Add lbt07

DESCRIPTION

@@ -79,6 +79,7 @@ Collate:
     'lbt01.R'
     'lbt04.R'
     'lbt05.R'
+    'lbt07.R'
     'lbt14.R'
     'mht01.R'
     'mng01.R'

NAMESPACE

@@ -147,6 +147,11 @@ export(lbt05_1_lyt)
 export(lbt05_1_main)
 export(lbt05_1_post)
 export(lbt05_1_pre)
+export(lbt07_1)
+export(lbt07_1_lyt)
+export(lbt07_1_main)
+export(lbt07_1_post)
+export(lbt07_1_pre)
 export(lbt14_1)
 export(lbt14_1_lyt)
 export(lbt14_1_main)

R/lbt07.R

@@ -0,0 +1,194 @@
+# lbt07_1 ----
+
+#' @describeIn lbt07_1 Main TLG function
+#'
+#' @inheritParams gen_args
+#' @param grade_var (`character`) `PARAM` and variables derived from the standard lab grade variable `ATOXGR`:
+#' * A grade direction variable (`GRADE_DIR`) is required in order to obtain
+#'   the correct denominators when building the layout as it is used to define row splitting.
+#' * A toxicity grade variable (e.g. `GRADE_ANL`) where all negative values from
+#'   `ATOXGR` are replaced by their absolute values.
+#' @param lbl_grade_var (`character`) label of the variables in `grade_var`. If `NULL`, uses the label
+#'   attribute of the columns selected in `grade_var`.
+#' @param ... not used.
+#'
+#' @details
+#'  * Split columns by arm, typically `ACTARM`.
+#'
+#' @note
+#'  * `adam_db` object must contain an `adlb` table with columns `"USUBJID"`, `"ATOXGR"`,
+#'  `"ONTRTFL"` and column specified by `armvar`.
+#'
+#' @export
+#'
+lbt07_1_main <- function(adam_db,
+                         armvar = "ACTARM",
+                         grade_var = c("PARAM", "GRADE_DIR", "GRADE_ANL"),
+                         deco = std_deco("LBT07"),
+                         lbl_grade_var = c("Parameter", "Direction of Abnormality", "Toxicity Grade"),
+                         ...) {
+
+  lbt07_1_check(adam_db, ...)
+
+  lbl_grade_var <- if (is.null(lbl_grade_var)) {
+    var_labels_for(adam_db$adlb, grade_var)
+  } else {
+    lbl_grade_var
+  }
+  map <- unique(adam_db$adlb[adam_db$adlb$GRADE_DIR != "ZERO", c("PARAM", "GRADE_DIR", "GRADE_ANL")]) %>%
+    lapply(as.character) %>%
+    as.data.frame() %>%
+    arrange(PARAM, desc(GRADE_DIR), GRADE_ANL)
+
+
+  lyt <- lbt07_1_lyt(
+    armvar = armvar,
+    grade_var = grade_var,
+    lbl_grade_var = lbl_grade_var,
+    deco = deco,
+    map = map,
+    ... = ...
+  )
+
+  tbl <- build_table(lyt, adam_db$adlb, alt_counts_df = adam_db$adsl)
+
+  tbl
+}
+
+#' @describeIn lbt07_1 Layout
+#'
+#' @inheritParams gen_args
+#'
+#' @param lbl_param (`character`) label of the `PARAM` variable.
+#' @param lbl_gradedir (`character`) label of the `GRADE_DIR` variable.
+#' @param map (`data.frame`) mapping of `PARAM`s to directions of abnormality.
+#' @param ... not used.
+#'
+#' @export
+#'
+lbt07_1_lyt <- function(armvar,
+                        lbl_gradedir,
+                        lbl_param,
+                        grade_var,
+                        lbl_grade_var,
+                        deco,
+                        map,
+                        ...) {
+  names(lbl_grade_var) <- grade_var
+
