TL Catalog
  1. Tables
  2. Adverse Events
  3. TSFAE21C
  • Introduction

  • Index

  • Tables
    • Adverse Events
      • TSFAE01A
      • TSFAE01B
      • TSFAE02
      • TSFAE02A
      • TSFAE03
      • TSFAE03A
      • TSFAE04
      • TSFAE04A
      • TSFAE05
      • TSFAE05A
      • TSFAE06A
      • TSFAE06B
      • TSFAE07A
      • TSFAE07B
      • TSFAE08
      • TSFAE09
      • TSFAE10
      • TSFAE11
      • TSFAE12
      • TSFAE13
      • TSFAE14
      • TSFAE15
      • TSFAE16
      • TSFAE17A
      • TSFAE17B
      • TSFAE17C
      • TSFAE17D
      • TSFAE19A
      • TSFAE19B
      • TSFAE19C
      • TSFAE19D
      • TSFAE20A
      • TSFAE20B
      • TSFAE20C
      • TSFAE21A
      • TSFAE21B
      • TSFAE21C
      • TSFAE21D
      • TSFAE22A
      • TSFAE22B
      • TSFAE22C
      • TSFAE23A
      • TSFAE23B
      • TSFAE23C
      • TSFAE23D
      • TSFAE24A
      • TSFAE24B
      • TSFAE24C
      • TSFAE24D
      • TSFAE24F
      • TSFDTH01
    • Clinical Laboratory Evaluation
      • TSFLAB01
      • TSFLAB01A
      • TSFLAB02
      • TSFLAB02A
      • TSFLAB02B
      • TSFLAB03
      • TSFLAB03A
      • TSFLAB04A
      • TSFLAB04B
      • TSFLAB05
      • TSFLAB06
      • TSFLAB07
    • Demographic
      • TSIDEM01
      • TSIDEM02
      • TSIMH01
    • Disposition of Subjects
      • TSIDS01
      • TSIDS02
      • TSIDS02A
    • Electrocardiograms
      • TSFECG01
      • TSFECG01A
      • TSFECG02
      • TSFECG03
      • TSFECG04
      • TSFECG05
    • Exposure
      • TSIEX01
      • TSIEX02
      • TSIEX03
      • TSIEX04
      • TSIEX06
      • TSIEX07
      • TSIEX08
      • TSIEX09
      • TSIEX10
      • TSIEX11
    • Pharmacokinetics
      • TPK01A
      • TPK01B
      • TPK02
      • TPK03
    • Prior and Concomitant Therapies
      • TSICM01
      • TSICM02
      • TSICM03
      • TSICM04
      • TSICM05
      • TSICM06
      • TSICM07
      • TSICM08
    • Vital Signs and Physical Findings
      • TSFVIT01
      • TSFVIT01A
      • TSFVIT02
      • TSFVIT03
      • TSFVIT04
      • TSFVIT05
      • TSFVIT06
  • Listings
    • Adverse Events
      • LSFAE01
      • LSFAE02
      • LSFAE03
      • LSFAE04
      • LSFAE05
      • LSFAE06A
      • LSFAE06B
      • LSFDTH01
    • Clinical Laboratory Evaluation
      • LSFLAB01
    • Demographic
      • LSIDEM01
      • LSIDEM02
      • LSIMH01
    • Disposition of Subjects
      • LSIDS01
      • LSIDS02
      • LSIDS03
      • LSIDS04
      • LSIDS05
    • Electrocardiograms
      • LSFECG01
      • LSFECG02
    • Exposure
      • LSIEX01
      • LSIEX02
      • LSIEX03
    • Prior and Concomitant Therapies
      • LSICM01
    • Vital Signs and Physical Findings
      • LSFVIT01
      • LSFVIT02

  • Reproducibility

  • Changelog

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  1. Tables
  2. Adverse Events
  3. TSFAE21C

TSFAE21C

Subjects With Treatment-emergent Adverse Events by System Organ Class, Preferred Term, and Severity


Output

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Code
# Program Name: tsfae21c.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSFAE21c"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

trtvar <- "TRT01A"
popfl <- "SAFFL"
combined_colspan_trt <- TRUE

if (combined_colspan_trt == TRUE) {
  # Set up levels and label for the required combined columns
  add_combo <- add_combo_facet(
    "Combined",
    label = "Combined",
    levels = c("Xanomeline High Dose", "Xanomeline Low Dose")
  )

