDECOD", "AESEV", "AEOUT", "AEACN")),
+        ~ reformat(.x, missing_rule)
+      )
+    ) %>%
+    mutate(
+      CPID = with_label(paste(.data$SITEID, .data$SUBJID, sep = "/"), "Center/Patient ID"),
+      ASR = with_label(paste(.data$AGE, .data$SEX, .data$RACE, sep = "/"), "Age/Sex/Race"),
+      Date_First = with_label(
+        toupper(format(as.Date(.data$TRTSDTM), "%d%b%Y")),
+        "Date of\nFirst Study\nDrug\nAdministration"
+      ),
+      Duration = with_label(.data$AENDY - .data$ASTDY + 1, "AE\nDuration\nin Days"),
+      Serious = with_label(ifelse(.data$AESER == "Y", "Yes", ifelse(.data$AESER == "N", "No", "")), "Serious"),
+      Related = with_label(
+        ifelse(.data$AEREL == "Y", "Yes", ifelse(.data$AEREL == "N", "No", "")),
+        "Caused by\nStudy\nDrug"
+      ),
+      Outcome = with_label(case_when(
+        AEOUT == "FATAL" ~ 1,
+        AEOUT == "NOT RECOVERED/NOT RESOLVED" ~ 2,
+        AEOUT == "RECOVERED/RESOLVED" ~ 3,
+        AEOUT == "RECOVERED/RESOLVED WITH SEQUELAE" ~ 4,
+        AEOUT == "RECOVERING/RESOLVING" ~ 5,
+        AEOUT == "UNKNOWN" ~ 6
+      ), "Outcome\n(1)"),
+      Treated = with_label(
+        ifelse(.data$AECONTRT == "Y", "Yes", ifelse(.data$AECONTRT == "N", "No", "")),
+        "Treatment\nfor AE"
+      ),
+      Action = with_label(case_when(
+        AEACN == "DOSE INCREASED" ~ 1,
+        AEACN == "DOSE NOT CHANGED" ~ 2,
+        AEACN == "DOSE REDUCED" | AEACN == "DOSE RATE REDUCED" ~ 3,
+        AEACN == "DRUG INTERRUPTED" ~ 4,
+        AEACN == "DRUG WITHDRAWN" ~ 5,
+        AEACN == "NOT APPLICABLE" | AEACN == "NOT EVALUABLE" ~ 6,
+        AEACN == "UNKNOWN" ~ 7
+      ), "Action\nTaken\n(2)"),
+      TRT01A = with_label(.data$TRT01A, "Treatment"),
+      AEDECOD = with_label(reformat(as.factor(.data$AEDECOD), nocoding), "Adverse\nEvent MedDRA\nPreferred Term"),
+      ASTDY = with_label(.data$ASTDY, "Study\nDay of\nOnset"),
+      AESEV = with_label(.data$AESEV, "Most\nExtreme\nIntensity")
+    ) %>%
+    select(all_of(c(
+      "CPID", "ASR", "TRT01A", "AEDECOD", "Date_First", "ASTDY", "Duration",
+      "Serious", "AESEV", "Related", "Outcome", "Treated", "Action"
+    )))
+
+  adam_db
+}
+
+#' @describeIn ael02 Postprocessing
+#'
+#' @inheritParams gen_args
+#'
+ael02_post <- function(tlg, ...) {
+  if (nrow(tlg) == 0) tlg <- null_report
+
+  tlg
+}
+
+#' `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,
+  postprocess = ael02_post
+)

R/ael03.R

@@ -0,0 +1,133 @@
+# ael03_main ----
+
+#' @describeIn ael03 Main TLG function
+#'
+#' @inheritParams gen_args
+#' @param dataset (`string`) 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`].