+  basic_table_deco(deco, show_colcount = TRUE) %>%
+    split_cols_by(armvar) %>%
+    split_rows_by(
+      "PARAM",
+      label_pos = "topleft",
+      split_label = lbl_grade_var[1]
+    ) %>%
+    summarize_num_patients(
+      var = "USUBJID",
+      required = "ATOXGR",
+      .stats = "unique_count"
+    ) %>%
+    split_rows_by(
+      "GRADE_DIR",
+      label_pos = "topleft",
+      split_label = lbl_grade_var[2],
+      split_fun = trim_levels_to_map(map)
+    ) %>%
+    count_abnormal_by_worst_grade(
+      var = "GRADE_ANL",
+      variables = list(id = "USUBJID", param = "PARAM", grade_dir = "GRADE_DIR"),
+      .formats = list(count_fraction = tern::format_count_fraction_fixed_dp),
+      .indent_mods = 4L
+    ) %>%
+    append_topleft("    Highest NCI CTCAE Grade")
+}
+
+#' @describeIn lbt07_1 Preprocessing
+#'
+#' @inheritParams gen_args
+#' @param ... not used.
+#'
+#' @export
+#'
+lbt07_1_pre <- function(adam_db, ...) {
+  checkmate::assert_class(adam_db, "dm")
+
+  db <- adam_db %>%
+    dm_zoom_to("adlb") %>%
+    filter(
+      .data$ATOXGR != "<Missing>",
+      .data$ONTRTFL == "Y"
+    ) %>%
+    mutate(
+      GRADE_DIR = factor(
+        case_when(
+          ATOXGR %in% c("-1", "-2", "-3", "-4") ~ "LOW",
+          ATOXGR == "0" ~ "ZERO",
+          ATOXGR %in% c("1", "2", "3", "4") ~ "HIGH"
+        ),
+        levels = c("LOW", "ZERO", "HIGH")
+      ),
+      GRADE_ANL = fct_relevel(
+        forcats::fct_recode(ATOXGR,
+          `1` = "-1", `2` = "-2", `3` = "-3", `4` = "-4"
+        ),
+        c("0", "1", "2", "3", "4")
+      ),
+      PARAM = as.factor(.data$PARAM)
+    ) %>%
+    dm_update_zoomed()
+}
+
+#' @describeIn lbt07_1 Checks
+#'
+#' @inheritParams gen_args
+#' @param ... not used.
+#'
+lbt07_1_check <- function(adam_db,
+                          req_tables = c("adsl", "adlb"),
+                          armvar = "ACTARM",
+                          ...) {
+  assert_all_tablenames(adam_db, req_tables)
+
+  msg <- NULL
+
+  adlb_layout_col <- c("USUBJID", "ATOXGR", "ONTRTFL")
+  adsl_layout_col <- c("USUBJID")
+
+  msg <- c(msg, check_all_colnames(adam_db$adlb, c(armvar, adlb_layout_col)))
+  msg <- c(msg, check_all_colnames(adam_db$adsl, c(adsl_layout_col)))
+
+  if (is.null(msg)) {
+    TRUE
+  } else {
+    stop(paste(msg, collapse = "\n  "))
+  }
+}
+
+
+#' @describeIn lbt07_1 Postprocessing
+#'
+#' @inheritParams gen_args
+#' @param ... not used.
+#'
+#' @export
+#'
+lbt07_1_post <- function(tlg, prune_0 = TRUE, ...) {
+  std_postprocess(tlg)
+}
+
+#' `LBT07` Table 1 (Default) Laboratory Test Results and Change from Baseline by Visit.
+#'
+#' The `LBT07` table provides an
+#' overview of the analysis values and its change from baseline of each respective arm over the course of the trial.
+#' @include chevron_tlg-S4class.R
+#' @export
+#'
+#' @examples
+#' run(lbt07_1, syn_data)
+lbt07_1 <- chevron_t(
+  main = lbt07_1_main,
+  preprocess = lbt07_1_pre,
+  postprocess = lbt07_1_post,
+  adam_datasets = c("adlb", "adsl")
+)

