AET06

Adverse Events by Baseline Characteristic

---

Output

Adverse Events by Sex

Preview

split_fun <- drop_split_levels

lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ARM") %>%
  split_cols_by("SEX") %>%
  analyze_num_patients(
    vars = "USUBJID",
    .stats = c("unique", "nonunique"),
    .labels = c(
      unique = "Total number of patients with at least one adverse event",
      nonunique = "Overall total number of events"
    )
  ) %>%
  split_rows_by(
    "AEBODSYS",
    child_labels = "visible",
    nested = FALSE,
    split_fun = split_fun,
    label_pos = "topleft",
    split_label = obj_label(adae$AEBODSYS)
  ) %>%
  summarize_num_patients(
    var = "USUBJID",
    .stats = c("unique", "nonunique"),
    .labels = c(
      unique = "Total number of patients with at least one adverse event",
      nonunique = "Total number of events"
    )
  ) %>%
  count_occurrences(vars = "AEDECOD", .indent_mods = -1L) %>%
  append_varlabels(adae, "AEDECOD", indent = 1L)

result <- build_table(
  lyt = lyt,
  df = adae,
  alt_counts_df = adsl
) %>%
  prune_table() %>%
  # Sorted by decreasing frequency across all groups by System Organ Class and Preferred Term.
  sort_at_path(
    path = c("AEBODSYS"),
    scorefun = cont_n_allcols
  ) %>%
  sort_at_path(
    path = c("AEBODSYS", "*", "AEDECOD"),
    scorefun = score_occurrences
  )

result

                                                                    A: Drug X                B: Placebo              C: Combination     
Body System or Organ Class                                       F            M            F            M            F            M     
  Dictionary-Derived Term                                      (N=79)       (N=55)       (N=82)       (N=52)       (N=70)       (N=62)  
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event     72 (91.1%)   50 (90.9%)   77 (93.9%)   46 (88.5%)   65 (92.9%)   55 (88.7%)
Overall total number of events                                  377          232          419          203          378          325    
cl A.1                                                                                                                                  
  Total number of patients with at least one adverse event   53 (67.1%)   25 (45.5%)   51 (62.2%)   24 (46.2%)   43 (61.4%)   46 (74.2%)
  Total number of events                                         85           47           93           37           86           74    
  dcd A.1.1.1.1                                              34 (43.0%)   16 (29.1%)   31 (37.8%)   14 (26.9%)   33 (47.1%)   30 (48.4%)
  dcd A.1.1.1.2                                              32 (40.5%)   16 (29.1%)   33 (40.2%)   15 (28.8%)   24 (34.3%)   26 (41.9%)
cl B.2                                                                                                                                  
  Total number of patients with at least one adverse event   46 (58.2%)   33 (60.0%)   45 (54.9%)   29 (55.8%)   44 (62.9%)   41 (66.1%)
  Total number of events                                         81           48           86           52           64           79    
  dcd B.2.2.3.1                                              30 (38.0%)   18 (32.7%)   32 (39.0%)   22 (42.3%)   26 (37.1%)   25 (40.3%)
  dcd B.2.1.2.1                                              29 (36.7%)   20 (36.4%)   30 (36.6%)   14 (26.9%)   22 (31.4%)   30 (48.4%)
cl D.1                                                                                                                                  
  Total number of patients with at least one adverse event   45 (57.0%)   34 (61.8%)   40 (48.8%)   27 (51.9%)   41 (58.6%)   39 (62.9%)
  Total number of events                                         72           55           64           42           73           62    
  dcd D.1.1.1.1                                              25 (31.6%)   25 (45.5%)   29 (35.4%)   13 (25.0%)   27 (38.6%)   24 (38.7%)
  dcd D.1.1.4.2                                              30 (38.0%)   18 (32.7%)   22 (26.8%)   20 (38.5%)   27 (38.6%)   23 (37.1%)
cl D.2                                                                                                                                  
  Total number of patients with at least one adverse event   26 (32.9%)   21 (38.2%)   40 (48.8%)   18 (34.6%)   34 (48.6%)   23 (37.1%)
  Total number of events                                         35           27           49           23           43           31    
  dcd D.2.1.5.3                                              26 (32.9%)   21 (38.2%)   40 (48.8%)   18 (34.6%)   34 (48.6%)   23 (37.1%)
cl B.1                                                                                                                                  
  Total number of patients with at least one adverse event   28 (35.4%)   19 (34.5%)   33 (40.2%)   16 (30.8%)   24 (34.3%)   19 (30.6%)
  Total number of events                                         33           23           36           24           35           27    
  dcd B.1.1.1.1                                              28 (35.4%)   19 (34.5%)   33 (40.2%)   16 (30.8%)   24 (34.3%)   19 (30.6%)
cl C.2                                                                                                                                  
  Total number of patients with at least one adverse event   23 (29.1%)   12 (21.8%)   36 (43.9%)   12 (23.1%)   30 (42.9%)   25 (40.3%)
  Total number of events                                         32           16           39           14           33           32    
  dcd C.2.1.2.1                                              23 (29.1%)   12 (21.8%)   36 (43.9%)   12 (23.1%)   30 (42.9%)   25 (40.3%)
cl C.1                                                                                                                                  
  Total number of patients with at least one adverse event   30 (38.0%)   13 (23.6%)   36 (43.9%)   10 (19.2%)   27 (38.6%)   16 (25.8%)
  Total number of events                                         39           16           52           11           44           20    
  dcd C.1.1.1.3                                              30 (38.0%)   13 (23.6%)   36 (43.9%)   10 (19.2%)   27 (38.6%)   16 (25.8%)

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Adverse Events by Other Baseline Characteristics (e.g. Biomarker Group)

