Code
grade_groups <- list("- Any Intensity -" = c("MILD", "MODERATE", "SEVERE", "LIFE THREATENING"))
split_fun <- trim_levels_in_group
lyt <- basic_table(show_colcounts = TRUE) %>%
split_cols_by("ACTARM") %>%
count_occurrences_by_grade(
var = "ASEV",
grade_groups = grade_groups
) %>%
split_rows_by(
"AEBODSYS",
child_labels = "visible",
nested = TRUE,
split_fun = split_fun("ASEV"),
label_pos = "topleft",
split_label = obj_label(adae$AEBODSYS)
) %>%
summarize_occurrences_by_grade(
var = "ASEV",
grade_groups = grade_groups
) %>%
split_rows_by(
"AEDECOD",
child_labels = "visible",
nested = TRUE,
indent_mod = -1L,
split_fun = split_fun("ASEV"),
label_pos = "topleft",
split_label = obj_label(adae$AEDECOD)
) %>%
summarize_num_patients(
var = "USUBJID",
.stats = "unique",
.labels = c("- Any Intensity -")
) %>%
count_occurrences_by_grade(
var = "ASEV",
.indent_mods = -1L
) %>%
append_varlabels(adae, "AESEV", indent = 2L)
result <- lyt %>%
build_table(
adae,
alt_counts_df = adsl
) %>%
sort_at_path(
path = "AEBODSYS",
scorefun = cont_n_allcols,
decreasing = TRUE
) %>%
sort_at_path(
path = c("AEBODSYS", "*", "AEDECOD"),
scorefun = cont_n_allcols,
decreasing = TRUE
)
resultMedDRA System Organ Class
MedDRA Preferred Term A: Drug X B: Placebo C: Combination
Severity/Intensity (N=134) (N=134) (N=132)
—————————————————————————————————————————————————————————————————————
- Any Intensity - 100 (74.6%) 98 (73.1%) 103 (78.0%)
MILD 5 (3.7%) 7 (5.2%) 4 (3.0%)
MODERATE 17 (12.7%) 21 (15.7%) 20 (15.2%)
SEVERE 77 (57.5%) 69 (51.5%) 77 (58.3%)
LIFE THREATENING 1 (0.7%) 1 (0.7%) 2 (1.5%)
cl A.1
- Any Intensity - 68 (50.7%) 58 (43.3%) 76 (57.6%)
MILD 27 (20.1%) 19 (14.2%) 34 (25.8%)
MODERATE 40 (29.9%) 39 (29.1%) 41 (31.1%)
LIFE THREATENING 1 (0.7%) 0 1 (0.8%)
dcd A.1.1.1.1
- Any Intensity - 45 (33.6%) 31 (23.1%) 52 (39.4%)
MILD 45 (33.6%) 31 (23.1%) 51 (38.6%)
LIFE THREATENING 0 0 1 (0.8%)
dcd A.1.1.1.2
- Any Intensity - 41 (30.6%) 39 (29.1%) 42 (31.8%)
MODERATE 40 (29.9%) 39 (29.1%) 41 (31.1%)
LIFE THREATENING 1 (0.7%) 0 1 (0.8%)
cl B.2
- Any Intensity - 62 (46.3%) 56 (41.8%) 74 (56.1%)
MILD 23 (17.2%) 22 (16.4%) 28 (21.2%)
MODERATE 38 (28.4%) 34 (25.4%) 45 (34.1%)
LIFE THREATENING 1 (0.7%) 0 1 (0.8%)
dcd B.2.2.3.1
- Any Intensity - 38 (28.4%) 40 (29.9%) 45 (34.1%)
MILD 38 (28.4%) 40 (29.9%) 45 (34.1%)
dcd B.2.1.2.1
- Any Intensity - 39 (29.1%) 34 (25.4%) 46 (34.8%)
MODERATE 38 (28.4%) 34 (25.4%) 45 (34.1%)
LIFE THREATENING 1 (0.7%) 0 1 (0.8%)
cl D.1
- Any Intensity - 64 (47.8%) 54 (40.3%) 68 (51.5%)
MODERATE 21 (15.7%) 22 (16.4%) 22 (16.7%)
SEVERE 42 (31.3%) 32 (23.9%) 44 (33.3%)
LIFE THREATENING 1 (0.7%) 0 2 (1.5%)
dcd D.1.1.1.1
- Any Intensity - 42 (31.3%) 32 (23.9%) 46 (34.8%)
SEVERE 42 (31.3%) 32 (23.9%) 45 (34.1%)
LIFE THREATENING 0 0 1 (0.8%)
dcd D.1.1.4.2
- Any Intensity - 38 (28.4%) 34 (25.4%) 40 (30.3%)
MODERATE 37 (27.6%) 34 (25.4%) 39 (29.5%)
LIFE THREATENING 1 (0.7%) 0 1 (0.8%)
cl D.2
- Any Intensity - 37 (27.6%) 46 (34.3%) 50 (37.9%)
MILD 37 (27.6%) 46 (34.3%) 49 (37.1%)
LIFE THREATENING 0 0 1 (0.8%)
dcd D.2.1.5.3
- Any Intensity - 37 (27.6%) 46 (34.3%) 50 (37.9%)
MILD 37 (27.6%) 46 (34.3%) 49 (37.1%)
LIFE THREATENING 0 0 1 (0.8%)
cl C.2
- Any Intensity - 28 (20.9%) 36 (26.9%) 48 (36.4%)
MODERATE 28 (20.9%) 36 (26.9%) 47 (35.6%)
LIFE THREATENING 0 0 1 (0.8%)
dcd C.2.1.2.1
- Any Intensity - 28 (20.9%) 36 (26.9%) 48 (36.4%)
MODERATE 28 (20.9%) 36 (26.9%) 47 (35.6%)
LIFE THREATENING 0 0 1 (0.8%)
cl B.1
- Any Intensity - 38 (28.4%) 37 (27.6%) 36 (27.3%)
SEVERE 38 (28.4%) 36 (26.9%) 36 (27.3%)
LIFE THREATENING 0 1 (0.7%) 0
dcd B.1.1.1.1
- Any Intensity - 38 (28.4%) 37 (27.6%) 36 (27.3%)
SEVERE 38 (28.4%) 36 (26.9%) 36 (27.3%)
LIFE THREATENING 0 1 (0.7%) 0
cl C.1
- Any Intensity - 36 (26.9%) 34 (25.4%) 36 (27.3%)
SEVERE 36 (26.9%) 34 (25.4%) 36 (27.3%)
dcd C.1.1.1.3
- Any Intensity - 36 (26.9%) 34 (25.4%) 36 (27.3%)
SEVERE 36 (26.9%) 34 (25.4%) 36 (27.3%) 