TL Catalog
  1. Tables
  2. Adverse Events
  3. TSFAE17C
  • 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

On this page

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  1. Tables
  2. Adverse Events
  3. TSFAE17C

TSFAE17C

Subjects With Treatment-emergent Adverse Events by Organ System, OCMQ (Narrow) / (Broad) and Preferred Term


Output

  • Preview
Code
# Program Name:              tsfae17c.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSFAE17c"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

trtvar <- "TRT01A"
popfl <- "SAFFL"
ocmqclass <- "Narrow"
combined_colspan_trt <- TRUE
risk_diff <- TRUE
rr_method <- "wald"
ctrl_grp <- "Placebo"

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::adaeocmq %>%
  filter(TRTEMFL == "Y" & OCMQCLSS == ocmqclass) %>%
  select(USUBJID, TRTEMFL, OCMQSOC, OCMQNAM, AEDECOD)

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

if (risk_diff == TRUE) {
  adsl$rrisk_header <- "Risk Difference (%) (95% CI)"
  adsl$rrisk_label <- paste(adsl[[trtvar]], paste("vs", ctrl_grp))
}

# join data together
ae <- adae %>% right_join(., adsl, by = c("USUBJID"))

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

# Define layout and build table:

ref_path <- c("colspan_trt", " ", "TRT01A", "Placebo")
extra_args_rr <- list(
  method = rr_method,
  ref_path = ref_path,
  .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)
}

if (risk_diff == TRUE) {
  lyt <- lyt %>%
    split_cols_by("rrisk_header", nested = FALSE) %>%
    split_cols_by(
      trtvar,
      labels_var = "rrisk_label",
      split_fun = remove_split_levels("Placebo")
    )
}

lyt <- lyt %>%
  split_rows_by(
    "OCMQSOC",
    split_label = "Organ System~[super a]",
    split_fun = trim_levels_in_group("OCMQNAM"),
    label_pos = "topleft",
    section_div = c(" "),
    nested = FALSE
  ) %>%
  summarize_row_groups(
    "OCMQSOC",
    cfun = a_freq_j,
    extra_args = append(extra_args_rr, NULL)
  ) %>%
  split_rows_by(
    "OCMQNAM",
    split_label = paste0("OCMQ (", ocmqclass, ")"),
    split_fun = trim_levels_in_group("AEDECOD"),
    label_pos = "topleft",
    nested = TRUE
  ) %>%
  summarize_row_groups(
    "OCMQNAM",
    cfun = a_freq_j,
    extra_args = append(extra_args_rr, NULL)
  ) %>%
  analyze(
    "AEDECOD",
    afun = a_freq_j,
    extra_args = append(extra_args_rr, NULL)
  ) %>%
  append_topleft("    Preferred Term, n (%)")

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

## Remove the N=xx column headers for the risk difference columns
result <- remove_col_count(result)

# If there is no data display "No data to display" text
if (nrow(adae) == 0) {
  result <- safe_prune_table(result)
}

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

if (nrow(adae) != 0) {
  result <- sort_at_path(
    result,
    c("root", "OCMQSOC"),
    scorefun = jj_complex_scorefun()
  )
  result <- sort_at_path(
    result,
    c("root", "OCMQSOC", "*", "OCMQNAM"),
    scorefun = jj_complex_scorefun()
  )
  result <- sort_at_path(
    result,
    c("root", "OCMQSOC", "*", "OCMQNAM", "*", "AEDECOD"),
    scorefun = jj_complex_scorefun()
  )
}

# 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")

TSFAE17c: Subjects With Treatment-emergent Adverse Events by System Organ Class, FDA Medical Query (Narrow) and Preferred Term; Safety Analysis Set (Study jjcs - core)

Organ Systema

Active Study Agent

Risk Difference (%) (95% CI)

OCMQ (Narrow)

Xanomeline High Dose

Xanomeline Low Dose

Combined

Placebo

Xanomeline High Dose vs Placebo

Xanomeline Low Dose vs Placebo

Preferred Term, n (%)

N=53

N=73

N=126

N=59

Skin and subcutaneous tissue
 disorders

39 (73.6%)

39 (53.4%)

78 (61.9%)

17 (28.8%)

44.8 (28.2, 61.3)

24.6 (8.3, 40.9)

Pruritus

36 (67.9%)

33 (45.2%)

69 (54.8%)

10 (16.9%)

