TSFAE24D

Subjects With Treatment-emergent Adverse Events Toxicity Grade =3 With Frequency =x% in Any Treatment Group by System Organ Class and Preferred Term

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# Program Name:              tsfae24d.R

# Prep environment:

library(envsetup)
library(tern)
library(dplyr)
library(rtables)
library(junco)

# Define script level parameters:

tblid <- "TSFAE24d"
fileid <- tblid
popfl <- "SAFFL"
trtvar <- "TRT01A"
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

# Process data:

adsl <- pharmaverseadamjnj::adsl %>%
  filter(!!rlang::sym(popfl) == "Y") %>%
  create_colspan_var(
    non_active_grp = "Placebo",
    non_active_grp_span_lbl = " ",
    active_grp_span_lbl = "Active Study Agent",
    colspan_var = "colspan_trt",
    trt_var = trtvar
  ) %>%
  mutate(COLSPAN_TOX = "AEs") %>%
  select(
    USUBJID,
    !!rlang::sym(popfl),
    !!rlang::sym(trtvar),
    colspan_trt,
    COLSPAN_TOX
  )

adae <- pharmaverseadamjnj::adae %>%
  filter(TRTEMFL == "Y") %>%
  mutate(TOXGE3 = ifelse(AETOXGRN == 3 | AETOXGRN > 3, ">= 3", "< 3")) %>%
  select(USUBJID, TRTEMFL, AEBODSYS, AEDECOD, AETOXGR, TOXGE3)

adae <- inner_join(adae, adsl, by = c("USUBJID"))

# Define layout and build table:

colspan_trt_map <- create_colspan_map(
  adsl,
  non_active_grp = "Placebo",
  non_active_grp_span_lbl = " ",
  active_grp_span_lbl = "Active Study Agent",
  colspan_var = "colspan_trt",
  trt_var = trtvar
)

add_active_combo <- make_split_fun(
  post = list(
    add_combo_facet(
      name = "Combined",
      label = "Combined",
      levels = c("Xanomeline High Dose", "Xanomeline Low Dose")
    ),
    cond_rm_facets(
      facets = "Combined",
      ancestor_pos = NA,
      value = " ",
      split = "colspan_trt"
    )
  )
)

# Create "TOX > 3" facet.
add_tox_levels <- make_split_fun(
  post = list(add_combo_facet(
    name = "TOXGR",
    label = ">= Grade 3 AEs",
    levels = c("AEs")
  ))
)

extra_args1 <- list(
  .stats = c("count_unique_fraction"),
  subcol_split = "TOXGR",
  subcol_var = "TOXGE3",
  subcol_val = ">= 3"
)

lyt <- basic_table(top_level_section_div = " ") %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  ) %>%
  split_cols_by(
    trtvar,
    split_fun = add_active_combo,
    show_colcounts = TRUE,
    colcount_format = "N=xx"
  ) %>%
  split_cols_by("COLSPAN_TOX", split_fun = add_tox_levels) %>%
  analyze(
    "TRTEMFL",
    nested = FALSE,
    afun = a_freq_subcol_j,
    extra_args = append(
      extra_args1,
      list(
        label = "Subjects with >= 1 AE",
        val = "Y"
      )
    )
  ) %>%
  split_rows_by(
    "AEBODSYS",
    split_label = "System Organ Class",
    label_pos = "topleft",
    split_fun = trim_levels_in_group("AEDECOD"),
    section_div = " ",
    nested = FALSE
  ) %>%
  summarize_row_groups(
    "AEBODSYS",
    cfun = a_freq_subcol_j,
    extra_args = extra_args1
  ) %>%
  analyze("AEDECOD", afun = a_freq_subcol_j, extra_args = extra_args1) %>%
  append_topleft(" Preferred Term, n (%)")

result <- build_table(lyt, adae, alt_counts_df = adsl)

# Post-Processing:

result <- result %>%
  sort_at_path(
    path = c("AEBODSYS"),
    scorefun = cont_n_onecol("Active Study Agent.Combined.TOXGR")
  ) %>%
  sort_at_path(
    path = c("AEBODSYS", "*", "AEDECOD"),
    scorefun = score_occurrences_cols("Active Study Agent.Combined.TOXGR")
  )

row_condition <- has_fraction_in_any_col(
  atleast = .02,
  col_names = c(
    "Active Study Agent.Xanomeline High Dose.TOXGR",
    "Active Study Agent.Xanomeline Low Dose.TOXGR",
    "Active Study Agent.Combined.TOXGR",
    " .Placebo.TOXGR"
  )
)

result <- safe_prune_table(result, keep_rows(row_condition))

