TL Catalog
  1. Tables
  2. Adverse Events
  3. TSFAE24C
  • 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

  • Output
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  1. Tables
  2. Adverse Events
  3. TSFAE24C

TSFAE24C

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


Output

  • Preview
Code
# Program Name:              tsfae24c.R

# Prep environment:

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

# Define script level parameters:

tblid <- "TSFAE24c"
fileid <- tblid
popfl <- "SAFFL"
trtvar <- "TRT01A"
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

# Process data:

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

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

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

# Define layout and build table:

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

combodf <- tribble(
  ~valname  , ~label        , ~levelcombo , ~exargs ,
  "RELATED" , "Related AEs" , c("AEs")    , list()
)

extra_args1 <- list(
  .stats = c("count_unique_fraction"),
  subcol_split = "RELATED",
  subcol_var = "AEREL",
  subcol_val = "RELATED"
)

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

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

# Post-Processing:

result <- result %>%
  sort_at_path(
    path = c("AEBODSYS"),
    scorefun = cont_n_onecol("AEs.Active Study Agent.Xanomeline High Dose")
  ) %>%
  sort_at_path(
    path = c("AEBODSYS", "*", "AEDECOD"),
    scorefun = score_occurrences_cols(
      "AEs.Active Study Agent.Xanomeline High Dose"
    )
  )

# 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")

TSFAE24c: Subjects With Treatment-emergent Adverse Events and Related Treatment-emergent Adverse Events by System Organ Class and Preferred Term; Safety Analysis Set (Study jjcs - core)

AEs

Related AEs

Active Study Agent

Active Study Agent

System Organ Class

Xanomeline High Dose

Xanomeline Low Dose

Placebo

Xanomeline High Dose

Xanomeline Low Dose

Placebo

Preferred Term, n (%)

N=53

N=73

N=59

N=53

N=73

N=59

Subjects with ≥ 1 AE

51 (96.2%)

62 (84.9%)

42 (71.2%)

15 (28.3%)

19 (26.0%)

19 (32.2%)

Skin and subcutaneous tissue
 disorders

34 (64.2%)

28 (38.4%)

16 (27.1%)

1 (1.9%)

0

4 (6.8%)

PRURITUS

20 (37.7%)

14 (19.2%)

6 (10.2%)

0

0

1 (1.7%)

ERYTHEMA

12 (22.6%)

8 (11.0%)

6 (10.2%)

0

0

0

HYPERHIDROSIS

8 (15.1%)

4 (5.5%)

2 (3.4%)

0

0

1 (1.7%)

RASH

5 (9.4%)

9 (12.3%)

4 (6.8%)

0

0

1 (1.7%)

SKIN IRRITATION

4 (7.5%)

4 (5.5%)

3 (5.1%)

0

0

0

RASH PRURITIC

2 (3.8%)

1 (1.4%)

0

0

0

0

ACTINIC KERATOSIS

1 (1.9%)

0

0

0

0

0

BLISTER

1 (1.9%)

2 (2.7%)

0

0

0

0

PRURITUS GENERALISED

1 (1.9%)

0

0

0

0

0

RASH MACULO-PAPULAR

1 (1.9%)

0

0

0

0

0

SKIN ODOUR ABNORMAL

1 (1.9%)

0

0

1 (1.9%)

0

0

URTICARIA

1 (1.9%)

1 (1.4%)

0

0

0

0

ALOPECIA

0

0

1 (1.7%)

0

0

1 (1.7%)

DRUG ERUPTION

0

0

1 (1.7%)

0

0

0

RASH ERYTHEMATOUS

0

1 (1.4%)

0

0

0

0

SKIN ULCER

0

0

1 (1.7%)

0

0

0

General disorders and
 administration site conditions

26 (49.1%)

38 (52.1%)

16 (27.1%)

5 (9.4%)

6 (8.2%)

1 (1.7%)

APPLICATION SITE PRURITUS

13 (24.5%)

18 (24.7%)

4 (6.8%)

0

0

0

APPLICATION SITE ERYTHEMA

10 (18.9%)

11 (15.1%)

2 (3.4%)

0

0

0

APPLICATION SITE IRRITATION

8 (15.1%)

7 (9.6%)