  # choose if any facets need to be removed - e.g remove the combined column for placebo
  rm_combo_from_placebo <- cond_rm_facets(
    facets = "Combined",
    ancestor_pos = NA,
    value = " ",
    split = "colspan_trt"
  )

  mysplit <- make_split_fun(post = list(add_combo, rm_combo_from_placebo))
}

# Process Data:

adsl <- pharmaverseadamjnj::adsl %>%
  filter(!!rlang::sym(popfl) == "Y") %>%
  select(STUDYID, USUBJID, all_of(trtvar), all_of(popfl))

adae <- pharmaverseadamjnj::adae %>%
  filter(TRTEMFL == "Y") %>%
  select(USUBJID, AEBODSYS, AEDECOD, TRTEMFL, AESEV)

# Take maximum severity
adaemax <- adae %>%
  mutate(
    AESEVN = case_when(
      toupper(AESEV) == "MILD" ~ 3,
      toupper(AESEV) == "MODERATE" ~ 2,
      toupper(AESEV) == "SEVERE" ~ 1,
      .default = 99
    )
  ) %>%
  arrange(USUBJID, AEBODSYS, AEDECOD, AESEVN) %>%
  group_by(USUBJID, AEBODSYS, AEDECOD) %>%
  slice(1) %>%
  ungroup()

adsl$colspan_trt <- factor(
  ifelse(adsl[[trtvar]] == "Placebo", " ", "Active Study Agent"),
  levels = c("Active Study Agent", " ")
)

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
)

# join data together
ae <- inner_join(adaemax, adsl, by = c("USUBJID"))

ae <- ae %>%
  mutate(AESEV2 = as.factor(ifelse(is.na(AESEV), "Missing", AESEV)))

if (length(adae$TRTEMFL) == 0) {
  ae <- right_join(adaemax, adsl, by = c("USUBJID"))

  ae <- ae %>%
    mutate(AESEV2 = as.factor(ifelse(is.na(AESEV), "Missing", AESEV)))
}

levels(ae$AESEV2) <- c(levels(ae$AESEV), "Missing")

# Define layout and build table:

extra_args_1 <- list(
  denom = "n_altdf",
  .stats = c("count_unique_fraction")
)

lyt <- basic_table(
  top_level_section_div = " ",
  show_colcounts = TRUE,
  colcount_format = "N=xx"
) %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  )

if (combined_colspan_trt == TRUE) {
  lyt <- lyt %>%
    split_cols_by(trtvar, split_fun = mysplit)
} else {
  lyt <- lyt %>%
    split_cols_by(trtvar)
}

lyt <- lyt %>%
  analyze(
    "TRTEMFL",
    afun = a_freq_j,
    show_labels = "hidden",
    extra_args = append(
      extra_args_1,
      list(label = "Subjects with >=1 AE", val = "Y")
    )
  ) %>%
  split_rows_by(
    "AEBODSYS",
    split_label = "System Organ Class",
    split_fun = trim_levels_in_group("AEDECOD"),
    label_pos = "topleft",
    section_div = c(" "),
    nested = FALSE
  ) %>%
  summarize_row_groups(
    "AEBODSYS",
    cfun = a_freq_j,
    extra_args = extra_args_1
  ) %>%
  split_rows_by(
    "AEDECOD",
    split_label = "Preferred Term, n (%)",
    section_div = c(" "),
    nested = TRUE
  ) %>%
  summarize_row_groups(
    "AEDECOD",
    cfun = a_freq_j,
    extra_args = extra_args_1
  ) %>%
  analyze("AESEV2", afun = a_freq_j, extra_args = extra_args_1) %>%
  append_topleft("  Preferred Term, n (%)")

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

# Post-Processing step to sort by descending count on chosen active treatment columns.

if (length(adae$TRTEMFL) != 0) {
  result <- sort_at_path(
    result,
    c("root", "AEBODSYS"),
    scorefun = jj_complex_scorefun()
  )
  result <- sort_at_path(
    result,
    c("root", "AEBODSYS", "*", "AEDECOD"),
    scorefun = jj_complex_scorefun()
  )

  #########################################################################################
  # Post-Processing step to remove all rows where counts are 0
  #########################################################################################

  result <- safe_prune_table(result, prune_func = prune_empty_level)
}

# 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 = "portrait",
  label_width_ins = 1.5
)

TSFAE21c: Subjects With Treatment-emergent Adverse Events by System Organ Class, Preferred Term, and Severity; Safety Analysis Set (Study jjcs - core)

Active Study Agent

System Organ Class

Xanomeline High Dose

Xanomeline Low Dose

Combined

Placebo

Preferred Term, n (%)

N=53

N=73

N=126

N=59

Subjects with ≥1 AE

51 (96.2%)