51.0 (35.2, 66.8)

28.3 (13.4, 43.2)

PRURITUS

20 (37.7%)

14 (19.2%)

34 (27.0%)

6 (10.2%)

27.6 (12.4, 42.7)

9.0 (-2.9, 20.9)

APPLICATION SITE PRURITUS

13 (24.5%)

18 (24.7%)

31 (24.6%)

4 (6.8%)

17.7 (4.5, 31.0)

17.9 (6.1, 29.7)

RASH PRURITIC

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

3.8 (-1.4, 8.9)

1.4 (-1.3, 4.0)

PRURITUS GENERALISED

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

EYE PRURITUS

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Erythema

21 (39.6%)

18 (24.7%)

39 (31.0%)

8 (13.6%)

26.1 (10.3, 41.9)

11.1 (-2.1, 24.3)

APPLICATION SITE
 ERYTHEMA

10 (18.9%)

11 (15.1%)

21 (16.7%)

2 (3.4%)

15.5 (4.0, 27.0)

11.7 (2.3, 21.1)

ERYTHEMA

12 (22.6%)

8 (11.0%)

20 (15.9%)

6 (10.2%)

12.5 (-1.2, 26.1)

0.8 (-9.7, 11.3)

RASH ERYTHEMATOUS

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Rash

14 (26.4%)

17 (23.3%)

31 (24.6%)

4 (6.8%)

19.6 (6.1, 33.1)

16.5 (4.9, 28.1)

RASH

5 (9.4%)

9 (12.3%)

14 (11.1%)

4 (6.8%)

2.7 (-7.5, 12.8)

5.5 (-4.4, 15.5)

APPLICATION SITE VESICLES

4 (7.5%)

4 (5.5%)

8 (6.3%)

0

7.5 (0.4, 14.7)

5.5 (0.3, 10.7)

BLISTER

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

1.9 (-1.8, 5.5)

2.7 (-1.0, 6.5)

RASH PRURITIC

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

3.8 (-1.4, 8.9)

1.4 (-1.3, 4.0)

URTICARIA

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

RASH ERYTHEMATOUS

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

RASH MACULO-PAPULAR

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Urticaria

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

1.9 (-1.8, 5.5)

2.7 (-1.0, 6.5)

APPLICATION SITE URTICARIA

0

2 (2.7%)

2 (1.6%)

0

0.0 (0.0, 0.0)

2.7 (-1.0, 6.5)

URTICARIA

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

Alopecia

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

ALOPECIA

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

General disorders and
 administration site conditions

20 (37.7%)

22 (30.1%)

42 (33.3%)

12 (20.3%)

17.4 (0.8, 34.0)

9.8 (-4.9, 24.5)

Dizziness

9 (17.0%)

10 (13.7%)

19 (15.1%)

0

17.0 (6.9, 27.1)

13.7 (5.8, 21.6)

DIZZINESS

8 (15.1%)

8 (11.0%)

16 (12.7%)

0

15.1 (5.5, 24.7)

11.0 (3.8, 18.1)

VERTIGO

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

BALANCE DISORDER

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Local Administration Reaction

7 (13.2%)

9 (12.3%)

16 (12.7%)

5 (8.5%)

4.7 (-6.8, 16.3)

3.9 (-6.5, 14.2)

APPLICATION SITE
 DERMATITIS

4 (7.5%)

7 (9.6%)

11 (8.7%)

5 (8.5%)

-0.9 (-11.0, 9.1)

1.1 (-8.7, 10.9)

APPLICATION SITE PAIN

2 (3.8%)

0

2 (1.6%)

0

3.8 (-1.4, 8.9)

0.0 (0.0, 0.0)

APPLICATION SITE URTICARIA

0

2 (2.7%)

2 (1.6%)

0

0.0 (0.0, 0.0)

2.7 (-1.0, 6.5)

APPLICATION SITE REACTION

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

Fatigue

7 (13.2%)

6 (8.2%)

13 (10.3%)

1 (1.7%)

11.5 (1.8, 21.2)

6.5 (-0.6, 13.6)

FATIGUE

5 (9.4%)

5 (6.8%)

10 (7.9%)

0

9.4 (1.6, 17.3)

6.8 (1.1, 12.6)

MALAISE

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

3.8 (-1.4, 8.9)

1.4 (-1.3, 4.0)

ASTHENIA

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

LETHARGY

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

LISTLESS

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Fall

1 (1.9%)