Preview

split_fun <- drop_split_levels

lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ARM") %>%
  split_cols_by("BMRKR2") %>%
  analyze_num_patients(
    vars = "USUBJID",
    .stats = c("unique", "nonunique"),
    .labels = c(
      unique = "Total number of patients with at least one adverse event",
      nonunique = "Overall total number of events"
    )
  ) %>%
  split_rows_by(
    "AEBODSYS",
    child_labels = "visible",
    nested = FALSE,
    split_fun = split_fun,
    label_pos = "topleft",
    split_label = obj_label(adae$AEBODSYS)
  ) %>%
  summarize_num_patients(
    var = "USUBJID",
    .stats = c("unique", "nonunique"),
    .labels = c(
      unique = "Total number of patients with at least one adverse event",
      nonunique = "Total number of events"
    )
  ) %>%
  count_occurrences(vars = "AEDECOD", .indent_mods = -1L) %>%
  append_varlabels(adae, "AEDECOD", indent = 1L)

result <- build_table(
  lyt = lyt,
  df = adae,
  alt_counts_df = adsl
) %>%
  prune_table() %>%
  # Sorted by decreasing frequency across all groups by System Organ Class and Preferred Term.
  sort_at_path(
    path = c("AEBODSYS"),
    scorefun = cont_n_allcols
  ) %>%
  sort_at_path(
    path = c("AEBODSYS", "*", "AEDECOD"),
    scorefun = score_occurrences
  )

result

                                                                          A: Drug X                              B: Placebo                           C: Combination           
Body System or Organ Class                                      LOW         MEDIUM        HIGH         LOW         MEDIUM        HIGH         LOW         MEDIUM        HIGH   
  Dictionary-Derived Term                                      (N=50)       (N=37)       (N=47)       (N=45)       (N=56)       (N=33)       (N=40)       (N=42)       (N=50)  
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event     46 (92.0%)   34 (91.9%)   42 (89.4%)   40 (88.9%)   53 (94.6%)   30 (90.9%)   36 (90.0%)   39 (92.9%)   45 (90.0%)
Overall total number of events                                  248          166          195          196          261          165          220          258          225    
cl A.1                                                                                                                                                                         
  Total number of patients with at least one adverse event   31 (62.0%)   19 (51.4%)   28 (59.6%)   25 (55.6%)   31 (55.4%)   19 (57.6%)   28 (70.0%)   30 (71.4%)   31 (62.0%)
  Total number of events                                         53           34           45           46           54           30           61           51           48    
  dcd A.1.1.1.1                                              22 (44.0%)   10 (27.0%)   18 (38.3%)   14 (31.1%)   20 (35.7%)   11 (33.3%)   21 (52.5%)   24 (57.1%)   18 (36.0%)
  dcd A.1.1.1.2                                              17 (34.0%)   13 (35.1%)   18 (38.3%)   18 (40.0%)   18 (32.1%)   12 (36.4%)   18 (45.0%)   14 (33.3%)   18 (36.0%)
cl B.2                                                                                                                                                                         
  Total number of patients with at least one adverse event   34 (68.0%)   21 (56.8%)   24 (51.1%)   23 (51.1%)   33 (58.9%)   18 (54.5%)   24 (60.0%)   27 (64.3%)   34 (68.0%)
  Total number of events                                         53           37           39           40           61           37           40           47           56    
  dcd B.2.2.3.1                                              21 (42.0%)   13 (35.1%)   14 (29.8%)   18 (40.0%)   22 (39.3%)   14 (42.4%)   16 (40.0%)   15 (35.7%)   20 (40.0%)
  dcd B.2.1.2.1                                              21 (42.0%)   11 (29.7%)   17 (36.2%)   11 (24.4%)   21 (37.5%)   12 (36.4%)   13 (32.5%)   17 (40.5%)   22 (44.0%)
cl D.1                                                                                                                                                                         
  Total number of patients with at least one adverse event   34 (68.0%)   21 (56.8%)   24 (51.1%)   18 (40.0%)   33 (58.9%)   16 (48.5%)   25 (62.5%)   31 (73.8%)   24 (48.0%)
  Total number of events                                         51           35           41           27           49           30           45           53           37    
  dcd D.1.1.1.1                                              19 (38.0%)   16 (43.2%)   15 (31.9%)   13 (28.9%)   19 (33.9%)   10 (30.3%)   14 (35.0%)   22 (52.4%)   15 (30.0%)
  dcd D.1.1.4.2                                              21 (42.0%)   9 (24.3%)    18 (38.3%)   9 (20.0%)    20 (35.7%)   13 (39.4%)   17 (42.5%)   18 (42.9%)   15 (30.0%)
cl D.2                                                                                                                                                                         
  Total number of patients with at least one adverse event   20 (40.0%)   12 (32.4%)   15 (31.9%)   19 (42.2%)   22 (39.3%)   17 (51.5%)   13 (32.5%)   23 (54.8%)   21 (42.0%)
  Total number of events                                         27           13           22           23           26           23           17           33           24    
  dcd D.2.1.5.3                                              20 (40.0%)   12 (32.4%)   15 (31.9%)   19 (42.2%)   22 (39.3%)   17 (51.5%)   13 (32.5%)   23 (54.8%)   21 (42.0%)
cl B.1                                                                                                                                                                         
  Total number of patients with at least one adverse event   14 (28.0%)   14 (37.8%)   19 (40.4%)   15 (33.3%)   24 (42.9%)   10 (30.3%)   14 (35.0%)   15 (35.7%)   14 (28.0%)
  Total number of events                                         16           19           21           18           25           17           19           25           18    
  dcd B.1.1.1.1                                              14 (28.0%)   14 (37.8%)   19 (40.4%)   15 (33.3%)   24 (42.9%)   10 (30.3%)   14 (35.0%)   15 (35.7%)   14 (28.0%)
cl C.2                                                                                                                                                                         
  Total number of patients with at least one adverse event   18 (36.0%)   8 (21.6%)    9 (19.1%)    15 (33.3%)   22 (39.3%)   11 (33.3%)   18 (45.0%)   17 (40.5%)   20 (40.0%)
  Total number of events                                         27           9            12           18           23           12           20           20           25    
  dcd C.2.1.2.1                                              18 (36.0%)   8 (21.6%)    9 (19.1%)    15 (33.3%)   22 (39.3%)   11 (33.3%)   18 (45.0%)   17 (40.5%)   20 (40.0%)
cl C.1                                                                                                                                                                         
  Total number of patients with at least one adverse event   17 (34.0%)   14 (37.8%)   12 (25.5%)   17 (37.8%)   17 (30.4%)   12 (36.4%)   12 (30.0%)   17 (40.5%)   14 (28.0%)
  Total number of events                                         21           19           15           24           23           16           18           29           17    
  dcd C.1.1.1.3                                              17 (34.0%)   14 (37.8%)   12 (25.5%)   17 (37.8%)   17 (30.4%)   12 (36.4%)   12 (30.0%)   17 (40.5%)   14 (28.0%)