62 (84.9%)

113 (89.7%)

42 (71.2%)

General disorders and
 administration site conditions

26 (49.1%)

38 (52.1%)

64 (50.8%)

16 (27.1%)

APPLICATION SITE PRURITUS

13 (24.5%)

18 (24.7%)

31 (24.6%)

4 (6.8%)

Mild

7 (13.2%)

11 (15.1%)

18 (14.3%)

3 (5.1%)

Moderate

6 (11.3%)

7 (9.6%)

13 (10.3%)

1 (1.7%)

APPLICATION SITE ERYTHEMA

10 (18.9%)

11 (15.1%)

21 (16.7%)

2 (3.4%)

Mild

7 (13.2%)

4 (5.5%)

11 (8.7%)

2 (3.4%)

Moderate

3 (5.7%)

6 (8.2%)

9 (7.1%)

0

Severe

0

1 (1.4%)

1 (0.8%)

0

APPLICATION SITE IRRITATION

8 (15.1%)

7 (9.6%)

15 (11.9%)

2 (3.4%)

Mild

3 (5.7%)

2 (2.7%)

5 (4.0%)

0

Moderate

5 (9.4%)

3 (4.1%)

8 (6.3%)

2 (3.4%)

Severe

0

2 (2.7%)

2 (1.6%)

0

APPLICATION SITE DERMATITIS

4 (7.5%)

7 (9.6%)

11 (8.7%)

5 (8.5%)

Mild

2 (3.8%)

3 (4.1%)

5 (4.0%)

5 (8.5%)

Moderate

2 (3.8%)

4 (5.5%)

6 (4.8%)

0

FATIGUE

5 (9.4%)

5 (6.8%)

10 (7.9%)

0

Mild

5 (9.4%)

3 (4.1%)

8 (6.3%)

0

Moderate

0

2 (2.7%)

2 (1.6%)

0

APPLICATION SITE VESICLES

4 (7.5%)

4 (5.5%)

8 (6.3%)

0

Mild

2 (3.8%)

2 (2.7%)

4 (3.2%)

0

Moderate

2 (3.8%)

2 (2.7%)

4 (3.2%)

0

APPLICATION SITE SWELLING

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

MALAISE

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

APPLICATION SITE PAIN

2 (3.8%)

0

2 (1.6%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

APPLICATION SITE
 PERSPIRATION

2 (3.8%)

0

2 (1.6%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

APPLICATION SITE URTICARIA

0

2 (2.7%)

2 (1.6%)

0

Mild

0

2 (2.7%)

2 (1.6%)

0

CHEST DISCOMFORT

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

CHEST PAIN

2 (3.8%)

0

2 (1.6%)

0

Mild

2 (3.8%)

0

2 (1.6%)

0

OEDEMA PERIPHERAL

1 (1.9%)

1 (1.4%)

2 (1.6%)

2 (3.4%)

Mild

0

0

0

2 (3.4%)

Moderate

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

APPLICATION SITE BLEEDING

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

APPLICATION SITE
 DESQUAMATION

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

APPLICATION SITE REACTION

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

Moderate

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

ASTHENIA

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Moderate

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

CHILLS

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

FEELING ABNORMAL

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

FEELING COLD

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

OEDEMA

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

PAIN

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

PYREXIA

0

1 (1.4%)

1 (0.8%)

2 (3.4%)

Mild

0

1 (1.4%)

1 (0.8%)

2 (3.4%)

SECRETION DISCHARGE

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

SUDDEN DEATH

0

1 (1.4%)

1 (0.8%)

0

Severe

0

1 (1.4%)

1 (0.8%)

0

ULCER

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

APPLICATION SITE INDURATION

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Skin and subcutaneous tissue
 disorders

34 (64.2%)

28 (38.4%)

62 (49.2%)

16 (27.1%)

PRURITUS

20 (37.7%)

14 (19.2%)

34 (27.0%)

6 (10.2%)

Mild

13 (24.5%)

6 (8.2%)

19 (15.1%)

5 (8.5%)

Moderate

7 (13.2%)

7 (9.6%)

14 (11.1%)

1 (1.7%)

Severe

0

1 (1.4%)

1 (0.8%)

0

ERYTHEMA

12 (22.6%)

8 (11.0%)

20 (15.9%)

6 (10.2%)

Mild

8 (15.1%)

3 (4.1%)

11 (8.7%)

2 (3.4%)

Moderate

4 (7.5%)

5 (6.8%)

9 (7.1%)

4 (6.8%)

RASH

5 (9.4%)