_pkgdown.yaml

@@ -67,6 +67,7 @@ reference:
       - lbt01_1
       - lbt04_1
       - lbt05_1
+      - lbt07_1
       - lbt14_1
       - lbt14_2
       - mht01_1

tests/testthat/_snaps/default_tlg.md

@@ -1007,11 +1007,55 @@
             Last or replicated                     3 (2.4%)     9 (6.9%)       5 (4.0%)   
             Any Abnormality                        4 (3.1%)     9 (6.9%)       6 (4.8%)   
 
+# lbt07_1 functions with default argument value return expected result with test data
 # lbt14_1 functions with default argument value return expected result with test data
 
     Code
       res
     Output
+        Parameter                                                                          
+          Direction of Abnormality                 A: Drug X    B: Placebo   C: Combination
+            Highest NCI CTCAE Grade                 (N=134)      (N=134)        (N=132)    
+        ———————————————————————————————————————————————————————————————————————————————————
+        Alanine Aminotransferase Measurement (n)      134          134            132      
+          LOW                                                                              
+                    1                              25 (18.7%)   22 (16.4%)     28 (21.2%)  
+                    2                              24 (17.9%)   22 (16.4%)     21 (15.9%)  
+                    3                              24 (17.9%)   20 (14.9%)     21 (15.9%)  
+                    4                              13 (9.7%)    10 (7.5%)      11 (8.3%)   
+                    Any                            68 (50.7%)   62 (46.3%)     61 (46.2%)  
+          HIGH                                                                             
+                    1                              23 (17.2%)   25 (18.7%)     27 (20.5%)  
+                    2                              22 (16.4%)   24 (17.9%)     24 (18.2%)  
+                    3                              18 (13.4%)   25 (18.7%)     23 (17.4%)  
+                    4                              16 (11.9%)   15 (11.2%)     16 (12.1%)  
+                    Any                            70 (52.2%)   70 (52.2%)     76 (57.6%)  
+        C-Reactive Protein Measurement (n)            134          134            132      
+          LOW                                                                              
+                    1                              32 (23.9%)   33 (24.6%)     22 (16.7%)  
+                    2                              34 (25.4%)   16 (11.9%)     22 (16.7%)  
+                    3                              18 (13.4%)   15 (11.2%)     22 (16.7%)  
+                    4                              14 (10.4%)   15 (11.2%)     12 (9.1%)   
+                    Any                            78 (58.2%)   63 (47.0%)     69 (52.3%)  
+          HIGH                                                                             
+                    1                              29 (21.6%)   29 (21.6%)     23 (17.4%)  
+                    2                              26 (19.4%)   26 (19.4%)     25 (18.9%)  
+                    3                              23 (17.2%)   17 (12.7%)     19 (14.4%)  
+                    4                              19 (14.2%)   20 (14.9%)     22 (16.7%)  
+                    Any                            79 (59.0%)   71 (53.0%)     76 (57.6%)  
+        Immunoglobulin A Measurement (n)              134          134            132      
+          LOW                                                                              
+                    1                              30 (22.4%)   34 (25.4%)     28 (21.2%)  
+                    2                              17 (12.7%)   25 (18.7%)     22 (16.7%)  
+                    3                              22 (16.4%)   16 (11.9%)     23 (17.4%)  
+                    4                              11 (8.2%)    21 (15.7%)     14 (10.6%)  
+                    Any                            73 (54.5%)   80 (59.7%)     70 (53.0%)  
+          HIGH                                                                             
+                    1                              31 (23.1%)   24 (17.9%)     25 (18.9%)  
+                    2                              23 (17.2%)   27 (20.1%)     23 (17.4%)  
+                    3                              19 (14.2%)   16 (11.9%)     24 (18.2%)  
+                    4                              16 (11.9%)   15 (11.2%)      6 (4.5%)   
+                    Any                            75 (56.0%)   71 (53.0%)     64 (48.5%)  
       LBT14 - Low Direction