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Adverse Events by Baseline Characteristic from ADSUB (e.g. BMI Category)

Preview

split_fun <- drop_split_levels

lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ARM") %>%
  split_cols_by("AVALCAT1") %>%
  analyze_num_patients(
    vars = "USUBJID",
    .stats = c("unique", "nonunique"),
    .labels = c(
      unique = "Total number of patients with at least one adverse event",
      nonunique = "Overall total number of events"
    )
  ) %>%
  split_rows_by(
    "AEBODSYS",
    child_labels = "visible",
    nested = FALSE,
    split_fun = split_fun,
    label_pos = "topleft",
    split_label = obj_label(adae$AEBODSYS)
  ) %>%
  summarize_num_patients(
    var = "USUBJID",
    .stats = c("unique", "nonunique"),
    .labels = c(
      unique = "Total number of patients with at least one adverse event",
      nonunique = "Total number of events"
    )
  ) %>%
  count_occurrences(vars = "AEDECOD", .indent_mods = -1L) %>%
  append_varlabels(adae, "AEDECOD", indent = 1L)

result <- build_table(
  lyt = lyt,
  df = adae,
  alt_counts_df = adsl
) %>%
  prune_table() %>%
  # Sorted by decreasing frequency across all groups by System Organ Class and Preferred Term.
  sort_at_path(
    path = c("AEBODSYS"),
    scorefun = cont_n_allcols
  ) %>%
  sort_at_path(
    path = c("AEBODSYS", "*", "AEDECOD"),
    scorefun = score_occurrences
  )

result

                                                                                 A: Drug X                                          B: Placebo                                         C: Combination                  
Body System or Organ Class                                     <18.5      18.5 - 24.9   25 - 29.9      >30         <18.5      18.5 - 24.9   25 - 29.9      >30         <18.5      18.5 - 24.9   25 - 29.9       >30    
  Dictionary-Derived Term                                      (N=44)       (N=17)       (N=11)       (N=62)       (N=37)       (N=18)       (N=10)       (N=69)       (N=28)       (N=20)        (N=18)       (N=66)  
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event     41 (93.2%)   14 (82.4%)    11 (100%)   56 (90.3%)   35 (94.6%)   16 (88.9%)    9 (90.0%)   63 (91.3%)   25 (89.3%)   19 (95.0%)    15 (83.3%)   61 (92.4%)
Overall total number of events                                  186           80           66          277          174           89           47          312          137           129          100          337    
cl A.1                                                                                                                                                                                                                 
  Total number of patients with at least one adverse event   23 (52.3%)   12 (70.6%)    7 (63.6%)   36 (58.1%)   19 (51.4%)   10 (55.6%)    6 (60.0%)   40 (58.0%)   16 (57.1%)   13 (65.0%)    14 (77.8%)   46 (69.7%)
  Total number of events                                         38           22           13           59           35           22            6           67           30           23            30           77    
  dcd A.1.1.1.1                                              14 (31.8%)    7 (41.2%)    3 (27.3%)   26 (41.9%)   12 (32.4%)    6 (33.3%)    4 (40.0%)   23 (33.3%)   12 (42.9%)    7 (35.0%)    13 (72.2%)   31 (47.0%)
  dcd A.1.1.1.2                                              15 (34.1%)    8 (47.1%)    5 (45.5%)   20 (32.3%)   12 (32.4%)    8 (44.4%)    2 (20.0%)   26 (37.7%)   9 (32.1%)     7 (35.0%)    7 (38.9%)    27 (40.9%)
cl B.2                                                                                                                                                                                                                 
  Total number of patients with at least one adverse event   23 (52.3%)   10 (58.8%)    8 (72.7%)   38 (61.3%)   21 (56.8%)    8 (44.4%)    7 (70.0%)   38 (55.1%)   16 (57.1%)   16 (80.0%)    12 (66.7%)   41 (62.1%)
  Total number of events                                         37           19           12           61           41           18           12           67           28           28            18           69    
  dcd B.2.2.3.1                                              13 (29.5%)    7 (41.2%)    6 (54.5%)   22 (35.5%)   14 (37.8%)    7 (38.9%)    6 (60.0%)   27 (39.1%)   7 (25.0%)    13 (65.0%)    5 (27.8%)    26 (39.4%)
  dcd B.2.1.2.1                                              14 (31.8%)    8 (47.1%)    4 (36.4%)   23 (37.1%)   14 (37.8%)    6 (33.3%)    4 (40.0%)   20 (29.0%)   13 (46.4%)    8 (40.0%)    8 (44.4%)    23 (34.8%)
cl D.1                                                                                                                                                                                                                 
  Total number of patients with at least one adverse event   24 (54.5%)    9 (52.9%)    8 (72.7%)   38 (61.3%)   18 (48.6%)    5 (27.8%)    7 (70.0%)   37 (53.6%)   15 (53.6%)   12 (60.0%)    11 (61.1%)   42 (63.6%)
  Total number of events                                         38           11           17           61           30           11           14           51           30           23            16           66    
  dcd D.1.1.1.1                                              13 (29.5%)    7 (41.2%)    7 (63.6%)   23 (37.1%)   13 (35.1%)    3 (16.7%)    4 (40.0%)   22 (31.9%)   12 (42.9%)    6 (30.0%)    8 (44.4%)    25 (37.9%)
  dcd D.1.1.4.2                                              16 (36.4%)    4 (23.5%)    6 (54.5%)   22 (35.5%)   10 (27.0%)    4 (22.2%)    5 (50.0%)   23 (33.3%)   10 (35.7%)    9 (45.0%)    6 (33.3%)    25 (37.9%)
cl D.2                                                                                                                                                                                                                 
  Total number of patients with at least one adverse event   14 (31.8%)    7 (41.2%)    5 (45.5%)   21 (33.9%)   14 (37.8%)   10 (55.6%)    4 (40.0%)   30 (43.5%)   13 (46.4%)   10 (50.0%)    7 (38.9%)    27 (40.9%)
  Total number of events                                         20            7           10           25           17           14            5           36           18           15            10           31    
  dcd D.2.1.5.3                                              14 (31.8%)    7 (41.2%)    5 (45.5%)   21 (33.9%)   14 (37.8%)   10 (55.6%)    4 (40.0%)   30 (43.5%)   13 (46.4%)   10 (50.0%)    7 (38.9%)    27 (40.9%)
cl B.1                                                                                                                                                                                                                 
  Total number of patients with at least one adverse event   17 (38.6%)    5 (29.4%)    7 (63.6%)   18 (29.0%)   14 (37.8%)    8 (44.4%)    4 (40.0%)   23 (33.3%)   7 (25.0%)    10 (50.0%)    7 (38.9%)    19 (28.8%)
  Total number of events                                         22            5            7           22           16           11            4           29           11           12            8            31    
  dcd B.1.1.1.1                                              17 (38.6%)    5 (29.4%)    7 (63.6%)   18 (29.0%)   14 (37.8%)    8 (44.4%)    4 (40.0%)   23 (33.3%)   7 (25.0%)    10 (50.0%)    7 (38.9%)    19 (28.8%)
cl C.2                                                                                                                                                                                                                 
  Total number of patients with at least one adverse event   14 (31.8%)    4 (23.5%)    2 (18.2%)   15 (24.2%)   15 (40.5%)    5 (27.8%)    4 (40.0%)   24 (34.8%)   10 (35.7%)   13 (65.0%)    8 (44.4%)    24 (36.4%)
  Total number of events                                         17            9            3           19           15            6            5           27           12           16            9            28    
  dcd C.2.1.2.1                                              14 (31.8%)    4 (23.5%)    2 (18.2%)   15 (24.2%)   15 (40.5%)    5 (27.8%)    4 (40.0%)   24 (34.8%)   10 (35.7%)   13 (65.0%)    8 (44.4%)    24 (36.4%)
cl C.1                                                                                                                                                                                                                 
  Total number of patients with at least one adverse event   11 (25.0%)    4 (23.5%)    4 (36.4%)   24 (38.7%)   13 (35.1%)    6 (33.3%)    1 (10.0%)   26 (37.7%)   6 (21.4%)     7 (35.0%)    6 (33.3%)    24 (36.4%)
  Total number of events                                         14            7            4           30           20            7            1           35           8            12            9            35    
  dcd C.1.1.1.3                                              11 (25.0%)    4 (23.5%)    4 (36.4%)   24 (38.7%)   13 (35.1%)    6 (33.3%)    1 (10.0%)   26 (37.7%)   6 (21.4%)     7 (35.0%)    6 (33.3%)    24 (36.4%)