2 (3.4%)

0

0

0

FATIGUE

5 (9.4%)

5 (6.8%)

0

1 (1.9%)

3 (4.1%)

0

APPLICATION SITE DERMATITIS

4 (7.5%)

7 (9.6%)

5 (8.5%)

0

0

0

APPLICATION SITE VESICLES

4 (7.5%)

4 (5.5%)

0

0

0

0

APPLICATION SITE PAIN

2 (3.8%)

0

0

0

0

0

APPLICATION SITE
 PERSPIRATION

2 (3.8%)

0

0

0

0

0

APPLICATION SITE SWELLING

2 (3.8%)

1 (1.4%)

0

0

0

0

CHEST PAIN

2 (3.8%)

0

0

2 (3.8%)

0

0

MALAISE

2 (3.8%)

1 (1.4%)

0

1 (1.9%)

0

0

APPLICATION SITE REACTION

1 (1.9%)

0

1 (1.7%)

0

0

0

CHEST DISCOMFORT

1 (1.9%)

1 (1.4%)

0

0

0

0

CHILLS

1 (1.9%)

0

0

1 (1.9%)

0

0

FEELING ABNORMAL

1 (1.9%)

0

0

0

0

0

FEELING COLD

1 (1.9%)

0

0

0

0

0

OEDEMA PERIPHERAL

1 (1.9%)

1 (1.4%)

2 (3.4%)

0

1 (1.4%)

1 (1.7%)

PAIN

1 (1.9%)

0

0

0

0

0

APPLICATION SITE BLEEDING

0

1 (1.4%)

0

0

0

0

APPLICATION SITE
 DESQUAMATION

0

1 (1.4%)

0

0

0

0

APPLICATION SITE INDURATION

0

0

1 (1.7%)

0

0

0

APPLICATION SITE URTICARIA

0

2 (2.7%)

0

0

0

0

ASTHENIA

0

1 (1.4%)

1 (1.7%)

0

1 (1.4%)

0

OEDEMA

0

1 (1.4%)

0

0

0

0

PYREXIA

0

1 (1.4%)

2 (3.4%)

0

1 (1.4%)

0

SECRETION DISCHARGE

0

1 (1.4%)

0

0

0

0

SUDDEN DEATH

0

1 (1.4%)

0

0

0

0

ULCER

0

1 (1.4%)

0

0

0

0

Nervous system disorders

18 (34.0%)

18 (24.7%)

5 (8.5%)

6 (11.3%)

5 (6.8%)

1 (1.7%)

DIZZINESS

8 (15.1%)

8 (11.0%)

0

4 (7.5%)

2 (2.7%)

0

HEADACHE

5 (9.4%)

3 (4.1%)

2 (3.4%)

2 (3.8%)

1 (1.4%)

0

BURNING SENSATION

1 (1.9%)

0

0

0

0

0

COGNITIVE DISORDER

1 (1.9%)

0

0

0

0

0

HYPERSOMNIA

1 (1.9%)

0

0

0

0

0

PARAESTHESIA

1 (1.9%)

0

0

0

0

0

PAROSMIA

1 (1.9%)

0

0

0

0

0

PARTIAL SEIZURES WITH
 SECONDARY
 GENERALISATION

1 (1.9%)

0

0

0

0

0

SOMNOLENCE

1 (1.9%)

2 (2.7%)

1 (1.7%)

1 (1.9%)

1 (1.4%)

0

SYNCOPE

1 (1.9%)

3 (4.1%)

0

0

0

0

SYNCOPE VASOVAGAL

1 (1.9%)

0

0

0

0

0

TRANSIENT ISCHAEMIC
 ATTACK

1 (1.9%)

2 (2.7%)

0

0

1 (1.4%)

0

BALANCE DISORDER

0

1 (1.4%)

0

0

0

0

COMPLEX PARTIAL SEIZURES

0

1 (1.4%)

0

0

0

0

COORDINATION ABNORMAL

0

1 (1.4%)

0

0

0

0

HEMIANOPIA HOMONYMOUS

0

1 (1.4%)

0

0

0

0

LETHARGY

0

1 (1.4%)

0

0

0

0

PARAESTHESIA ORAL

0

1 (1.4%)