# Add titles and footnotes:

result <- set_titles(result, tab_titles)

# Convert to tbl file and output table:

tt_to_tlgrtf(string_map = string_map, tt = 
  result,
  file = fileid,
  orientation = "landscape",
  nosplitin = list(cols = c(trtvar))
)

TSFAE24d: Subjects With Treatment-emergent Adverse Events Toxicity Grade =3 With Frequency =[x]% in [Any Treatment Group] by System Organ Class and Preferred Term; Safety Analysis Set (Study jjcs - core)
	Active Study Agent
	Xanomeline High Dose		Xanomeline Low Dose		Combined		Placebo
System Organ Class	N=53		N=73		N=126		N=59
Preferred Term, n (%)	AEs	≥ Grade 3 AEs	AEs	≥ Grade 3 AEs	AEs	≥ Grade 3 AEs	AEs	≥ Grade 3 AEs
Subjects with ≥ 1 AE	51 (96.2%)	48 (90.6%)	62 (84.9%)	52 (71.2%)	113 (89.7%)	100 (79.4%)	42 (71.2%)	35 (59.3%)
General disorders and  administration site conditions	26 (49.1%)	23 (43.4%)	38 (52.1%)	26 (35.6%)	64 (50.8%)	49 (38.9%)	16 (27.1%)	10 (16.9%)
APPLICATION SITE PRURITUS	13 (24.5%)	8 (15.1%)	18 (24.7%)	8 (11.0%)	31 (24.6%)	16 (12.7%)	4 (6.8%)	4 (6.8%)
APPLICATION SITE ERYTHEMA	10 (18.9%)	6 (11.3%)	11 (15.1%)	7 (9.6%)	21 (16.7%)	13 (10.3%)	2 (3.4%)	0
APPLICATION SITE IRRITATION	8 (15.1%)	5 (9.4%)	7 (9.6%)	6 (8.2%)	15 (11.9%)	11 (8.7%)	2 (3.4%)	1 (1.7%)
APPLICATION SITE VESICLES	4 (7.5%)	3 (5.7%)	4 (5.5%)	3 (4.1%)	8 (6.3%)	6 (4.8%)	0	0
APPLICATION SITE DERMATITIS	4 (7.5%)	3 (5.7%)	7 (9.6%)	2 (2.7%)	11 (8.7%)	5 (4.0%)	5 (8.5%)	3 (5.1%)
FATIGUE	5 (9.4%)	2 (3.8%)	5 (6.8%)	3 (4.1%)	10 (7.9%)	5 (4.0%)	0	0
APPLICATION SITE SWELLING	2 (3.8%)	2 (3.8%)	1 (1.4%)	1 (1.4%)	3 (2.4%)	3 (2.4%)	0	0
APPLICATION SITE  PERSPIRATION	2 (3.8%)	2 (3.8%)	0	0	2 (1.6%)	2 (1.6%)	0	0
OEDEMA PERIPHERAL	1 (1.9%)	1 (1.9%)	1 (1.4%)	0	2 (1.6%)	1 (0.8%)	2 (3.4%)	2 (3.4%)
Skin and subcutaneous tissue  disorders	34 (64.2%)	21 (39.6%)	28 (38.4%)	18 (24.7%)	62 (49.2%)	39 (31.0%)	16 (27.1%)	8 (13.6%)
PRURITUS	20 (37.7%)	11 (20.8%)	14 (19.2%)	9 (12.3%)	34 (27.0%)	20 (15.9%)	6 (10.2%)	2 (3.4%)
RASH	5 (9.4%)	4 (7.5%)	9 (12.3%)	6 (8.2%)	14 (11.1%)	10 (7.9%)	4 (6.8%)	2 (3.4%)
ERYTHEMA	12 (22.6%)	5 (9.4%)	8 (11.0%)	3 (4.1%)	20 (15.9%)	8 (6.3%)	6 (10.2%)	3 (5.1%)
HYPERHIDROSIS	8 (15.1%)	4 (7.5%)	4 (5.5%)	2 (2.7%)	12 (9.5%)	6 (4.8%)	2 (3.4%)	2 (3.4%)