2 (2.7%)

3 (2.4%)

1 (1.7%)

0.2 (-4.7, 5.1)

1.0 (-3.9, 6.0)

FALL

1 (1.9%)

2 (2.7%)

3 (2.4%)

1 (1.7%)

0.2 (-4.7, 5.1)

1.0 (-3.9, 6.0)

Peripheral Edema

1 (1.9%)

1 (1.4%)

2 (1.6%)

2 (3.4%)

-1.5 (-7.4, 4.4)

-2.0 (-7.4, 3.3)

OEDEMA PERIPHERAL

1 (1.9%)

1 (1.4%)

2 (1.6%)

2 (3.4%)

-1.5 (-7.4, 4.4)

-2.0 (-7.4, 3.3)

Pyrexia

0

2 (2.7%)

2 (1.6%)

2 (3.4%)

-3.4 (-8.0, 1.2)

-0.7 (-6.6, 5.3)

BODY TEMPERATURE
 INCREASED

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

PYREXIA

0

1 (1.4%)

1 (0.8%)

2 (3.4%)

-3.4 (-8.0, 1.2)

-2.0 (-7.4, 3.3)

Decreased Appetite

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

DECREASED APPETITE

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Volume Depletion

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

DEHYDRATION

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Nervous system disorders

12 (22.6%)

14 (19.2%)

26 (20.6%)

5 (8.5%)

14.2 (0.8, 27.5)

10.7 (-0.8, 22.2)

Headache

5 (9.4%)

3 (4.1%)

8 (6.3%)

2 (3.4%)

6.0 (-3.1, 15.2)

0.7 (-5.8, 7.2)

HEADACHE

5 (9.4%)

3 (4.1%)

8 (6.3%)

2 (3.4%)

6.0 (-3.1, 15.2)

0.7 (-5.8, 7.2)

Somnolence

2 (3.8%)

4 (5.5%)

6 (4.8%)

1 (1.7%)

2.1 (-4.0, 8.2)

3.8 (-2.4, 10.0)

SOMNOLENCE

1 (1.9%)

2 (2.7%)

3 (2.4%)

1 (1.7%)

0.2 (-4.7, 5.1)

1.0 (-3.9, 6.0)

HYPERSOMNIA

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

LETHARGY

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

STUPOR

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Confusional State

2 (3.8%)

3 (4.1%)

5 (4.0%)

3 (5.1%)

-1.3 (-8.9, 6.3)

-1.0 (-8.2, 6.2)

CONFUSIONAL STATE

1 (1.9%)

3 (4.1%)

4 (3.2%)

2 (3.4%)

-1.5 (-7.4, 4.4)

0.7 (-5.8, 7.2)

DELIRIUM

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

DISORIENTATION

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Syncope

2 (3.8%)

3 (4.1%)

5 (4.0%)

0

3.8 (-1.4, 8.9)

4.1 (-0.4, 8.7)

SYNCOPE

1 (1.9%)

3 (4.1%)

4 (3.2%)

0

1.9 (-1.8, 5.5)

4.1 (-0.4, 8.7)

SYNCOPE VASOVAGAL

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Paresthesia

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

3.8 (-1.4, 8.9)

1.4 (-1.3, 4.0)

BURNING SENSATION

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

PARAESTHESIA

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

PARAESTHESIA ORAL

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Stroke and TIA

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

1.9 (-1.8, 5.5)

2.7 (-1.0, 6.5)

TRANSIENT ISCHAEMIC
 ATTACK

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

1.9 (-1.8, 5.5)

2.7 (-1.0, 6.5)

Seizure

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

COMPLEX PARTIAL SEIZURES

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

PARTIAL SEIZURES WITH
 SECONDARY
 GENERALISATION

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Cardiac disorders

11 (20.8%)

12 (16.4%)

23 (18.3%)

8 (13.6%)

7.2 (-6.8, 21.2)

2.9 (-9.3, 15.1)

Arrhythmia

9 (17.0%)

9 (12.3%)

18 (14.3%)

3 (5.1%)

11.9 (0.3, 23.5)

7.2 (-2.2, 16.6)

SINUS BRADYCARDIA

7 (13.2%)

4 (5.5%)

11 (8.7%)

0

13.2 (4.1, 22.3)

5.5 (0.3, 10.7)

ATRIAL FIBRILLATION

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

1.9 (-1.8, 5.5)