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Adverse Events by Regrouped Baseline Characteristics (e.g. Race)

Preview

split_fun <- drop_split_levels

lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ARM") %>%
  split_cols_by("RACE1") %>%
  analyze_num_patients(
    vars = "USUBJID",
    .stats = c("unique", "nonunique"),
    .labels = c(
      unique = "Total number of patients with at least one adverse event",
      nonunique = "Overall total number of events"
    )
  ) %>%
  split_rows_by(
    "AEBODSYS",
    child_labels = "visible",
    nested = FALSE,
    split_fun = split_fun,
    label_pos = "topleft",
    split_label = obj_label(adae$AEBODSYS)
  ) %>%
  summarize_num_patients(
    var = "USUBJID",
    .stats = c("unique", "nonunique"),
    .labels = c(
      unique = "Total number of patients with at least one adverse event",
      nonunique = "Total number of events"
    )
  ) %>%
  count_occurrences(vars = "AEDECOD", .indent_mods = -1L) %>%
  append_varlabels(adae, "AEDECOD", indent = 1L)

result <- build_table(
  lyt = lyt,
  df = adae,
  alt_counts_df = adsl
) %>%
  prune_table() %>%
  prune_table() %>%
  # Sorted by decreasing frequency across all groups by System Organ Class and Preferred Term.
  sort_at_path(
    path = c("AEBODSYS"),
    scorefun = cont_n_allcols
  ) %>%
  sort_at_path(
    path = c("AEBODSYS", "*", "AEDECOD"),
    scorefun = score_occurrences
  )