0

0

0

0

PARKINSON'S DISEASE

0

0

1 (1.7%)

0

0

0

PSYCHOMOTOR
 HYPERACTIVITY

0

0

1 (1.7%)

0

0

1 (1.7%)

STUPOR

0

1 (1.4%)

0

0

0

0

Gastrointestinal disorders

14 (26.4%)

10 (13.7%)

7 (11.9%)

4 (7.5%)

2 (2.7%)

2 (3.4%)

NAUSEA

5 (9.4%)

2 (2.7%)

0

2 (3.8%)

0

0

VOMITING

5 (9.4%)

2 (2.7%)

0

2 (3.8%)

0

0

SALIVARY HYPERSECRETION

4 (7.5%)

0

0

0

0

0

DIARRHOEA

2 (3.8%)

3 (4.1%)

3 (5.1%)

1 (1.9%)

1 (1.4%)

1 (1.7%)

ABDOMINAL DISCOMFORT

1 (1.9%)

0

0

1 (1.9%)

0

0

STOMACH DISCOMFORT

1 (1.9%)

0

0

0

0

0

ABDOMINAL PAIN

0

2 (2.7%)

1 (1.7%)

0

1 (1.4%)

1 (1.7%)

CONSTIPATION

0

0

1 (1.7%)

0

0

1 (1.7%)

DYSPEPSIA

0

1 (1.4%)

1 (1.7%)

0

0

0

GASTROOESOPHAGEAL REFLUX
 DISEASE

0

0

1 (1.7%)

0

0

0

GLOSSITIS

0

0

1 (1.7%)

0

0

0

HIATUS HERNIA

0

0

1 (1.7%)

0

0

0

RECTAL HAEMORRHAGE

0

1 (1.4%)

0

0

0

0

Cardiac disorders

11 (20.8%)

11 (15.1%)

7 (11.9%)

2 (3.8%)

3 (4.1%)

3 (5.1%)

SINUS BRADYCARDIA

7 (13.2%)

4 (5.5%)

0

2 (3.8%)

1 (1.4%)

0

MYOCARDIAL INFARCTION

3 (5.7%)

1 (1.4%)

3 (5.1%)

0

0

2 (3.4%)

ATRIAL FIBRILLATION

1 (1.9%)

2 (2.7%)

0

0

0

0

ATRIAL FLUTTER

1 (1.9%)

1 (1.4%)

0

0

0

0

CARDIAC DISORDER

1 (1.9%)

0

0

0

0

0

VENTRICULAR EXTRASYSTOLES

1 (1.9%)

2 (2.7%)

0

0

1 (1.4%)

0

ATRIOVENTRICULAR BLOCK
 FIRST DEGREE

0

1 (1.4%)

0

0

0

0

ATRIOVENTRICULAR BLOCK
 SECOND DEGREE

0

0

1 (1.7%)

0

0

0

BUNDLE BRANCH BLOCK LEFT

0

0

1 (1.7%)

0

0

0

BUNDLE BRANCH BLOCK RIGHT

0

1 (1.4%)

1 (1.7%)

0

0

1 (1.7%)

PALPITATIONS

0

2 (2.7%)

0

0

1 (1.4%)

0

SINUS ARRHYTHMIA

0

0

1 (1.7%)

0

0

0

SUPRAVENTRICULAR
 EXTRASYSTOLES

0

1 (1.4%)

1 (1.7%)

0

0

1 (1.7%)

SUPRAVENTRICULAR
 TACHYCARDIA

0

1 (1.4%)

0

0

0

0

TACHYCARDIA

0

0

1 (1.7%)

0

0

1 (1.7%)

WOLFF-PARKINSON-WHITE
 SYNDROME

0

1 (1.4%)

0

0

0

0

Infections and infestations

9 (17.0%)

6 (8.2%)

14 (23.7%)

0

0

4 (6.8%)

NASOPHARYNGITIS

3 (5.7%)

3 (4.1%)

2 (3.4%)

0

0

0

UPPER RESPIRATORY TRACT
 INFECTION

2 (3.8%)

0

5 (8.5%)

0

0

3 (5.1%)

HORDEOLUM

1 (1.9%)

0

0

0

0

0

INFLUENZA

1 (1.9%)