9 (12.3%)

14 (11.1%)

4 (6.8%)

Mild

4 (7.5%)

5 (6.8%)

9 (7.1%)

1 (1.7%)

Moderate

1 (1.9%)

3 (4.1%)

4 (3.2%)

3 (5.1%)

Severe

0

1 (1.4%)

1 (0.8%)

0

HYPERHIDROSIS

8 (15.1%)

4 (5.5%)

12 (9.5%)

2 (3.4%)

Mild

8 (15.1%)

1 (1.4%)

9 (7.1%)

2 (3.4%)

Moderate

0

3 (4.1%)

3 (2.4%)

0

SKIN IRRITATION

4 (7.5%)

4 (5.5%)

8 (6.3%)

3 (5.1%)

Mild

3 (5.7%)

1 (1.4%)

4 (3.2%)

2 (3.4%)

Moderate

1 (1.9%)

2 (2.7%)

3 (2.4%)

1 (1.7%)

Severe

0

1 (1.4%)

1 (0.8%)

0

BLISTER

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Severe

0

1 (1.4%)

1 (0.8%)

0

RASH PRURITIC

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

URTICARIA

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

ACTINIC KERATOSIS

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

PRURITUS GENERALISED

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

RASH ERYTHEMATOUS

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

RASH MACULO-PAPULAR

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

SKIN ODOUR ABNORMAL

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

ALOPECIA

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

DRUG ERUPTION

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

SKIN ULCER

0

0

0

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

Nervous system disorders

18 (34.0%)

18 (24.7%)

36 (28.6%)

5 (8.5%)

DIZZINESS

8 (15.1%)

8 (11.0%)

16 (12.7%)

0

Mild

5 (9.4%)

5 (6.8%)

10 (7.9%)

0

Moderate

3 (5.7%)

3 (4.1%)

6 (4.8%)

0

HEADACHE

5 (9.4%)

3 (4.1%)

8 (6.3%)

2 (3.4%)

Mild

4 (7.5%)

2 (2.7%)

6 (4.8%)

2 (3.4%)

Moderate

1 (1.9%)

0

1 (0.8%)

0

Severe

0

1 (1.4%)

1 (0.8%)

0

SYNCOPE

1 (1.9%)

3 (4.1%)

4 (3.2%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

Moderate

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Severe

0

1 (1.4%)

1 (0.8%)

0

SOMNOLENCE

1 (1.9%)

2 (2.7%)

3 (2.4%)

1 (1.7%)

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

TRANSIENT ISCHAEMIC
 ATTACK

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

Severe

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

BALANCE DISORDER

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

BURNING SENSATION

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

COGNITIVE DISORDER

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

COMPLEX PARTIAL SEIZURES

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

COORDINATION ABNORMAL

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

HEMIANOPIA HOMONYMOUS

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

HYPERSOMNIA

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

LETHARGY

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

PARAESTHESIA

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

PARAESTHESIA ORAL

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

PAROSMIA

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

PARTIAL SEIZURES WITH
 SECONDARY
 GENERALISATION

1 (1.9%)

0

1 (0.8%)

0

Severe

1 (1.9%)

0

1 (0.8%)

0

STUPOR

0

1 (1.4%)

1 (0.8%)

0

Severe

0

1 (1.4%)

1 (0.8%)

0

SYNCOPE VASOVAGAL

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

PARKINSON'S DISEASE

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

PSYCHOMOTOR
 HYPERACTIVITY

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Gastrointestinal disorders

14 (26.4%)

10 (13.7%)

24 (19.0%)

7 (11.9%)

NAUSEA

5 (9.4%)

2 (2.7%)

7 (5.6%)

0

Mild

5 (9.4%)

2 (2.7%)

7 (5.6%)

0

VOMITING

5 (9.4%)

2 (2.7%)

7 (5.6%)

0

Mild

4 (7.5%)

1 (1.4%)

5 (4.0%)

0

Moderate

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

DIARRHOEA

2 (3.8%)

3 (4.1%)

5 (4.0%)

3 (5.1%)

Mild

2 (3.8%)

2 (2.7%)

4 (3.2%)

3 (5.1%)

Moderate

0

1 (1.4%)

1 (0.8%)

0

SALIVARY HYPERSECRETION

4 (7.5%)

0

4 (3.2%)

0

Mild

4 (7.5%)

0

4 (3.2%)

0

ABDOMINAL PAIN

0

2 (2.7%)

2 (1.6%)

1 (1.7%)

Mild

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Moderate

0

1 (1.4%)

1 (0.8%)