result

                                                                    A: Drug X                B: Placebo              C: Combination     
Body System or Organ Class                                     WHITE      NON-WHITE      WHITE      NON-WHITE      WHITE      NON-WHITE 
  Dictionary-Derived Term                                      (N=27)      (N=107)       (N=26)      (N=108)       (N=21)      (N=111)  
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event     26 (96.3%)   96 (89.7%)   25 (96.2%)   98 (90.7%)   21 (100%)    99 (89.2%)
Overall total number of events                                  109          500          144          478          114          589    
cl A.1                                                                                                                                  
  Total number of patients with at least one adverse event   16 (59.3%)   62 (57.9%)   21 (80.8%)   54 (50.0%)   15 (71.4%)   74 (66.7%)
  Total number of events                                         30          102           37           93           25          135    
  dcd A.1.1.1.1                                              9 (33.3%)    41 (38.3%)   14 (53.8%)   31 (28.7%)   10 (47.6%)   53 (47.7%)
  dcd A.1.1.1.2                                              11 (40.7%)   37 (34.6%)   13 (50.0%)   35 (32.4%)   9 (42.9%)    41 (36.9%)
cl B.2                                                                                                                                  
  Total number of patients with at least one adverse event   15 (55.6%)   64 (59.8%)   16 (61.5%)   58 (53.7%)   12 (57.1%)   73 (65.8%)
  Total number of events                                         18          111           28          110           17          126    
  dcd B.2.2.3.1                                              4 (14.8%)    44 (41.1%)   10 (38.5%)   44 (40.7%)   5 (23.8%)    46 (41.4%)
  dcd B.2.1.2.1                                              12 (44.4%)   37 (34.6%)   9 (34.6%)    35 (32.4%)   7 (33.3%)    45 (40.5%)
cl D.1                                                                                                                                  
  Total number of patients with at least one adverse event   18 (66.7%)   61 (57.0%)   15 (57.7%)   52 (48.1%)   14 (66.7%)   66 (59.5%)
  Total number of events                                         27          100           23           83           27          108    
  dcd D.1.1.1.1                                              11 (40.7%)   39 (36.4%)   14 (53.8%)   28 (25.9%)   12 (57.1%)   39 (35.1%)
  dcd D.1.1.4.2                                              11 (40.7%)   37 (34.6%)   7 (26.9%)    35 (32.4%)   9 (42.9%)    41 (36.9%)
cl D.2                                                                                                                                  
  Total number of patients with at least one adverse event   6 (22.2%)    41 (38.3%)   15 (57.7%)   43 (39.8%)   9 (42.9%)    48 (43.2%)
  Total number of events                                         6            56           18           54           12           62    
  dcd D.2.1.5.3                                              6 (22.2%)    41 (38.3%)   15 (57.7%)   43 (39.8%)   9 (42.9%)    48 (43.2%)
cl B.1                                                                                                                                  
  Total number of patients with at least one adverse event   12 (44.4%)   35 (32.7%)   7 (26.9%)    42 (38.9%)   6 (28.6%)    37 (33.3%)
  Total number of events                                         15           41           8            52           8            54    
  dcd B.1.1.1.1                                              12 (44.4%)   35 (32.7%)   7 (26.9%)    42 (38.9%)   6 (28.6%)    37 (33.3%)
cl C.2                                                                                                                                  
  Total number of patients with at least one adverse event   5 (18.5%)    30 (28.0%)   11 (42.3%)   37 (34.3%)   11 (52.4%)   44 (39.6%)
  Total number of events                                         8            40           12           41           12           53    
  dcd C.2.1.2.1                                              5 (18.5%)    30 (28.0%)   11 (42.3%)   37 (34.3%)   11 (52.4%)   44 (39.6%)
cl C.1                                                                                                                                  
  Total number of patients with at least one adverse event   5 (18.5%)    38 (35.5%)   13 (50.0%)   33 (30.6%)   8 (38.1%)    35 (31.5%)
  Total number of events                                         5            50           18           45           13           51    
  dcd C.1.1.1.3                                              5 (18.5%)    38 (35.5%)   13 (50.0%)   33 (30.6%)   8 (38.1%)    35 (31.5%)

Try this using WebR

Experimental use!

WebR is a tool allowing you to run R code in the web browser. Modify the code below and click run to see the results. Alternatively, copy the code and click here to open WebR in a new tab.

Adverse Events by Baseline Characteristics (e.g. Sex) Including High-Level Terms

Preview

split_fun <- drop_split_levels

lyt <- basic_table(show_colcounts = TRUE) %>%
  split_cols_by("ARM") %>%
  split_cols_by("SEX") %>%
  analyze_num_patients(
    vars = "USUBJID",
    .stats = c("unique", "nonunique"),
    .labels = c(
      unique = "Total number of patients with at least one adverse event",
      nonunique = "Overall total number of events"
    )
  ) %>%
  split_rows_by(
    "AEBODSYS",
    child_labels = "visible",
    nested = FALSE,
    split_fun = split_fun,
    label_pos = "topleft",
    split_label = obj_label(adae$AEBODSYS)
  ) %>%
  summarize_num_patients(
    var = "USUBJID",
    .stats = c("unique", "nonunique"),
    .labels = c(
      unique = "Total number of patients with at least one adverse event",
      nonunique = "Total number of events"
    )
  ) %>%
  split_rows_by(
    "AEHLT",
    child_labels = "visible",
    indent_mod = -1L,
    split_fun = split_fun,
    label_pos = "topleft",
    split_label = obj_label(adae$AEHLT)
  ) %>%
  summarize_num_patients(
    var = "USUBJID",
    .stats = c("unique", "nonunique"),
    .labels = c(
      unique = "Total number of patients with at least one adverse event",
      nonunique = "Total number of events"
    )
  ) %>%
  count_occurrences("AEDECOD", .indent_mods = -1L) %>%
  append_varlabels(adae, "AEDECOD", indent = 2L)

result <- build_table(
  lyt = lyt,
  df = adae,
  alt_counts_df = adsl
) %>%
  prune_table() %>%
  # Sorted by decreasing frequency across all groups by System Organ Class, High-Level Term and Preferred Term.
  sort_at_path(
    path = c("AEBODSYS"),
    scorefun = cont_n_allcols
  ) %>%
  sort_at_path(
    path = c("AEBODSYS", "*", "AEHLT"),
    scorefun = cont_n_allcols
  ) %>%
  sort_at_path(
    path = c("AEBODSYS", "*", "AEHLT", "*", "AEDECOD"),
    scorefun = score_occurrences
  )