2.7 (-1.0, 6.5)

VENTRICULAR
 EXTRASYSTOLES

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

1.9 (-1.8, 5.5)

2.7 (-1.0, 6.5)

ATRIAL FLUTTER

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

SUPRAVENTRICULAR
 EXTRASYSTOLES

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

SUPRAVENTRICULAR
 TACHYCARDIA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

SINUS ARRHYTHMIA

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

TACHYCARDIA

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Acute Coronary Syndrome

3 (5.7%)

1 (1.4%)

4 (3.2%)

3 (5.1%)

0.6 (-7.8, 8.9)

-3.7 (-9.9, 2.5)

MYOCARDIAL INFARCTION

3 (5.7%)

1 (1.4%)

4 (3.2%)

3 (5.1%)

0.6 (-7.8, 8.9)

-3.7 (-9.9, 2.5)

Myocardial Infarction

3 (5.7%)

1 (1.4%)

4 (3.2%)

3 (5.1%)

0.6 (-7.8, 8.9)

-3.7 (-9.9, 2.5)

MYOCARDIAL INFARCTION

3 (5.7%)

1 (1.4%)

4 (3.2%)

3 (5.1%)

0.6 (-7.8, 8.9)

-3.7 (-9.9, 2.5)

Myocardial Ischemia

3 (5.7%)

1 (1.4%)

4 (3.2%)

3 (5.1%)

0.6 (-7.8, 8.9)

-3.7 (-9.9, 2.5)

MYOCARDIAL INFARCTION

3 (5.7%)

1 (1.4%)

4 (3.2%)

3 (5.1%)

0.6 (-7.8, 8.9)

-3.7 (-9.9, 2.5)

Cardiac Conduction
 Disturbance

0

3 (4.1%)

3 (2.4%)

3 (5.1%)

-5.1 (-10.7, 0.5)

-1.0 (-8.2, 6.2)

ATRIOVENTRICULAR BLOCK
 FIRST DEGREE

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

BUNDLE BRANCH BLOCK
 RIGHT

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

WOLFF-PARKINSON-WHITE
 SYNDROME

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

ATRIOVENTRICULAR BLOCK
 SECOND DEGREE

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

BUNDLE BRANCH BLOCK
 LEFT

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Palpitations

0

2 (2.7%)

2 (1.6%)

0

0.0 (0.0, 0.0)

2.7 (-1.0, 6.5)

PALPITATIONS

0

2 (2.7%)

2 (1.6%)

0

0.0 (0.0, 0.0)

2.7 (-1.0, 6.5)

Systemic Hypertension

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

HYPERTENSION

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

Tachycardia

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

SUPRAVENTRICULAR
 TACHYCARDIA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

TACHYCARDIA

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Gastrointestinal disorders

11 (20.8%)

9 (12.3%)

20 (15.9%)

5 (8.5%)

12.3 (-0.7, 25.3)

3.9 (-6.5, 14.2)

Nausea

5 (9.4%)

2 (2.7%)

7 (5.6%)

0

9.4 (1.6, 17.3)

2.7 (-1.0, 6.5)

NAUSEA

5 (9.4%)

2 (2.7%)

7 (5.6%)

0

9.4 (1.6, 17.3)

2.7 (-1.0, 6.5)

Vomiting

5 (9.4%)

2 (2.7%)

7 (5.6%)

0

9.4 (1.6, 17.3)

2.7 (-1.0, 6.5)

VOMITING

5 (9.4%)

2 (2.7%)

7 (5.6%)

0

9.4 (1.6, 17.3)

2.7 (-1.0, 6.5)

Diarrhea

2 (3.8%)

3 (4.1%)

5 (4.0%)

3 (5.1%)

-1.3 (-8.9, 6.3)

-1.0 (-8.2, 6.2)

DIARRHOEA

2 (3.8%)

3 (4.1%)

5 (4.0%)

3 (5.1%)

-1.3 (-8.9, 6.3)

-1.0 (-8.2, 6.2)

Abdominal Pain

2 (3.8%)

2 (2.7%)

4 (3.2%)

1 (1.7%)

2.1 (-4.0, 8.2)

1.0 (-3.9, 6.0)

ABDOMINAL PAIN

0

2 (2.7%)

2 (1.6%)

1 (1.7%)

-1.7 (-5.0, 1.6)

1.0 (-3.9, 6.0)