0

ABDOMINAL DISCOMFORT

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

DYSPEPSIA

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Moderate

0

1 (1.4%)

1 (0.8%)

0

RECTAL HAEMORRHAGE

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

STOMACH DISCOMFORT

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

CONSTIPATION

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

GASTROOESOPHAGEAL REFLUX
 DISEASE

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

GLOSSITIS

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

HIATUS HERNIA

0

0

0

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

Cardiac disorders

11 (20.8%)

11 (15.1%)

22 (17.5%)

7 (11.9%)

SINUS BRADYCARDIA

7 (13.2%)

4 (5.5%)

11 (8.7%)

0

Mild

3 (5.7%)

3 (4.1%)

6 (4.8%)

0

Moderate

4 (7.5%)

1 (1.4%)

5 (4.0%)

0

MYOCARDIAL INFARCTION

3 (5.7%)

1 (1.4%)

4 (3.2%)

3 (5.1%)

Mild

2 (3.8%)

1 (1.4%)

3 (2.4%)

1 (1.7%)

Moderate

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

Severe

0

0

0

1 (1.7%)

ATRIAL FIBRILLATION

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

VENTRICULAR EXTRASYSTOLES

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

ATRIAL FLUTTER

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

PALPITATIONS

0

2 (2.7%)

2 (1.6%)

0

Moderate

0

2 (2.7%)

2 (1.6%)

0

ATRIOVENTRICULAR BLOCK
 FIRST DEGREE

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

BUNDLE BRANCH BLOCK RIGHT

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Moderate

0

1 (1.4%)

1 (0.8%)

0

CARDIAC DISORDER

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

SUPRAVENTRICULAR
 EXTRASYSTOLES

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Mild

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

SUPRAVENTRICULAR
 TACHYCARDIA

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

WOLFF-PARKINSON-WHITE
 SYNDROME

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

ATRIOVENTRICULAR BLOCK
 SECOND DEGREE

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

BUNDLE BRANCH BLOCK LEFT

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

SINUS ARRHYTHMIA

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

TACHYCARDIA

0

0

0

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

Infections and infestations

9 (17.0%)

6 (8.2%)

15 (11.9%)

14 (23.7%)

NASOPHARYNGITIS

3 (5.7%)

3 (4.1%)

6 (4.8%)

2 (3.4%)

Mild

3 (5.7%)

2 (2.7%)

5 (4.0%)

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

Severe

0

1 (1.4%)

1 (0.8%)

0

INFLUENZA

1 (1.9%)

1 (1.4%)

2 (1.6%)

1 (1.7%)

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

1 (1.7%)

UPPER RESPIRATORY TRACT
 INFECTION

2 (3.8%)

0

2 (1.6%)

5 (8.5%)

Mild

2 (3.8%)

0

2 (1.6%)

4 (6.8%)

Moderate

0

0

0

1 (1.7%)

CELLULITIS

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

HORDEOLUM

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

LOWER RESPIRATORY TRACT
 INFECTION

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

PNEUMONIA

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

RHINITIS

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

URINARY TRACT INFECTION

1 (1.9%)

0

1 (0.8%)

2 (3.4%)

Mild

1 (1.9%)

0

1 (0.8%)

2 (3.4%)

BRONCHITIS

0

0

0

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

CERVICITIS

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

EAR INFECTION

0

0

0

2 (3.4%)

Mild

0

0

0

2 (3.4%)

GASTROENTERITIS VIRAL

0

0

0

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

LOCALISED INFECTION

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

VAGINAL MYCOSIS

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Psychiatric disorders

6 (11.3%)

8 (11.0%)

14 (11.1%)

7 (11.9%)

CONFUSIONAL STATE

1 (1.9%)

3 (4.1%)

4 (3.2%)

2 (3.4%)

Mild

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

Moderate

0

3 (4.1%)

3 (2.4%)

1 (1.7%)

AGITATION

0

2 (2.7%)

2 (1.6%)

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Moderate

0

1 (1.4%)

1 (0.8%)

0

Severe

0

1 (1.4%)

1 (0.8%)

0

ANXIETY

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

DELIRIUM

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

DELUSION

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Moderate

1 (1.9%)

0

1 (0.8%)

0

DEPRESSED MOOD

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

HALLUCINATION

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

HALLUCINATION, VISUAL

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

INSOMNIA

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

Mild

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

IRRITABILITY

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

LIBIDO DECREASED

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

LISTLESS

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

NIGHTMARE

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

RESTLESSNESS

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

DISORIENTATION

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

DISTURBANCE IN SEXUAL
 AROUSAL

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Respiratory, thoracic and
 mediastinal disorders

