TL Catalog
  1. Tables
  2. Adverse Events
  3. TSFAE17D
  • 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. TSFAE17D

TSFAE17D

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


Output

  • Preview
Code
# Program Name:              tsfae17d.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSFAE17d"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

trtvar <- "TRT01A"
popfl <- "SAFFL"
ocmqclass <- "Broad"
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")

TSFAE17d: Subjects With Treatment-emergent Adverse Events by System Organ Class, FDA Medical Query (Broad) and Preferred Term; Safety Analysis Set (Study jjcs - core)

Organ Systema

Active Study Agent

Risk Difference (%) (95% CI)

OCMQ (Broad)

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

Immune system disorders

42 (79.2%)

38 (52.1%)

80 (63.5%)

19 (32.2%)

47.0 (30.9, 63.2)

19.9 (3.3, 36.4)

Hypersensitivity

41 (77.4%)

38 (52.1%)

79 (62.7%)

19 (32.2%)

45.2 (28.8, 61.6)

19.9 (3.3, 36.4)

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)

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

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
 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)

RASH PRURITIC

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

3.8 (-1.4, 8.9)

1.4 (-1.3, 4.0)

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)

OEDEMA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

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)

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)

EYE SWELLING

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Angioedema

1 (1.9%)

0

1 (0.8%)

2 (3.4%)

-1.5 (-7.4, 4.4)

-3.4 (-8.0, 1.2)

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)

EYE SWELLING

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Skin and subcutaneous tissue
 disorders

24 (45.3%)

22 (30.1%)

46 (36.5%)

12 (20.3%)

24.9 (8.1, 41.8)

9.8 (-4.9, 24.5)

Rash

16 (30.2%)

12 (16.4%)

28 (22.2%)

8 (13.6%)

16.6 (1.5, 31.8)

2.9 (-9.3, 15.1)

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)

SKIN IRRITATION

4 (7.5%)

4 (5.5%)

8 (6.3%)

3 (5.1%)

2.5 (-6.6, 11.5)

0.4 (-7.3, 8.1)

Urticaria

9 (17.0%)

11 (15.1%)

20 (15.9%)

5 (8.5%)

8.5 (-3.8, 20.9)

6.6 (-4.3, 17.4)

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)

RASH PRURITIC

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

3.8 (-1.4, 8.9)

1.4 (-1.3, 4.0)

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)

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)

DRUG ERUPTION

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Erythema

4 (7.5%)

4 (5.5%)

8 (6.3%)

3 (5.1%)

2.5 (-6.6, 11.5)

0.4 (-7.3, 8.1)

SKIN IRRITATION

4 (7.5%)

4 (5.5%)

8 (6.3%)

3 (5.1%)

2.5 (-6.6, 11.5)

0.4 (-7.3, 8.1)

Pruritus

4 (7.5%)

4 (5.5%)

8 (6.3%)

3 (5.1%)

2.5 (-6.6, 11.5)

0.4 (-7.3, 8.1)

SKIN IRRITATION

4 (7.5%)

4 (5.5%)

8 (6.3%)

3 (5.1%)

2.5 (-6.6, 11.5)

0.4 (-7.3, 8.1)

Nervous system disorders

15 (28.3%)

15 (20.5%)

30 (23.8%)

3 (5.1%)

23.2 (9.9, 36.6)

15.5 (4.6, 26.3)

Syncope

8 (15.1%)

8 (11.0%)

16 (12.7%)

2 (3.4%)

11.7 (1.0, 22.4)

7.6 (-1.0, 16.1)

DIZZINESS

8 (15.1%)

8 (11.0%)

16 (12.7%)

0

15.1 (5.5, 24.7)

11.0 (3.8, 18.1)

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)

Somnolence

5 (9.4%)

5 (6.8%)

10 (7.9%)

0

9.4 (1.6, 17.3)

6.8 (1.1, 12.6)

FATIGUE

5 (9.4%)

5 (6.8%)

10 (7.9%)

0

9.4 (1.6, 17.3)

6.8 (1.1, 12.6)

Confusional State

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)

Dysgeusia

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

PAROSMIA

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Stroke and TIA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

HEMIANOPIA HOMONYMOUS

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

General disorders and
 administration site conditions

11 (20.8%)

15 (20.5%)

26 (20.6%)

3 (5.1%)

15.7 (3.4, 27.9)

15.5 (4.6, 26.3)

Fall

10 (18.9%)

12 (16.4%)

22 (17.5%)

2 (3.4%)

15.5 (4.0, 27.0)

13.0 (3.4, 22.7)

DIZZINESS

8 (15.1%)

8 (11.0%)

16 (12.7%)

0

15.1 (5.5, 24.7)

11.0 (3.8, 18.1)

SYNCOPE

1 (1.9%)