1 (1.4%)

1 (1.7%)

0

0

0

LOWER RESPIRATORY TRACT
 INFECTION

1 (1.9%)

0

0

0

0

0

RHINITIS

1 (1.9%)

0

0

0

0

0

URINARY TRACT INFECTION

1 (1.9%)

0

2 (3.4%)

0

0

1 (1.7%)

BRONCHITIS

0

0

1 (1.7%)

0

0

0

CELLULITIS

0

1 (1.4%)

0

0

0

0

CERVICITIS

0

0

1 (1.7%)

0

0

1 (1.7%)

EAR INFECTION

0

0

2 (3.4%)

0

0

0

GASTROENTERITIS VIRAL

0

0

1 (1.7%)

0

0

1 (1.7%)

LOCALISED INFECTION

0

0

1 (1.7%)

0

0

0

PNEUMONIA

0

1 (1.4%)

0

0

0

0

VAGINAL MYCOSIS

0

0

1 (1.7%)

0

0

1 (1.7%)

Respiratory, thoracic and
 mediastinal disorders

7 (13.2%)

6 (8.2%)

5 (8.5%)

2 (3.8%)

2 (2.7%)

2 (3.4%)

COUGH

3 (5.7%)

4 (5.5%)

1 (1.7%)

0

1 (1.4%)

1 (1.7%)

NASAL CONGESTION

3 (5.7%)

0

2 (3.4%)

1 (1.9%)

0

1 (1.7%)

EPISTAXIS

2 (3.8%)

0

0

1 (1.9%)

0

0

ALLERGIC GRANULOMATOUS
 ANGIITIS

1 (1.9%)

0

0

0

0

0

PHARYNGOLARYNGEAL PAIN

1 (1.9%)

0

0

0

0

0

PRODUCTIVE COUGH

1 (1.9%)

0

0

0

0

0

RESPIRATORY TRACT
 CONGESTION

1 (1.9%)

0

0

0

0

0

RHINORRHOEA

1 (1.9%)

1 (1.4%)

0

0

1 (1.4%)

0

DYSPHONIA

0

1 (1.4%)

0

0

1 (1.4%)

0

DYSPNOEA

0

1 (1.4%)

0

0

0

0

EMPHYSEMA

0

0

1 (1.7%)

0

0

0

POSTNASAL DRIP

0

0

1 (1.7%)

0

0

0

Psychiatric disorders

6 (11.3%)

8 (11.0%)

7 (11.9%)

2 (3.8%)

0

5 (8.5%)

CONFUSIONAL STATE

1 (1.9%)

3 (4.1%)

2 (3.4%)

1 (1.9%)

0

1 (1.7%)

DELIRIUM

1 (1.9%)

0

0

0

0

0

DELUSION

1 (1.9%)

0

1 (1.7%)

0

0

1 (1.7%)

HALLUCINATION

1 (1.9%)

0

0

0

0

0

HALLUCINATION, VISUAL

1 (1.9%)

0

0

0

0

0

INSOMNIA

1 (1.9%)

0

1 (1.7%)

0

0

0

LIBIDO DECREASED

1 (1.9%)

0

0

0

0

0

LISTLESS

1 (1.9%)

0

0

0

0

0

NIGHTMARE

1 (1.9%)

0

0

1 (1.9%)

0

0

AGITATION

0

2 (2.7%)

1 (1.7%)

0

0

1 (1.7%)

ANXIETY

0

1 (1.4%)

0

0

0

0

DEPRESSED MOOD

0

1 (1.4%)

0

0

0

0

DISORIENTATION

0

0

1 (1.7%)

0

0

1 (1.7%)

DISTURBANCE IN SEXUAL
 AROUSAL

0

0

1 (1.7%)

0

0

1 (1.7%)

IRRITABILITY

0

1 (1.4%)

0

0

0

0

RESTLESSNESS

0

1 (1.4%)

0

0

0

0

Investigations

5 (9.4%)

7 (9.6%)

7 (11.9%)

0

1 (1.4%)

3 (5.1%)

BIOPSY

1 (1.9%)

0

0

0

0

0

BIOPSY PROSTATE

1 (1.9%)

0

0

0

0

0

BLOOD CHOLESTEROL
 INCREASED

1 (1.9%)