7 (13.2%)

6 (8.2%)

13 (10.3%)

5 (8.5%)

COUGH

3 (5.7%)

4 (5.5%)

7 (5.6%)

1 (1.7%)

Mild

2 (3.8%)

3 (4.1%)

5 (4.0%)

1 (1.7%)

Moderate

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

NASAL CONGESTION

3 (5.7%)

0

3 (2.4%)

2 (3.4%)

Mild

3 (5.7%)

0

3 (2.4%)

2 (3.4%)

EPISTAXIS

2 (3.8%)

0

2 (1.6%)

0

Mild

2 (3.8%)

0

2 (1.6%)

0

RHINORRHOEA

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

ALLERGIC GRANULOMATOUS
 ANGIITIS

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

DYSPHONIA

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

DYSPNOEA

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

PHARYNGOLARYNGEAL PAIN

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

PRODUCTIVE COUGH

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

RESPIRATORY TRACT
 CONGESTION

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

EMPHYSEMA

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

POSTNASAL DRIP

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Investigations

5 (9.4%)

7 (9.6%)

12 (9.5%)

7 (11.9%)

BLOOD GLUCOSE INCREASED

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

ELECTROCARDIOGRAM T WAVE
 INVERSION

1 (1.9%)

1 (1.4%)

2 (1.6%)

2 (3.4%)

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

2 (3.4%)

BIOPSY

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

BIOPSY PROSTATE

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

BLOOD CHOLESTEROL
 INCREASED

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

BODY TEMPERATURE
 INCREASED

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

ELECTROCARDIOGRAM ST
 SEGMENT DEPRESSION

0

1 (1.4%)

1 (0.8%)

3 (5.1%)

Mild

0

1 (1.4%)

1 (0.8%)

3 (5.1%)

ELECTROCARDIOGRAM T WAVE
 AMPLITUDE DECREASED

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Mild

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

NASAL MUCOSA BIOPSY

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

WEIGHT DECREASED

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

BLOOD ALKALINE
 PHOSPHATASE INCREASED

0

0

0

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

BLOOD CREATINE
 PHOSPHOKINASE INCREASED

0

0

0

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

BLOOD URINE PRESENT

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

CYSTOSCOPY

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Musculoskeletal and connective
 tissue disorders

4 (7.5%)

5 (6.8%)

9 (7.1%)

2 (3.4%)

BACK PAIN

2 (3.8%)

1 (1.4%)

3 (2.4%)

1 (1.7%)

Mild

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

Moderate

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

ARTHRALGIA

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Moderate

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

FLANK PAIN

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

MUSCLE SPASMS

0

1 (1.4%)

1 (0.8%)

0

Severe

0

1 (1.4%)

1 (0.8%)

0

MUSCULAR WEAKNESS

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

MYALGIA

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

SHOULDER PAIN

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Mild

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

0

0

1 (1.7%)

Injury, poisoning and
 procedural complications

3 (5.7%)

5 (6.8%)

8 (6.3%)

2 (3.4%)

CONTUSION

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

Mild

2 (3.8%)

0

2 (1.6%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

FALL

1 (1.9%)

2 (2.7%)

3 (2.4%)

1 (1.7%)

Mild

1 (1.9%)

1 (1.4%)

2 (1.6%)

1 (1.7%)

Moderate

0

1 (1.4%)

1 (0.8%)

0

EXCORIATION

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Moderate

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

SKIN LACERATION

0

2 (2.7%)

2 (1.6%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

FACIAL BONES FRACTURE

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

JOINT DISLOCATION

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

WOUND

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

HIP FRACTURE

0

0

0

1 (1.7%)

Severe

0

0

0

1 (1.7%)

Renal and urinary disorders

2 (3.8%)

3 (4.1%)

5 (4.0%)

2 (3.4%)

CALCULUS URETHRAL

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

DYSURIA

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Mild

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

INCONTINENCE

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

MICTURITION URGENCY

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Mild

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

NEPHROLITHIASIS

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

Vascular disorders

1 (1.9%)

3 (4.1%)

4 (3.2%)

3 (5.1%)

HOT FLUSH

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

HYPERTENSION

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Mild

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

0

0

1 (1.7%)

HYPOTENSION

0

1 (1.4%)

1 (0.8%)

2 (3.4%)

Mild

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

WOUND HAEMORRHAGE

1 (1.9%)

0

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

ORTHOSTATIC HYPOTENSION

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Ear and labyrinth disorders

1 (1.9%)

2 (2.7%)