+#'
+#' @export
+#'
+ael03_main <- function(adam_db,
+                       dataset = "adae",
+                       key_cols = c("CPID", "ASR", "TRT01A"),
+                       disp_cols = names(adam_db[[dataset]]),
+                       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$", dataset))
+  assert_list(default_formatting, types = "fmt_config", names = "unique")
+  assert_list(col_formatting, null.ok = TRUE, types = "fmt_config", names = "unique")
+  assert_flag(unique_rows)
+
+  as_listing(
+    adam_db[[dataset]],
+    key_cols = key_cols,
+    disp_cols = disp_cols,
+    default_formatting = default_formatting,
+    col_formatting = col_formatting,
+    unique_rows = unique_rows
+  )
+}
+
+#' @describeIn ael03 Preprocessing
+#'
+#' @inheritParams ael03_main
+#'
+#' @export
+#'
+ael03_pre <- function(adam_db,
+                      dataset = "adae",
+                      ...) {
+  adam_db[[dataset]] <- adam_db[[dataset]] %>%
+    filter(.data$ANL01FL == "Y") %>%
+    filter(.data$AESER == "Y") %>%
+    mutate(
+      across(
+        all_of(c("TRT01A", "AEDECOD", "AESEV", "AEOUT", "AEACN")),
+        ~ reformat(.x, missing_rule)
+      )
+    ) %>%
+    mutate(
+      CPID = with_label(paste(.data$SITEID, .data$SUBJID, sep = "/"), "Center/Patient ID"),
+      ASR = with_label(paste(.data$AGE, .data$SEX, .data$RACE, sep = "/"), "Age/Sex/Race"),
+      Date_First = with_label(
+        toupper(format(as.Date(.data$TRTSDTM), "%d%b%Y")),
+        "Date of\nFirst Study\nDrug\nAdministration"
+      ),
+      Duration = with_label(.data$AENDY - .data$ASTDY + 1, "AE\nDuration\nin Days"),
+      Related = with_label(
+        ifelse(.data$AEREL == "Y", "Yes", ifelse(.data$AEREL == "N", "No", "")),
+        "Caused by\nStudy\nDrug"
+      ),
+      Outcome = with_label(case_when(
+        AEOUT == "FATAL" ~ 1,
+        AEOUT == "NOT RECOVERED/NOT RESOLVED" ~ 2,
+        AEOUT == "RECOVERED/RESOLVED" ~ 3,
+        AEOUT == "RECOVERED/RESOLVED WITH SEQUELAE" ~ 4,
+        AEOUT == "RECOVERING/RESOLVING" ~ 5,
+        AEOUT == "UNKNOWN" ~ 6
+      ), "Outcome\n(1)"),
+      Treated = with_label(
+        ifelse(.data$AECONTRT == "Y", "Yes", ifelse(.data$AECONTRT == "N", "No", "")),
+        "Treatment\nfor AE"
+      ),
+      Action = with_label(case_when(
+        AEACN == "DOSE INCREASED" ~ 1,
+        AEACN == "DOSE NOT CHANGED" ~ 2,
+        AEACN == "DOSE REDUCED" | AEACN == "DOSE RATE REDUCED" ~ 3,
+        AEACN == "DRUG INTERRUPTED" ~ 4,
+        AEACN == "DRUG WITHDRAWN" ~ 5,
+        AEACN == "NOT APPLICABLE" | AEACN == "NOT EVALUABLE" ~ 6,
+        AEACN == "UNKNOWN" ~ 7
+      ), "Action\nTaken\n(2)"),
+      SERREAS = with_label(case_when(
+        AESDTH == "Y" ~ "1",
+        AESLIFE == "Y" ~ "2",
+        AESHOSP == "Y" ~ "3",
+        AESDISAB == "Y" ~ "4",
+        AESCONG == "Y" ~ "5",
+        AESMIE == "Y" ~ "6",
+        TRUE ~ " "
+      ), "Reason\nClassified\nas Serious\n(3)"),
+      TRT01A = with_label(.data$TRT01A, "Treatment"),
+      AEDECOD = with_label(reformat(as.factor(.data$AEDECOD), nocoding), "Adverse\nEvent MedDRA\nPreferred Term"),
+      ASTDY = with_label(.data$ASTDY, "Study\nDay of\nOnset"),
+      AESEV = with_label(.data$AESEV, "Most\nExtreme\nIntensity")
+    ) %>%
+    select(all_of(c(
+      "CPID", "ASR", "TRT01A", "AEDECOD", "Date_First", "ASTDY", "Duration",
+      "AESEV", "Related", "Outcome", "Treated", "Action", "SERREAS"
+    )))
+
+  adam_db
+}
+
+#' @describeIn ael03 Postprocessing
+#'
+#' @inheritParams gen_args
+#'
+ael03_post <- function(tlg, ...) {
+  if (nrow(tlg) == 0) tlg <- null_report
+
+  tlg
+}
+
+#' `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,
+  postprocess = ael03_post
+)

R/ael04.R

@@ -0,0 +1,97 @@
+# ael04_main ----
+
+#' @describeIn ael04 Main TLG function
+#'
+#' @inheritParams gen_args
+#' @param dataset (`string`) 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`].