0

0

0

0

0

BLOOD GLUCOSE INCREASED

1 (1.9%)

1 (1.4%)

0

0

0

0

ELECTROCARDIOGRAM T WAVE
 INVERSION

1 (1.9%)

1 (1.4%)

2 (3.4%)

0

0

2 (3.4%)

BLOOD ALKALINE
 PHOSPHATASE INCREASED

0

0

1 (1.7%)

0

0

0

BLOOD CREATINE
 PHOSPHOKINASE INCREASED

0

0

1 (1.7%)

0

0

0

BLOOD URINE PRESENT

0

0

1 (1.7%)

0

0

0

BODY TEMPERATURE
 INCREASED

0

1 (1.4%)

0

0

0

0

CYSTOSCOPY

0

0

1 (1.7%)

0

0

0

ELECTROCARDIOGRAM ST
 SEGMENT DEPRESSION

0

1 (1.4%)

3 (5.1%)

0

0

2 (3.4%)

ELECTROCARDIOGRAM T WAVE
 AMPLITUDE DECREASED

0

1 (1.4%)

1 (1.7%)

0

1 (1.4%)

1 (1.7%)

NASAL MUCOSA BIOPSY

0

1 (1.4%)

0

0

0

0

WEIGHT DECREASED

0

1 (1.4%)

0

0

0

0

Musculoskeletal and connective
 tissue disorders

4 (7.5%)

5 (6.8%)

2 (3.4%)

1 (1.9%)

0

0

BACK PAIN

2 (3.8%)

1 (1.4%)

1 (1.7%)

1 (1.9%)

0

0

ARTHRALGIA

1 (1.9%)

1 (1.4%)

0

0

0

0

FLANK PAIN

1 (1.9%)

0

0

0

0

0

MYALGIA

1 (1.9%)

0

0

0

0

0

MUSCLE SPASMS

0

1 (1.4%)

0

0

0

0

MUSCULAR WEAKNESS

0

1 (1.4%)

0

0

0

0

SHOULDER PAIN

0

1 (1.4%)

1 (1.7%)

0

0

0

Injury, poisoning and
 procedural complications

3 (5.7%)

5 (6.8%)

2 (3.4%)

1 (1.9%)

1 (1.4%)

0

CONTUSION

2 (3.8%)

1 (1.4%)

0

1 (1.9%)

1 (1.4%)

0

EXCORIATION

1 (1.9%)

1 (1.4%)

0

0

0

0

FACIAL BONES FRACTURE

1 (1.9%)

0

0

0

0

0

FALL

1 (1.9%)

2 (2.7%)

1 (1.7%)

0

1 (1.4%)

0

HIP FRACTURE

0

0

1 (1.7%)

0

0

0

JOINT DISLOCATION

0

1 (1.4%)

0

0

0

0

SKIN LACERATION

0

2 (2.7%)

0

0

0

0

WOUND

0

1 (1.4%)

0

0

0

0

Reproductive system and breast
 disorders

3 (5.7%)

0

3 (5.1%)

0

0

0

ABNORMAL UTERINE BLEEDING

1 (1.9%)

0

0

0

0

0

BENIGN PROSTATIC
 HYPERPLASIA

1 (1.9%)

0

1 (1.7%)

0

0

0

ERECTILE DYSFUNCTION

1 (1.9%)

0

1 (1.7%)

0

0

0

PELVIC PAIN

0

0

1 (1.7%)

0

0

0

Renal and urinary disorders

2 (3.8%)

3 (4.1%)

2 (3.4%)

0

1 (1.4%)

1 (1.7%)

CALCULUS URETHRAL

1 (1.9%)

0

0

0

0

0

NEPHROLITHIASIS

1 (1.9%)

0

0

0

0

0

DYSURIA

0

1 (1.4%)

1 (1.7%)

0

1 (1.4%)

1 (1.7%)

INCONTINENCE

0

1 (1.4%)

0

0

0

0

MICTURITION URGENCY

0

1 (1.4%)

1 (1.7%)

0

0

0

Congenital, familial and genetic
 disorders

1 (1.9%)

1 (1.4%)

0

0

0

0

VENTRICULAR SEPTAL DEFECT

1 (1.9%)