ABDOMINAL DISCOMFORT

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

STOMACH DISCOMFORT

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Dyspepsia

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

DYSPEPSIA

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

Constipation

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

CONSTIPATION

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Vascular disorders

7 (13.2%)

8 (11.0%)

15 (11.9%)

4 (6.8%)

6.4 (-4.7, 17.6)

4.2 (-5.4, 13.8)

Hemorrhage

3 (5.7%)

4 (5.5%)

7 (5.6%)

1 (1.7%)

4.0 (-3.1, 11.0)

3.8 (-2.4, 10.0)

CONTUSION

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

3.8 (-1.4, 8.9)

1.4 (-1.3, 4.0)

EPISTAXIS

2 (3.8%)

0

2 (1.6%)

0

3.8 (-1.4, 8.9)

0.0 (0.0, 0.0)

APPLICATION SITE BLEEDING

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

CONJUNCTIVAL
 HAEMORRHAGE

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

RECTAL HAEMORRHAGE

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

BLOOD URINE PRESENT

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Thrombosis

4 (7.5%)

3 (4.1%)

7 (5.6%)

3 (5.1%)

2.5 (-6.6, 11.5)

-1.0 (-8.2, 6.2)

MYOCARDIAL INFARCTION

3 (5.7%)

1 (1.4%)

4 (3.2%)

3 (5.1%)

0.6 (-7.8, 8.9)

-3.7 (-9.9, 2.5)

TRANSIENT ISCHAEMIC
 ATTACK

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

1.9 (-1.8, 5.5)

2.7 (-1.0, 6.5)

Thrombosis Arterial

4 (7.5%)

3 (4.1%)

7 (5.6%)

3 (5.1%)

2.5 (-6.6, 11.5)

-1.0 (-8.2, 6.2)

MYOCARDIAL INFARCTION

3 (5.7%)

1 (1.4%)

4 (3.2%)

3 (5.1%)

0.6 (-7.8, 8.9)

-3.7 (-9.9, 2.5)

TRANSIENT ISCHAEMIC
 ATTACK

1 (1.9%)

2 (2.7%)

3 (2.4%)

0

1.9 (-1.8, 5.5)

2.7 (-1.0, 6.5)

Hypotension

0

1 (1.4%)

1 (0.8%)

2 (3.4%)

-3.4 (-8.0, 1.2)

-2.0 (-7.4, 3.3)

HYPOTENSION

0

1 (1.4%)

1 (0.8%)

2 (3.4%)

-3.4 (-8.0, 1.2)

-2.0 (-7.4, 3.3)

ORTHOSTATIC
 HYPOTENSION

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Infections and infestations

8 (15.1%)

6 (8.2%)

14 (11.1%)

10 (16.9%)

-1.9 (-15.4, 11.7)

-8.7 (-20.2, 2.7)

Nasopharyngitis

6 (11.3%)

3 (4.1%)

9 (7.1%)

7 (11.9%)

-0.5 (-12.4, 11.3)

-7.8 (-17.2, 1.7)

NASOPHARYNGITIS

3 (5.7%)

3 (4.1%)

6 (4.8%)

2 (3.4%)

2.3 (-5.5, 10.0)

0.7 (-5.8, 7.2)

UPPER RESPIRATORY TRACT
 INFECTION

2 (3.8%)

0

2 (1.6%)

5 (8.5%)

-4.7 (-13.5, 4.1)

-8.5 (-15.6, -1.4)

RHINITIS

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Bacterial Infection

2 (3.8%)

1 (1.4%)

3 (2.4%)

2 (3.4%)

0.4 (-6.5, 7.3)

-2.0 (-7.4, 3.3)

CELLULITIS

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

HORDEOLUM

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

URINARY TRACT INFECTION

1 (1.9%)

0

1 (0.8%)

2 (3.4%)

-1.5 (-7.4, 4.4)

-3.4 (-8.0, 1.2)

Viral Infection

1 (1.9%)

1 (1.4%)

2 (1.6%)

2 (3.4%)

-1.5 (-7.4, 4.4)

-2.0 (-7.4, 3.3)

INFLUENZA

1 (1.9%)

1 (1.4%)

2 (1.6%)

1 (1.7%)

0.2 (-4.7, 5.1)

-0.3 (-4.6, 3.9)

GASTROENTERITIS VIRAL

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Pneumonia

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

PNEUMONIA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Psychiatric disorders