result

Body System or Organ Class                                            A: Drug X                B: Placebo              C: Combination     
  High Level Term                                                  F            M            F            M            F            M     
    Dictionary-Derived Term                                      (N=79)       (N=55)       (N=82)       (N=52)       (N=70)       (N=62)  
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event       72 (91.1%)   50 (90.9%)   77 (93.9%)   46 (88.5%)   65 (92.9%)   55 (88.7%)
Overall total number of events                                    377          232          419          203          378          325    
cl A.1                                                                                                                                    
  Total number of patients with at least one adverse event     53 (67.1%)   25 (45.5%)   51 (62.2%)   24 (46.2%)   43 (61.4%)   46 (74.2%)
  Total number of events                                           85           47           93           37           86           74    
  hlt A.1.1.1                                                                                                                             
    Total number of patients with at least one adverse event   53 (67.1%)   25 (45.5%)   51 (62.2%)   24 (46.2%)   43 (61.4%)   46 (74.2%)
    Total number of events                                         85           47           93           37           86           74    
    dcd A.1.1.1.1                                              34 (43.0%)   16 (29.1%)   31 (37.8%)   14 (26.9%)   33 (47.1%)   30 (48.4%)
    dcd A.1.1.1.2                                              32 (40.5%)   16 (29.1%)   33 (40.2%)   15 (28.8%)   24 (34.3%)   26 (41.9%)
cl B.2                                                                                                                                    
  Total number of patients with at least one adverse event     46 (58.2%)   33 (60.0%)   45 (54.9%)   29 (55.8%)   44 (62.9%)   41 (66.1%)
  Total number of events                                           81           48           86           52           64           79    
  hlt B.2.2.3                                                                                                                             
    Total number of patients with at least one adverse event   30 (38.0%)   18 (32.7%)   32 (39.0%)   22 (42.3%)   26 (37.1%)   25 (40.3%)
    Total number of events                                         40           24           43           33           37           40    
    dcd B.2.2.3.1                                              30 (38.0%)   18 (32.7%)   32 (39.0%)   22 (42.3%)   26 (37.1%)   25 (40.3%)
  hlt B.2.1.2                                                                                                                             
    Total number of patients with at least one adverse event   29 (36.7%)   20 (36.4%)   30 (36.6%)   14 (26.9%)   22 (31.4%)   30 (48.4%)
    Total number of events                                         41           24           43           19           27           39    
    dcd B.2.1.2.1                                              29 (36.7%)   20 (36.4%)   30 (36.6%)   14 (26.9%)   22 (31.4%)   30 (48.4%)
cl D.1                                                                                                                                    
  Total number of patients with at least one adverse event     45 (57.0%)   34 (61.8%)   40 (48.8%)   27 (51.9%)   41 (58.6%)   39 (62.9%)
  Total number of events                                           72           55           64           42           73           62    
  hlt D.1.1.1                                                                                                                             
    Total number of patients with at least one adverse event   25 (31.6%)   25 (45.5%)   29 (35.4%)   13 (25.0%)   27 (38.6%)   24 (38.7%)
    Total number of events                                         32           29           36           15           39           32    
    dcd D.1.1.1.1                                              25 (31.6%)   25 (45.5%)   29 (35.4%)   13 (25.0%)   27 (38.6%)   24 (38.7%)
  hlt D.1.1.4                                                                                                                             
    Total number of patients with at least one adverse event   30 (38.0%)   18 (32.7%)   22 (26.8%)   20 (38.5%)   27 (38.6%)   23 (37.1%)
    Total number of events                                         40           26           28           27           34           30    
    dcd D.1.1.4.2                                              30 (38.0%)   18 (32.7%)   22 (26.8%)   20 (38.5%)   27 (38.6%)   23 (37.1%)
cl D.2                                                                                                                                    
  Total number of patients with at least one adverse event     26 (32.9%)   21 (38.2%)   40 (48.8%)   18 (34.6%)   34 (48.6%)   23 (37.1%)
  Total number of events                                           35           27           49           23           43           31    
  hlt D.2.1.5                                                                                                                             
    Total number of patients with at least one adverse event   26 (32.9%)   21 (38.2%)   40 (48.8%)   18 (34.6%)   34 (48.6%)   23 (37.1%)
    Total number of events                                         35           27           49           23           43           31    
    dcd D.2.1.5.3                                              26 (32.9%)   21 (38.2%)   40 (48.8%)   18 (34.6%)   34 (48.6%)   23 (37.1%)
cl B.1                                                                                                                                    
  Total number of patients with at least one adverse event     28 (35.4%)   19 (34.5%)   33 (40.2%)   16 (30.8%)   24 (34.3%)   19 (30.6%)
  Total number of events                                           33           23           36           24           35           27    
  hlt B.1.1.1                                                                                                                             
    Total number of patients with at least one adverse event   28 (35.4%)   19 (34.5%)   33 (40.2%)   16 (30.8%)   24 (34.3%)   19 (30.6%)
    Total number of events                                         33           23           36           24           35           27    
    dcd B.1.1.1.1                                              28 (35.4%)   19 (34.5%)   33 (40.2%)   16 (30.8%)   24 (34.3%)   19 (30.6%)
cl C.2                                                                                                                                    
  Total number of patients with at least one adverse event     23 (29.1%)   12 (21.8%)   36 (43.9%)   12 (23.1%)   30 (42.9%)   25 (40.3%)
  Total number of events                                           32           16           39           14           33           32    
  hlt C.2.1.2                                                                                                                             
    Total number of patients with at least one adverse event   23 (29.1%)   12 (21.8%)   36 (43.9%)   12 (23.1%)   30 (42.9%)   25 (40.3%)
    Total number of events                                         32           16           39           14           33           32    
    dcd C.2.1.2.1                                              23 (29.1%)   12 (21.8%)   36 (43.9%)   12 (23.1%)   30 (42.9%)   25 (40.3%)
cl C.1                                                                                                                                    
  Total number of patients with at least one adverse event     30 (38.0%)   13 (23.6%)   36 (43.9%)   10 (19.2%)   27 (38.6%)   16 (25.8%)
  Total number of events                                           39           16           52           11           44           20    
  hlt C.1.1.1                                                                                                                             
    Total number of patients with at least one adverse event   30 (38.0%)   13 (23.6%)   36 (43.9%)   10 (19.2%)   27 (38.6%)   16 (25.8%)
    Total number of events                                         39           16           52           11           44           20    
    dcd C.1.1.1.3                                              30 (38.0%)   13 (23.6%)   36 (43.9%)   10 (19.2%)   27 (38.6%)   16 (25.8%)

Try this using WebR

Experimental use!