3 (2.4%)

1 (1.7%)

VERTIGO

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Moderate

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

CERUMEN IMPACTION

0

1 (1.4%)

1 (0.8%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

EAR PAIN

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Eye disorders

1 (1.9%)

2 (2.7%)

3 (2.4%)

2 (3.4%)

VISION BLURRED

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Mild

0

1 (1.4%)

1 (0.8%)

0

Moderate

1 (1.9%)

0

1 (0.8%)

0

CONJUNCTIVAL HAEMORRHAGE

0

1 (1.4%)

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

CONJUNCTIVITIS

0

0

0

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

EYE ALLERGY

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

EYE PRURITUS

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

EYE SWELLING

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Reproductive system and breast
 disorders

3 (5.7%)

0

3 (2.4%)

3 (5.1%)

ABNORMAL UTERINE BLEEDING

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

BENIGN PROSTATIC
 HYPERPLASIA

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

Moderate

1 (1.9%)

0

1 (0.8%)

0

Severe

0

0

0

1 (1.7%)

ERECTILE DYSFUNCTION

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

Mild

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

PELVIC PAIN

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Congenital, familial and genetic
 disorders

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

VENTRICULAR SEPTAL DEFECT

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

Moderate

0

1 (1.4%)

1 (0.8%)

0

Neoplasms benign, malignant
 and unspecified (incl cysts
 and polyps)

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

COLON CANCER

0

1 (1.4%)

1 (0.8%)

0

Severe

0

1 (1.4%)

1 (0.8%)

0

PROSTATE CANCER

1 (1.9%)

0

1 (0.8%)

0

Severe

1 (1.9%)

0

1 (0.8%)

0

Endocrine disorders

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

BLEEDING ANOVULATORY

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Mild

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

Metabolism and nutrition
 disorders

1 (1.9%)

0

1 (0.8%)

2 (3.4%)

INCREASED APPETITE

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

DECREASED APPETITE

0

0

0

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

DEHYDRATION

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Surgical and medical
 procedures

1 (1.9%)

0

1 (0.8%)

2 (3.4%)

ACROCHORDON EXCISION

1 (1.9%)

0

1 (0.8%)

0

Mild

1 (1.9%)

0

1 (0.8%)

0

CATARACT OPERATION

0

0

0

1 (1.7%)

Moderate

0

0

0

1 (1.7%)

EYE LASER SURGERY

0

0

0

1 (1.7%)

Mild

0

0

0

1 (1.7%)

Note: Subjects are counted only once for any given event, regardless of the number of times they actually experienced the event. The event experienced by the subject with the worst severity is used.

Note: Adverse events are coded using MedDRA version 26.0.

Download RTF file

TSFAE21B
TSFAE21D
Source Code
---
title: TSFAE21C
subtitle: Subjects With Treatment-emergent Adverse Events by System Organ Class, Preferred Term, and Severity
---

------------------------------------------------------------------------

{{< include ../../_utils/envir_hook.qmd >}}

```{r setup, echo = FALSE, warning = FALSE, message = FALSE}
options(docx.add_datetime = FALSE, tidytlg.add_datetime = FALSE)
envsetup_config_name <- "default"

# Path to the combined config file
envsetup_file_path <- file.path("../..", "envsetup.yml")

Sys.setenv(ENVSETUP_ENVIRON = '')
library(envsetup)
loaded_config <- config::get(config = envsetup_config_name, file = envsetup_file_path)
envsetup::rprofile(loaded_config)


dpscomp <- compound
dpspdr <- paste(protocol,dbrelease,rpteff,sep="__")

aptcomp <- compound
aptpdr <- paste(protocol,dbrelease,rpteff,sep="__")

###### Study specific updates (formerly in envre)

dpscomp <- "standards"
dpspdr <- "jjcs__NULL__jjcs - core"

apt <- FALSE
library(junco)
default_str_map <- rbind(default_str_map, c("&ctcae", "5.0"))