3 (4.1%)

4 (3.2%)

0

1.9 (-1.8, 5.5)

4.1 (-0.4, 8.7)

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)

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)

Fatigue

2 (3.8%)

2 (2.7%)

4 (3.2%)

1 (1.7%)

2.1 (-4.0, 8.2)

1.0 (-3.9, 6.0)

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)

Peripheral Edema

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

OEDEMA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Pyrexia

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

CHILLS

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Cardiac disorders

10 (18.9%)

14 (19.2%)

24 (19.0%)

7 (11.9%)

7.0 (-6.4, 20.4)

7.3 (-4.9, 19.5)

Arrhythmia

9 (17.0%)

11 (15.1%)

20 (15.9%)

0

17.0 (6.9, 27.1)

15.1 (6.9, 23.3)

DIZZINESS

8 (15.1%)

8 (11.0%)

16 (12.7%)

0

15.1 (5.5, 24.7)

11.0 (3.8, 18.1)

SYNCOPE

1 (1.9%)

3 (4.1%)

4 (3.2%)

0

1.9 (-1.8, 5.5)

4.1 (-0.4, 8.7)

PALPITATIONS

0

2 (2.7%)

2 (1.6%)

0

0.0 (0.0, 0.0)

2.7 (-1.0, 6.5)

SYNCOPE VASOVAGAL

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

WOLFF-PARKINSON-WHITE
 SYNDROME

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Heart Failure

1 (1.9%)

3 (4.1%)

4 (3.2%)

2 (3.4%)

-1.5 (-7.4, 4.4)

0.7 (-5.8, 7.2)

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)

DYSPNOEA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

OEDEMA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Myocardial Ischemia

1 (1.9%)

3 (4.1%)

4 (3.2%)

4 (6.8%)

-4.9 (-12.3, 2.5)

-2.7 (-10.5, 5.2)

ELECTROCARDIOGRAM T
 WAVE INVERSION

1 (1.9%)

1 (1.4%)

2 (1.6%)

2 (3.4%)

-1.5 (-7.4, 4.4)

-2.0 (-7.4, 3.3)

ELECTROCARDIOGRAM ST
 SEGMENT DEPRESSION

0

1 (1.4%)

1 (0.8%)

3 (5.1%)

-5.1 (-10.7, 0.5)

-3.7 (-9.9, 2.5)

SUDDEN DEATH

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Acute Coronary Syndrome

0

1 (1.4%)

1 (0.8%)

4 (6.8%)

-6.8 (-13.2, -0.4)

-5.4 (-12.4, 1.5)

ELECTROCARDIOGRAM ST
 SEGMENT DEPRESSION

0

1 (1.4%)

1 (0.8%)

3 (5.1%)

-5.1 (-10.7, 0.5)

-3.7 (-9.9, 2.5)

BLOOD CREATINE
 PHOSPHOKINASE
 INCREASED

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Myocardial Infarction

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

SUDDEN DEATH

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Ear and labyrinth disorders

8 (15.1%)

9 (12.3%)

17 (13.5%)

0

15.1 (5.5, 24.7)

12.3 (4.8, 19.9)

Vertigo

8 (15.1%)

9 (12.3%)

17 (13.5%)

0

15.1 (5.5, 24.7)

12.3 (4.8, 19.9)

DIZZINESS

8 (15.1%)

8 (11.0%)

16 (12.7%)

0

15.1 (5.5, 24.7)

11.0 (3.8, 18.1)

BALANCE DISORDER

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Gastrointestinal disorders

12 (22.6%)

4 (5.5%)

16 (12.7%)

1 (1.7%)

20.9 (9.2, 32.7)

3.8 (-2.4, 10.0)

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%)

1 (1.7%)

7.7 (-0.8, 16.3)

1.0 (-3.9, 6.0)

NAUSEA

5 (9.4%)

2 (2.7%)

7 (5.6%)

0

9.4 (1.6, 17.3)

2.7 (-1.0, 6.5)

GASTROENTERITIS VIRAL

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Dyspepsia

5 (9.4%)

1 (1.4%)

6 (4.8%)

1 (1.7%)

7.7 (-0.8, 16.3)

-0.3 (-4.6, 3.9)

CHEST DISCOMFORT

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

CHEST PAIN

2 (3.8%)

0

2 (1.6%)

0

3.8 (-1.4, 8.9)

0.0 (0.0, 0.0)

ABDOMINAL DISCOMFORT

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

BURNING SENSATION

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

GASTROOESOPHAGEAL
 REFLUX DISEASE

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Diarrhea

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

GASTROENTERITIS VIRAL

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Psychiatric disorders

6 (11.3%)

4 (5.5%)

10 (7.9%)

2 (3.4%)

7.9 (-1.8, 17.6)