WebR is a tool allowing you to run R code in the web browser. Modify the code below and click run to see the results. Alternatively, copy the code and click here to open WebR in a new tab.

Data Setup

library(dplyr)
library(tern)

adsl <- random.cdisc.data::cadsl
adae <- random.cdisc.data::cadae
adsub <- random.cdisc.data::cadsub

adsub_bmi <- adsub %>%
  filter(PARAMCD == "BBMISI") %>%
  select(STUDYID, USUBJID, AVALCAT1) %>%
  mutate(
    AVALCAT1 = factor(AVALCAT1, levels = c("<18.5", "18.5 - 24.9", "25 - 29.9", ">30"))
  )

adsl <- adsl %>%
  mutate(
    RACE1 = case_when(
      RACE == "WHITE" ~ "WHITE",
      TRUE ~ "NON-WHITE"
    ),
    RACE1 = factor(
      RACE1,
      levels = c("WHITE", "NON-WHITE")
    )
  ) %>%
  left_join(
    y = adsub_bmi,
    by = c("STUDYID", "USUBJID")
  )

adae_labels <- var_labels(adae)

adae <- adae %>%
  mutate(
    RACE1 = case_when(
      RACE == "WHITE" ~ "WHITE",
      TRUE ~ "NON-WHITE"
    ),
    RACE1 = factor(
      RACE1,
      levels = c("WHITE", "NON-WHITE")
    )
  ) %>%
  left_join(
    y = adsub_bmi,
    by = c("STUDYID", "USUBJID")
  )

var_labels(adae) <- c(adae_labels, "RACE1" = "RACE WHITE/NON-WHITE", "AVALCAT1" = "Baseline BMI Category")

# Ensure character variables are converted to factors and empty strings and NAs are explicit missing levels.
adsl <- df_explicit_na(adsl)
adae <- df_explicit_na(adae)
adsub_bmi <- df_explicit_na(adsub_bmi)

teal App

Preview

library(teal.modules.clinical)

## Data reproducible code
data <- teal_data()
data <- within(data, {
  ADSL <- random.cdisc.data::cadsl
  ADAE <- random.cdisc.data::cadae

  # Ensure character variables are converted to factors and empty strings and NAs are explicit missing levels.
  ADSL <- df_explicit_na(ADSL)
  ADAE <- df_explicit_na(ADAE)
})
datanames <- c("ADSL", "ADAE")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

## Reusable Configuration For Modules
ADAE <- data[["ADAE"]]

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_t_events(
      label = "Adverse Event Table",
      dataname = "ADAE",
      arm_var = choices_selected(c("ARM", "ARMCD", "SEX"), c("ARM", "SEX")),
      llt = choices_selected(
        choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
        selected = c("AEDECOD")
      ),
      hlt = choices_selected(
        choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
        selected = "AEBODSYS"
      ),
      add_total = TRUE,
      event_type = "adverse event"
    )
  )
)

shinyApp(app$ui, app$server)

Try this using shinylive

Experimental use!

shinylive allow you to modify to run shiny application entirely in the web browser. Modify the code below and click re-run the app to see the results. The performance is slighly worse and some of the features (e.g. downloading) might not work at all.

#| '!! shinylive warning !!': |
#|   shinylive does not work in self-contained HTML documents.
#|   Please set `embed-resources: false` in your metadata.
#| standalone: true
#| viewerHeight: 800
#| editorHeight: 200
#| components: [viewer, editor]
#| layout: vertical

# -- WEBR HELPERS --
options(webr_pkg_repos = c("r-universe" = "https://insightsengineering.r-universe.dev", getOption("webr_pkg_repos")))

# -- APP CODE --
library(teal.modules.clinical)

## Data reproducible code
data <- teal_data()
data <- within(data, {
  ADSL <- random.cdisc.data::cadsl
  ADAE <- random.cdisc.data::cadae

  # Ensure character variables are converted to factors and empty strings and NAs are explicit missing levels.
  ADSL <- df_explicit_na(ADSL)
  ADAE <- df_explicit_na(ADAE)
})
datanames <- c("ADSL", "ADAE")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

## Reusable Configuration For Modules
ADAE <- data[["ADAE"]]

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_t_events(
      label = "Adverse Event Table",
      dataname = "ADAE",
      arm_var = choices_selected(c("ARM", "ARMCD", "SEX"), c("ARM", "SEX")),
      llt = choices_selected(
        choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
        selected = c("AEDECOD")
      ),
      hlt = choices_selected(
        choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
        selected = "AEBODSYS"
      ),
      add_total = TRUE,
      event_type = "adverse event"
    )
  )
)

shinyApp(app$ui, app$server)