```

## Output

:::: panel-tabset
## {{< fa regular file-lines sm fw >}} Preview

```{r variant1, results='hide', warning = FALSE, message = FALSE}

# Program Name: tsfae21c.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSFAE21c"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

trtvar <- "TRT01A"
popfl <- "SAFFL"
combined_colspan_trt <- TRUE

if (combined_colspan_trt == TRUE) {
  # Set up levels and label for the required combined columns
  add_combo <- add_combo_facet(
    "Combined",
    label = "Combined",
    levels = c("Xanomeline High Dose", "Xanomeline Low Dose")
  )

  # choose if any facets need to be removed - e.g remove the combined column for placebo
  rm_combo_from_placebo <- cond_rm_facets(
    facets = "Combined",
    ancestor_pos = NA,
    value = " ",
    split = "colspan_trt"
  )

  mysplit <- make_split_fun(post = list(add_combo, rm_combo_from_placebo))
}

# Process Data:

adsl <- pharmaverseadamjnj::adsl %>%
  filter(!!rlang::sym(popfl) == "Y") %>%
  select(STUDYID, USUBJID, all_of(trtvar), all_of(popfl))

adae <- pharmaverseadamjnj::adae %>%
  filter(TRTEMFL == "Y") %>%
  select(USUBJID, AEBODSYS, AEDECOD, TRTEMFL, AESEV)

# Take maximum severity
adaemax <- adae %>%
  mutate(
    AESEVN = case_when(
      toupper(AESEV) == "MILD" ~ 3,
      toupper(AESEV) == "MODERATE" ~ 2,
      toupper(AESEV) == "SEVERE" ~ 1,
      .default = 99
    )
  ) %>%
  arrange(USUBJID, AEBODSYS, AEDECOD, AESEVN) %>%
  group_by(USUBJID, AEBODSYS, AEDECOD) %>%
  slice(1) %>%
  ungroup()

adsl$colspan_trt <- factor(
  ifelse(adsl[[trtvar]] == "Placebo", " ", "Active Study Agent"),
  levels = c("Active Study Agent", " ")
)

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
)

# join data together
ae <- inner_join(adaemax, adsl, by = c("USUBJID"))

ae <- ae %>%
  mutate(AESEV2 = as.factor(ifelse(is.na(AESEV), "Missing", AESEV)))

if (length(adae$TRTEMFL) == 0) {
  ae <- right_join(adaemax, adsl, by = c("USUBJID"))

  ae <- ae %>%
    mutate(AESEV2 = as.factor(ifelse(is.na(AESEV), "Missing", AESEV)))
}

levels(ae$AESEV2) <- c(levels(ae$AESEV), "Missing")

# Define layout and build table:

extra_args_1 <- list(
  denom = "n_altdf",
  .stats = c("count_unique_fraction")
)

lyt <- basic_table(
  top_level_section_div = " ",
  show_colcounts = TRUE,
  colcount_format = "N=xx"
) %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  )

if (combined_colspan_trt == TRUE) {
  lyt <- lyt %>%
    split_cols_by(trtvar, split_fun = mysplit)
} else {
  lyt <- lyt %>%
    split_cols_by(trtvar)
}

lyt <- lyt %>%
  analyze(
    "TRTEMFL",
    afun = a_freq_j,
    show_labels = "hidden",
    extra_args = append(
      extra_args_1,
      list(label = "Subjects with >=1 AE", val = "Y")
    )
  ) %>%
  split_rows_by(
    "AEBODSYS",
    split_label = "System Organ Class",
    split_fun = trim_levels_in_group("AEDECOD"),
    label_pos = "topleft",
    section_div = c(" "),
    nested = FALSE
  ) %>%
  summarize_row_groups(
    "AEBODSYS",
    cfun = a_freq_j,
    extra_args = extra_args_1
  ) %>%
  split_rows_by(
    "AEDECOD",
    split_label = "Preferred Term, n (%)",
    section_div = c(" "),
    nested = TRUE
  ) %>%
  summarize_row_groups(
    "AEDECOD",
    cfun = a_freq_j,
    extra_args = extra_args_1
  ) %>%
  analyze("AESEV2", afun = a_freq_j, extra_args = extra_args_1) %>%
  append_topleft("  Preferred Term, n (%)")

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

# Post-Processing step to sort by descending count on chosen active treatment columns.

if (length(adae$TRTEMFL) != 0) {
  result <- sort_at_path(
    result,
    c("root", "AEBODSYS"),
    scorefun = jj_complex_scorefun()
  )
  result <- sort_at_path(
    result,
    c("root", "AEBODSYS", "*", "AEDECOD"),
    scorefun = jj_complex_scorefun()
  )

  #########################################################################################
  # Post-Processing step to remove all rows where counts are 0
  #########################################################################################

  result <- safe_prune_table(result, prune_func = prune_empty_level)
}

# 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 = "portrait",
  label_width_ins = 1.5
)
```
```{r result1, echo=FALSE, message=FALSE, warning=FALSE, test = list(result_v1 = "result")}
tt_to_flextable_j(result, tblid, string_map = string_map) 
```

[Download RTF file](`r paste0(tolower(tblid), '.rtf')`)
::::

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