2.1 (-4.9, 9.1)

Anxiety

1 (1.9%)

4 (5.5%)

5 (4.0%)

1 (1.7%)

0.2 (-4.7, 5.1)

3.8 (-2.4, 10.0)

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)

NIGHTMARE

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

RESTLESSNESS

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Mania

0

3 (4.1%)

3 (2.4%)

2 (3.4%)

-3.4 (-8.0, 1.2)

0.7 (-5.8, 7.2)

AGITATION

0

2 (2.7%)

2 (1.6%)

1 (1.7%)

-1.7 (-5.0, 1.6)

1.0 (-3.9, 6.0)

RESTLESSNESS

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

PSYCHOMOTOR
 HYPERACTIVITY

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Psychosis

3 (5.7%)

0

3 (2.4%)

0

5.7 (-0.6, 11.9)

0.0 (0.0, 0.0)

DELIRIUM

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

HALLUCINATION

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)

Study Agent Abuse Potential

3 (5.7%)

0

3 (2.4%)

1 (1.7%)

4.0 (-3.1, 11.0)

-1.7 (-5.0, 1.6)

HALLUCINATION

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

HALLUCINATION, VISUAL

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

HYPERSOMNIA

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

PSYCHOMOTOR
 HYPERACTIVITY

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Infections and infestations

4 (7.5%)

2 (2.7%)

6 (4.8%)

10 (16.9%)

-9.4 (-21.3, 2.5)

-14.2 (-24.5, -3.9)

Viral Infection

3 (5.7%)

1 (1.4%)

4 (3.2%)

6 (10.2%)

-4.5 (-14.4, 5.4)

-8.8 (-17.0, -0.6)

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)

LOWER RESPIRATORY TRACT
 INFECTION

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

PNEUMONIA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

CONJUNCTIVITIS

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Pneumonia

2 (3.8%)

1 (1.4%)

3 (2.4%)

1 (1.7%)

2.1 (-4.0, 8.2)

-0.3 (-4.6, 3.9)

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)

LOWER RESPIRATORY TRACT
 INFECTION

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

Bacterial Infection

1 (1.9%)

1 (1.4%)

2 (1.6%)

3 (5.1%)

-3.2 (-9.9, 3.5)

-3.7 (-9.9, 2.5)

LOWER RESPIRATORY TRACT
 INFECTION

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

PNEUMONIA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

CERVICITIS

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

EAR INFECTION

0

0

0

2 (3.4%)

-3.4 (-8.0, 1.2)

-3.4 (-8.0, 1.2)

Renal and urinary disorders

1 (1.9%)

3 (4.1%)

4 (3.2%)

3 (5.1%)

-3.2 (-9.9, 3.5)

-1.0 (-8.2, 6.2)

Urinary Retention

1 (1.9%)

3 (4.1%)

4 (3.2%)

3 (5.1%)

-3.2 (-9.9, 3.5)

-1.0 (-8.2, 6.2)

BENIGN PROSTATIC
 HYPERPLASIA

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

DYSURIA

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

INCONTINENCE

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

MICTURITION URGENCY

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

Renal & Urinary Tract
 Infection

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

DYSURIA

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

Musculoskeletal and connective
 tissue disorders

1 (1.9%)

2 (2.7%)

3 (2.4%)

1 (1.7%)

0.2 (-4.7, 5.1)

1.0 (-3.9, 6.0)

Arthritis

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)

Myalgia

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

MUSCLE SPASMS

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Muscle Injury

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

BLOOD CREATINE
 PHOSPHOKINASE
 INCREASED

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Metabolism and nutrition
 disorders

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Cachexia

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

WEIGHT DECREASED

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Reproductive system and breast
 disorders

0

1 (1.4%)

1 (0.8%)

3 (5.1%)

-5.1 (-10.7, 0.5)

-3.7 (-9.9, 2.5)

Abnormal Uterine Bleeding

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

BLEEDING ANOVULATORY

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

Erectile Dysfunction

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

DISTURBANCE IN SEXUAL
 AROUSAL

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Sexual Dysfunction

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

PELVIC PAIN

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Respiratory, thoracic and
 mediastinal disorders

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

Bronchospasm

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)

Respiratory Failure

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)

Cough

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

POSTNASAL DRIP

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Eye disorders

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Glaucoma

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

EYE SWELLING

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Hepatobiliary disorders

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Hepatic Injury

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

BLOOD ALKALINE
 PHOSPHATASE INCREASED

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Vascular disorders

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Hypotension

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)

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

TSFAE17C
TSFAE19A
Source Code
---
title: TSFAE17D
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:              tsfae17d.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSFAE17d"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

trtvar <- "TRT01A"
popfl <- "SAFFL"
ocmqclass <- "Broad"
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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