5 (9.4%)

7 (9.6%)

12 (9.5%)

4 (6.8%)

2.7 (-7.5, 12.8)

2.8 (-6.5, 12.1)

Study Agent Abuse Potential

1 (1.9%)

3 (4.1%)

4 (3.2%)

1 (1.7%)

0.2 (-4.7, 5.1)

2.4 (-3.2, 8.0)

SOMNOLENCE

1 (1.9%)

2 (2.7%)

3 (2.4%)

1 (1.7%)

0.2 (-4.7, 5.1)

1.0 (-3.9, 6.0)

STUPOR

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Irritability

0

3 (4.1%)

3 (2.4%)

1 (1.7%)

-1.7 (-5.0, 1.6)

2.4 (-3.2, 8.0)

AGITATION

0

2 (2.7%)

2 (1.6%)

1 (1.7%)

-1.7 (-5.0, 1.6)

1.0 (-3.9, 6.0)

IRRITABILITY

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Psychosis

2 (3.8%)

0

2 (1.6%)

1 (1.7%)

2.1 (-4.0, 8.2)

-1.7 (-5.0, 1.6)

DELUSION

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

HALLUCINATION, VISUAL

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Anxiety

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

ANXIETY

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Depression

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

DEPRESSED MOOD

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Insomnia

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

INSOMNIA

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

Parasomnia

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

NIGHTMARE

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Respiratory, thoracic and
 mediastinal disorders

4 (7.5%)

5 (6.8%)

9 (7.1%)

1 (1.7%)

5.9 (-2.0, 13.7)

5.2 (-1.5, 11.8)

Cough

4 (7.5%)

4 (5.5%)

8 (6.3%)

1 (1.7%)

5.9 (-2.0, 13.7)

3.8 (-2.4, 10.0)

COUGH

3 (5.7%)

4 (5.5%)

7 (5.6%)

1 (1.7%)

4.0 (-3.1, 11.0)

3.8 (-2.4, 10.0)

PRODUCTIVE COUGH

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Dyspnea

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

DYSPNOEA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Musculoskeletal and connective
 tissue disorders

5 (9.4%)

2 (2.7%)

7 (5.6%)

2 (3.4%)

6.0 (-3.1, 15.2)

-0.7 (-6.6, 5.3)

Back Pain

3 (5.7%)

1 (1.4%)

4 (3.2%)

1 (1.7%)

4.0 (-3.1, 11.0)

-0.3 (-4.6, 3.9)

BACK PAIN

2 (3.8%)

1 (1.4%)

3 (2.4%)

1 (1.7%)

2.1 (-4.0, 8.2)

-0.3 (-4.6, 3.9)

FLANK PAIN

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Arthralgia

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

ARTHRALGIA

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

Fracture

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

FACIAL BONES FRACTURE

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

HIP FRACTURE

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Myalgia

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

MYALGIA

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Osteoporosis

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

HIP FRACTURE

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Reproductive system and breast
 disorders

3 (5.7%)

0

3 (2.4%)

2 (3.4%)

2.3 (-5.5, 10.0)

-3.4 (-8.0, 1.2)

Sexual Dysfunction

2 (3.8%)

0

2 (1.6%)

2 (3.4%)

0.4 (-6.5, 7.3)

-3.4 (-8.0, 1.2)

ERECTILE DYSFUNCTION

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

LIBIDO DECREASED

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

DISTURBANCE IN SEXUAL
 AROUSAL

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Abnormal Uterine Bleeding

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

ABNORMAL UTERINE
 BLEEDING

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Erectile Dysfunction

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

ERECTILE DYSFUNCTION

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

Excessive Menstrual Bleeding

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

ABNORMAL UTERINE
 BLEEDING

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Ear and labyrinth disorders

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

Vertigo

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

VERTIGO

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

Endocrine disorders

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

Hyperglycemia

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

BLOOD GLUCOSE INCREASED

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

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

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

Malignancy

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

COLON CANCER

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

PROSTATE CANCER

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Metabolism and nutrition
 disorders

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Lipid Disorder

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

BLOOD CHOLESTEROL
 INCREASED

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Renal and urinary disorders

1 (1.9%)

0

1 (0.8%)

2 (3.4%)

-1.5 (-7.4, 4.4)

-3.4 (-8.0, 1.2)

Renal & Urinary Tract
 Infection

1 (1.9%)

0

1 (0.8%)