Reproducibility

Timestamp

[1] "2024-11-21 15:17:44 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       Ubuntu 22.04.5 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2024-11-21
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package               * version  date (UTC) lib source
 backports               1.5.0    2024-05-23 [1] RSPM
 brio                    1.1.5    2024-04-24 [1] RSPM
 broom                   1.0.7    2024-09-26 [1] RSPM
 bslib                   0.8.0    2024-07-29 [1] RSPM
 cachem                  1.1.0    2024-05-16 [1] RSPM
 callr                   3.7.6    2024-03-25 [1] RSPM
 checkmate               2.3.2    2024-07-29 [1] RSPM
 chromote                0.3.1    2024-08-30 [1] RSPM
 cli                     3.6.3    2024-06-21 [1] RSPM
 coda                    0.19-4.1 2024-01-31 [1] CRAN (R 4.4.1)
 codetools               0.2-20   2024-03-31 [2] CRAN (R 4.4.1)
 colorspace              2.1-1    2024-07-26 [1] RSPM
 curl                    6.0.1    2024-11-14 [1] RSPM
 digest                  0.6.37   2024-08-19 [1] RSPM
 dplyr                 * 1.1.4    2023-11-17 [1] RSPM
 emmeans                 1.10.5   2024-10-14 [1] RSPM
 estimability            1.5.1    2024-05-12 [1] RSPM
 evaluate                1.0.1    2024-10-10 [1] RSPM
 fansi                   1.0.6    2023-12-08 [1] RSPM
 fastmap                 1.2.0    2024-05-15 [1] RSPM
 fontawesome             0.5.3    2024-11-16 [1] RSPM
 forcats                 1.0.0    2023-01-29 [1] RSPM
 formatR                 1.14     2023-01-17 [1] CRAN (R 4.4.1)
 formatters            * 0.5.9    2024-09-12 [1] RSPM
 geepack                 1.3.12   2024-09-23 [1] RSPM
 generics                0.1.3    2022-07-05 [1] RSPM
 ggplot2                 3.5.1    2024-04-23 [1] RSPM
 glue                    1.8.0    2024-09-30 [1] RSPM
 gtable                  0.3.6    2024-10-25 [1] RSPM
 htmltools               0.5.8.1  2024-04-04 [1] RSPM
 htmlwidgets             1.6.4    2023-12-06 [1] RSPM
 httpuv                  1.6.15   2024-03-26 [1] RSPM
 jquerylib               0.1.4    2021-04-26 [1] RSPM
 jsonlite                1.8.9    2024-09-20 [1] RSPM
 knitr                   1.49     2024-11-08 [1] RSPM
 later                   1.3.2    2023-12-06 [1] RSPM
 lattice                 0.22-6   2024-03-20 [2] CRAN (R 4.4.1)
 lifecycle               1.0.4    2023-11-07 [1] RSPM
 logger                  0.4.0    2024-10-22 [1] RSPM
 magrittr              * 2.0.3    2022-03-30 [1] RSPM
 MASS                    7.3-61   2024-06-13 [2] CRAN (R 4.4.1)
 Matrix                  1.7-1    2024-10-18 [1] RSPM
 memoise                 2.0.1    2021-11-26 [1] RSPM
 mime                    0.12     2021-09-28 [1] RSPM
 multcomp                1.4-26   2024-07-18 [1] CRAN (R 4.4.1)
 munsell                 0.5.1    2024-04-01 [1] RSPM
 mvtnorm                 1.3-2    2024-11-04 [1] RSPM
 nlme                    3.1-166  2024-08-14 [2] CRAN (R 4.4.1)
 pillar                  1.9.0    2023-03-22 [1] RSPM
 pkgcache                2.2.3    2024-09-12 [1] RSPM
 pkgconfig               2.0.3    2019-09-22 [1] RSPM
 processx                3.8.4    2024-03-16 [1] RSPM
 promises                1.3.0    2024-04-05 [1] RSPM
 ps                      1.8.1    2024-10-28 [1] RSPM
 purrr                   1.0.2    2023-08-10 [1] RSPM
 R6                      2.5.1    2021-08-19 [1] RSPM
 random.cdisc.data       0.3.16   2024-10-10 [1] RSPM
 rbibutils               2.3      2024-10-04 [1] RSPM
 Rcpp                    1.0.13-1 2024-11-02 [1] RSPM
 Rdpack                  2.6.2    2024-11-15 [1] RSPM
 rlang                   1.1.4    2024-06-04 [1] RSPM
 rmarkdown               2.29     2024-11-04 [1] RSPM
 rtables               * 0.6.10   2024-09-20 [1] RSPM
 sandwich                3.1-1    2024-09-15 [1] CRAN (R 4.4.1)
 sass                    0.4.9    2024-03-15 [1] RSPM
 scales                  1.3.0    2023-11-28 [1] RSPM
 sessioninfo             1.2.2    2021-12-06 [1] any (@1.2.2)
 shiny                 * 1.9.1    2024-08-01 [1] RSPM
 shinycssloaders         1.1.0    2024-07-30 [1] RSPM
 shinyjs                 2.1.0    2021-12-23 [1] RSPM
 shinyvalidate           0.1.3    2023-10-04 [1] RSPM
 shinyWidgets            0.8.7    2024-09-23 [1] RSPM
 stringi                 1.8.4    2024-05-06 [1] RSPM
 stringr                 1.5.1    2023-11-14 [1] RSPM
 survival                3.7-0    2024-06-05 [2] CRAN (R 4.4.1)
 teal                  * 0.15.2   2024-03-07 [1] RSPM
 teal.code             * 0.5.0    2024-01-11 [1] RSPM
 teal.data             * 0.6.0    2024-04-30 [1] RSPM
 teal.logger             0.3.0    2024-10-24 [1] RSPM
 teal.modules.clinical * 0.9.1    2024-04-27 [1] RSPM
 teal.reporter           0.3.1    2024-03-15 [1] RSPM
 teal.slice            * 0.5.1    2024-04-30 [1] RSPM
 teal.transform        * 0.5.0    2024-02-17 [1] RSPM
 teal.widgets            0.4.2    2023-12-14 [1] RSPM
 tern                  * 0.9.6    2024-09-24 [1] RSPM
 tern.gee                0.1.5    2024-08-23 [1] RSPM
 testthat                3.2.1.1  2024-04-14 [1] RSPM
 TH.data                 1.1-2    2023-04-17 [1] CRAN (R 4.4.1)
 tibble                  3.2.1    2023-03-20 [1] RSPM
 tidyr                   1.3.1    2024-01-24 [1] RSPM
 tidyselect              1.2.1    2024-03-11 [1] RSPM
 utf8                    1.2.4    2023-10-22 [1] RSPM
 vctrs                   0.6.5    2023-12-01 [1] RSPM
 webshot                 0.5.5    2023-06-26 [1] CRAN (R 4.4.1)
 webshot2                0.1.1    2023-08-11 [1] RSPM
 websocket               1.4.2    2024-07-22 [1] RSPM
 withr                   3.0.2    2024-10-28 [1] RSPM
 xfun                    0.49     2024-10-31 [1] RSPM
 xtable                  1.8-4    2019-04-21 [1] RSPM
 yaml                    2.3.10   2024-07-26 [1] RSPM
 zoo                     1.8-12   2023-04-13 [1] CRAN (R 4.4.1)

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

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