SKIN IRRITATION	4 (7.5%)	2 (3.8%)	4 (5.5%)	2 (2.7%)	8 (6.3%)	4 (3.2%)	3 (5.1%)	2 (3.4%)
BLISTER	1 (1.9%)	1 (1.9%)	2 (2.7%)	2 (2.7%)	3 (2.4%)	3 (2.4%)	0	0
RASH PRURITIC	2 (3.8%)	2 (3.8%)	1 (1.4%)	1 (1.4%)	3 (2.4%)	3 (2.4%)	0	0
Nervous system disorders	18 (34.0%)	11 (20.8%)	18 (24.7%)	11 (15.1%)	36 (28.6%)	22 (17.5%)	5 (8.5%)	4 (6.8%)
DIZZINESS	8 (15.1%)	4 (7.5%)	8 (11.0%)	3 (4.1%)	16 (12.7%)	7 (5.6%)	0	0
HEADACHE	5 (9.4%)	3 (5.7%)	3 (4.1%)	2 (2.7%)	8 (6.3%)	5 (4.0%)	2 (3.4%)	1 (1.7%)
Gastrointestinal disorders	14 (26.4%)	10 (18.9%)	10 (13.7%)	7 (9.6%)	24 (19.0%)	17 (13.5%)	7 (11.9%)	5 (8.5%)
NAUSEA	5 (9.4%)	3 (5.7%)	2 (2.7%)	2 (2.7%)	7 (5.6%)	5 (4.0%)	0	0
DIARRHOEA	2 (3.8%)	1 (1.9%)	3 (4.1%)	3 (4.1%)	5 (4.0%)	4 (3.2%)	3 (5.1%)	2 (3.4%)
VOMITING	5 (9.4%)	4 (7.5%)	2 (2.7%)	0	7 (5.6%)	4 (3.2%)	0	0
SALIVARY HYPERSECRETION	4 (7.5%)	2 (3.8%)	0	0	4 (3.2%)	2 (1.6%)	0	0
Cardiac disorders	11 (20.8%)	7 (13.2%)	11 (15.1%)	8 (11.0%)	22 (17.5%)	15 (11.9%)	7 (11.9%)	5 (8.5%)
SINUS BRADYCARDIA	7 (13.2%)	4 (7.5%)	4 (5.5%)	1 (1.4%)	11 (8.7%)	5 (4.0%)	0	0
ATRIAL FIBRILLATION	1 (1.9%)	1 (1.9%)	2 (2.7%)	2 (2.7%)	3 (2.4%)	3 (2.4%)	0	0
MYOCARDIAL INFARCTION	3 (5.7%)	0	1 (1.4%)	1 (1.4%)	4 (3.2%)	1 (0.8%)	3 (5.1%)	2 (3.4%)
Infections and infestations	9 (17.0%)	7 (13.2%)	6 (8.2%)	5 (6.8%)	15 (11.9%)	12 (9.5%)	14 (23.7%)	8 (13.6%)
NASOPHARYNGITIS	3 (5.7%)	2 (3.8%)	3 (4.1%)	3 (4.1%)	6 (4.8%)	5 (4.0%)	2 (3.4%)	2 (3.4%)
Respiratory, thoracic and  mediastinal disorders	7 (13.2%)	5 (9.4%)	6 (8.2%)	4 (5.5%)	13 (10.3%)	9 (7.1%)	5 (8.5%)	4 (6.8%)
COUGH	3 (5.7%)	0	4 (5.5%)	3 (4.1%)	7 (5.6%)	3 (2.4%)	1 (1.7%)	1 (1.7%)
Psychiatric disorders	6 (11.3%)	3 (5.7%)	8 (11.0%)	5 (6.8%)	14 (11.1%)	8 (6.3%)	7 (11.9%)	4 (6.8%)
CONFUSIONAL STATE	1 (1.9%)	0	3 (4.1%)	2 (2.7%)	4 (3.2%)	2 (1.6%)	2 (3.4%)	1 (1.7%)
Musculoskeletal and connective  tissue disorders	4 (7.5%)	4 (7.5%)	5 (6.8%)	2 (2.7%)	9 (7.1%)	6 (4.8%)	2 (3.4%)	2 (3.4%)
BACK PAIN	2 (3.8%)	2 (3.8%)	1 (1.4%)	0	3 (2.4%)	2 (1.6%)	1 (1.7%)	1 (1.7%)
Note: Subjects are counted only once for any given event, regardless of the number of times they actually experienced the event.
Note: Adverse events are coded using MedDRA version 26.0; toxicity grade is evaluated according to NCI-CTCAE version 5.0..

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