1 (1.4%)

0

0

0

0

Ear and labyrinth disorders

1 (1.9%)

2 (2.7%)

1 (1.7%)

0

0

0

VERTIGO

1 (1.9%)

1 (1.4%)

0

0

0

0

CERUMEN IMPACTION

0

1 (1.4%)

0

0

0

0

EAR PAIN

0

0

1 (1.7%)

0

0

0

Eye disorders

1 (1.9%)

2 (2.7%)

2 (3.4%)

0

1 (1.4%)

2 (3.4%)

VISION BLURRED

1 (1.9%)

1 (1.4%)

0

0

0

0

CONJUNCTIVAL HAEMORRHAGE

0

1 (1.4%)

0

0

1 (1.4%)

0

CONJUNCTIVITIS

0

0

1 (1.7%)

0

0

1 (1.7%)

EYE ALLERGY

0

0

1 (1.7%)

0

0

0

EYE PRURITUS

0

0

1 (1.7%)

0

0

1 (1.7%)

EYE SWELLING

0

0

1 (1.7%)

0

0

0

Metabolism and nutrition
 disorders

1 (1.9%)

0

2 (3.4%)

1 (1.9%)

0

0

INCREASED APPETITE

1 (1.9%)

0

0

1 (1.9%)

0

0

DECREASED APPETITE

0

0

1 (1.7%)

0

0

0

DEHYDRATION

0

0

1 (1.7%)

0

0

0

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

1 (1.9%)

1 (1.4%)

0

0

0

0

PROSTATE CANCER

1 (1.9%)

0

0

0

0

0

COLON CANCER

0

1 (1.4%)

0

0

0

0

Surgical and medical
 procedures

1 (1.9%)

0

2 (3.4%)

0

0

0

ACROCHORDON EXCISION

1 (1.9%)

0

0

0

0

0

CATARACT OPERATION

0

0

1 (1.7%)

0

0

0

EYE LASER SURGERY

0

0

1 (1.7%)

0

0

0

Vascular disorders

1 (1.9%)

3 (4.1%)

3 (5.1%)

0

0

2 (3.4%)

WOUND HAEMORRHAGE

1 (1.9%)

0

0

0

0

0

HOT FLUSH

0

1 (1.4%)

0

0

0

0

HYPERTENSION

0

1 (1.4%)

1 (1.7%)

0

0

1 (1.7%)

HYPOTENSION

0

1 (1.4%)

2 (3.4%)

0

0

1 (1.7%)

ORTHOSTATIC HYPOTENSION

0

0

1 (1.7%)

0

0

0

Endocrine disorders

0

1 (1.4%)

1 (1.7%)

0

0

1 (1.7%)

BLEEDING ANOVULATORY

0

1 (1.4%)

1 (1.7%)

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. An AE is assessed by the investigator as related.

Note: Adverse events are coded using MedDRA version 26.0.

Download RTF file

TSFAE24B
TSFAE24D
Source Code
---
title: TSFAE24C
subtitle: Subjects With Treatment-emergent Adverse Events and Related Treatment-emergent Adverse Events by System Organ Class 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:              tsfae24c.R

# Prep environment:

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

# Define script level parameters:

tblid <- "TSFAE24c"
fileid <- tblid
popfl <- "SAFFL"
trtvar <- "TRT01A"
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

# Process data:

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

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

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

# Define layout and build table:

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

combodf <- tribble(
  ~valname  , ~label        , ~levelcombo , ~exargs ,
  "RELATED" , "Related AEs" , c("AEs")    , list()
)

extra_args1 <- list(
  .stats = c("count_unique_fraction"),
  subcol_split = "RELATED",
  subcol_var = "AEREL",
  subcol_val = "RELATED"
)

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

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

# Post-Processing:

result <- result %>%
  sort_at_path(
    path = c("AEBODSYS"),
    scorefun = cont_n_onecol("AEs.Active Study Agent.Xanomeline High Dose")
  ) %>%
  sort_at_path(
    path = c("AEBODSYS", "*", "AEDECOD"),
    scorefun = score_occurrences_cols(
      "AEs.Active Study Agent.Xanomeline High Dose"
    )
  )

# 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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