+#'
+#' @export
+#'
+ael04_main <- function(adam_db,
+                       dataset = "adsl",
+                       key_cols = c("CPID"),
+                       disp_cols = names(adam_db[[dataset]]),
+                       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$", dataset))
+  assert_list(default_formatting, types = "fmt_config", names = "unique")
+  assert_list(col_formatting, null.ok = TRUE, types = "fmt_config", names = "unique")
+  assert_flag(unique_rows)
+
+  as_listing(
+    adam_db[[dataset]],
+    key_cols = key_cols,
+    disp_cols = disp_cols,
+    default_formatting = default_formatting,
+    col_formatting = col_formatting,
+    unique_rows = unique_rows
+  )
+}
+
+#' @describeIn ael04 Preprocessing
+#'
+#' @inheritParams ael04_main
+#'
+#' @export
+#'
+ael04_pre <- function(adam_db,
+                      dataset = "adsl",
+                      ...) {
+  adam_db[[dataset]] <- adam_db[[dataset]] %>%
+    filter(!is.na(.data$DTHADY)) %>%
+    mutate(
+      across(
+        all_of(c("TRT01A", "DTHCAUS", "ADTHAUT")),
+        ~ reformat(.x, missing_rule)
+      )
+    ) %>%
+    mutate(
+      CPID = with_label(paste(.data$SITEID, .data$SUBJID, sep = "/"), "Center/Patient ID"),
+      ASR = with_label(paste(.data$AGE, .data$SEX, .data$RACE, sep = "/"), "Age/Sex/Race"),
+      Date_First = with_label(
+        toupper(format(as.Date(.data$TRTSDTM), "%d%b%Y")),
+        "Date of\nFirst Study\nDrug\nAdministration"
+      ),
+      TRT01A = with_label(.data$TRT01A, "Treatment"),
+      EOSDY = with_label(.data$EOSDY, "Day of Last\nStudy Drug\nAdministration"),
+      DTHADY = with_label(.data$DTHADY, "Day of\nDeath"),
+      DTHCAUS = with_label(.data$DTHCAUS, "Cause of Death"),
+      ADTHAUT = with_label(.data$ADTHAUT, "Autopsy\nPerformed?")
+    ) %>%
+    select(all_of(c(
+      "CPID", "ASR", "TRT01A", "Date_First", "EOSDY", "DTHADY", "DTHCAUS", "ADTHAUT"
+    )))
+
+  adam_db
+}
+
+#' @describeIn ael04 Postprocessing
+#'
+#' @inheritParams gen_args
+#'
+ael04_post <- function(tlg, ...) {
+  if (nrow(tlg) == 0) tlg <- null_report
+
+  tlg
+}
+
+#' `AEL04` Listing 1 (Default) Listing of Patient Deaths.
+#'
+#' @include chevron_tlg-S4class.R
+#' @export
+#'
+#' @examples
+#' res <- run(ael04, syn_data)
+ael04 <- chevron_l(
+  main = ael04_main,
+  preprocess = ael04_pre,
+  postprocess = ael04_post
+)