2 (3.4%)

-1.5 (-7.4, 4.4)

-3.4 (-8.0, 1.2)

URINARY TRACT INFECTION

1 (1.9%)

0

1 (0.8%)

2 (3.4%)

-1.5 (-7.4, 4.4)

-3.4 (-8.0, 1.2)

Immune system disorders

0

0

0

2 (3.4%)

-3.4 (-8.0, 1.2)

-3.4 (-8.0, 1.2)

Hypersensitivity

0

0

0

2 (3.4%)

-3.4 (-8.0, 1.2)

-3.4 (-8.0, 1.2)

DRUG ERUPTION

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

EYE ALLERGY

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Key: FMQ=FDA Medical Query

a Each FMQ is aligned to a single system organ class based on clinical judgment, as defined by FDA. However, some FMQs may contain preferred terms from more than one system organ class. Preferred terms that are not included in any FMQ are not summarized.

Note: Adverse events are coded using MedDRA version 26.0.

Download RTF file

TSFAE17B
TSFAE17D
Source Code
---
title: TSFAE17C
subtitle: Subjects With Treatment-emergent Adverse Events by Organ System, OCMQ (Narrow) / (Broad) and Preferred Term
---

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

{{< 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:              tsfae17c.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSFAE17c"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

trtvar <- "TRT01A"
popfl <- "SAFFL"
ocmqclass <- "Narrow"
combined_colspan_trt <- TRUE
risk_diff <- TRUE
rr_method <- "wald"
ctrl_grp <- "Placebo"

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::adaeocmq %>%
  filter(TRTEMFL == "Y" & OCMQCLSS == ocmqclass) %>%
  select(USUBJID, TRTEMFL, OCMQSOC, OCMQNAM, AEDECOD)

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

if (risk_diff == TRUE) {
  adsl$rrisk_header <- "Risk Difference (%) (95% CI)"
  adsl$rrisk_label <- paste(adsl[[trtvar]], paste("vs", ctrl_grp))
}

# join data together
ae <- adae %>% right_join(., adsl, by = c("USUBJID"))

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

# Define layout and build table:

ref_path <- c("colspan_trt", " ", "TRT01A", "Placebo")
extra_args_rr <- list(
  method = rr_method,
  ref_path = ref_path,
  .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)
}

if (risk_diff == TRUE) {
  lyt <- lyt %>%
    split_cols_by("rrisk_header", nested = FALSE) %>%
    split_cols_by(
      trtvar,
      labels_var = "rrisk_label",
      split_fun = remove_split_levels("Placebo")
    )
}

lyt <- lyt %>%
  split_rows_by(
    "OCMQSOC",
    split_label = "Organ System~[super a]",
    split_fun = trim_levels_in_group("OCMQNAM"),
    label_pos = "topleft",
    section_div = c(" "),
    nested = FALSE
  ) %>%
  summarize_row_groups(
    "OCMQSOC",
    cfun = a_freq_j,
    extra_args = append(extra_args_rr, NULL)
  ) %>%
  split_rows_by(
    "OCMQNAM",
    split_label = paste0("OCMQ (", ocmqclass, ")"),
    split_fun = trim_levels_in_group("AEDECOD"),
    label_pos = "topleft",
    nested = TRUE
  ) %>%
  summarize_row_groups(
    "OCMQNAM",
    cfun = a_freq_j,
    extra_args = append(extra_args_rr, NULL)
  ) %>%
  analyze(
    "AEDECOD",
    afun = a_freq_j,
    extra_args = append(extra_args_rr, NULL)
  ) %>%
  append_topleft("    Preferred Term, n (%)")

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

## Remove the N=xx column headers for the risk difference columns
result <- remove_col_count(result)

# If there is no data display "No data to display" text
if (nrow(adae) == 0) {
  result <- safe_prune_table(result)
}

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

if (nrow(adae) != 0) {
  result <- sort_at_path(
    result,
    c("root", "OCMQSOC"),
    scorefun = jj_complex_scorefun()
  )
  result <- sort_at_path(
    result,
    c("root", "OCMQSOC", "*", "OCMQNAM"),
    scorefun = jj_complex_scorefun()
  )
  result <- sort_at_path(
    result,
    c("root", "OCMQSOC", "*", "OCMQNAM", "*", "AEDECOD"),
    scorefun = jj_complex_scorefun()
  )
}

# 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")
```
```{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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