TL Catalog
  1. Tables
  2. Adverse Events
  3. TSFAE12
  • 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. TSFAE12

TSFAE12

Subjects With Treatment-emergent Adverse Events Leading to Dose Modification of Study Treatment by System Organ Class and Preferred Term


Output

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Code
# Program Name:              tsfae12.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSFAE12"
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
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::adae %>%
  filter(
    TRTEMFL == "Y" &
      !(AEACN %in%
        c(
          "",
          NA_character_,
          "DRUG WITHDRAWN",
          "DOSE NOT CHANGED",
          "UNKNOWN",
          "NOT APPLICABLE"
        ))
  ) %>%
  select(USUBJID, TRTEMFL, AEACN, AEBODSYS, 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", " ", trtvar, ctrl_grp)
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 %>%
  analyze(
    "TRTEMFL",
    afun = a_freq_j,
    show_labels = "hidden",
    extra_args = append(
      extra_args_rr,
      list(label = "Subjects with >=1 AE", NULL)
    )
  ) %>%
  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 = 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)

# 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()
  )
}

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

# If there is no data remove top row and display "No data to display" text
if (length(adae$TRTEMFL) == 0) {
  result <- safe_prune_table(
    result,
    prune_func = remove_rows(removerowtext = "Subjects with >=1 AE")
  )
}

# 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")

TSFAE12: Subjects With Treatment-emergent Adverse Events Leading to [Dose Modification of Study Treatment] by System Organ Class and Preferred Term; Safety Analysis Set (Study jjcs - core)

Active Study Agent

Risk Difference (%) (95% CI)

System Organ Class

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

Subjects with ≥1 AE

49 (92.5%)

53 (72.6%)

102 (81.0%)

39 (66.1%)

26.4 (12.3, 40.4)

6.5 (-9.3, 22.3)

Skin and subcutaneous tissue
 disorders

26 (49.1%)

23 (31.5%)

49 (38.9%)

12 (20.3%)

28.7 (11.8, 45.6)

11.2 (-3.6, 26.0)

PRURITUS

14 (26.4%)

12 (16.4%)

26 (20.6%)

4 (6.8%)

19.6 (6.1, 33.1)

9.7 (-1.0, 20.3)

ERYTHEMA

8 (15.1%)

6 (8.2%)

14 (11.1%)

5 (8.5%)

6.6 (-5.4, 18.6)

-0.3 (-9.8, 9.2)

HYPERHIDROSIS

7 (13.2%)

2 (2.7%)

9 (7.1%)

1 (1.7%)

11.5 (1.8, 21.2)

1.0 (-3.9, 6.0)

RASH

4 (7.5%)

5 (6.8%)

9 (7.1%)

3 (5.1%)

2.5 (-6.6, 11.5)

1.8 (-6.3, 9.8)

SKIN IRRITATION

1 (1.9%)

3 (4.1%)

4 (3.2%)

2 (3.4%)

-1.5 (-7.4, 4.4)

0.7 (-5.8, 7.2)

BLISTER

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

RASH PRURITIC

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

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)

General disorders and
 administration site conditions

23 (43.4%)

23 (31.5%)

46 (36.5%)

12 (20.3%)

23.1 (6.2, 39.9)

11.2 (-3.6, 26.0)

APPLICATION SITE PRURITUS

9 (17.0%)

11 (15.1%)

20 (15.9%)

4 (6.8%)

10.2 (-1.8, 22.2)

8.3 (-2.1, 18.7)

APPLICATION SITE ERYTHEMA

9 (17.0%)

6 (8.2%)

15 (11.9%)

0

17.0 (6.9, 27.1)

8.2 (1.9, 14.5)

APPLICATION SITE IRRITATION

8 (15.1%)

5 (6.8%)

13 (10.3%)

2 (3.4%)

11.7 (1.0, 22.4)

3.5 (-3.9, 10.9)

FATIGUE

4 (7.5%)

3 (4.1%)

7 (5.6%)

0

7.5 (0.4, 14.7)

4.1 (-0.4, 8.7)

APPLICATION SITE DERMATITIS

2 (3.8%)

4 (5.5%)

6 (4.8%)

3 (5.1%)

-1.3 (-8.9, 6.3)

0.4 (-7.3, 8.1)

APPLICATION SITE VESICLES

2 (3.8%)

3 (4.1%)

5 (4.0%)

0

3.8 (-1.4, 8.9)

4.1 (-0.4, 8.7)

MALAISE

2 (3.8%)

1 (1.4%)

3 (2.4%)

0

3.8 (-1.4, 8.9)

1.4 (-1.3, 4.0)

APPLICATION SITE
 PERSPIRATION

2 (3.8%)

0

2 (1.6%)

0

3.8 (-1.4, 8.9)

0.0 (0.0, 0.0)

APPLICATION SITE SWELLING

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)

APPLICATION SITE
 DESQUAMATION

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

CHEST PAIN

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)

FEELING ABNORMAL

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

FEELING COLD

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

OEDEMA PERIPHERAL

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

PYREXIA

0

1 (1.4%)

1 (0.8%)

2 (3.4%)

-3.4 (-8.0, 1.2)

-2.0 (-7.4, 3.3)

SUDDEN DEATH

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

ASTHENIA

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Nervous system disorders

8 (15.1%)

10 (13.7%)

18 (14.3%)

4 (6.8%)

8.3 (-3.3, 19.9)

6.9 (-3.2, 17.1)

DIZZINESS

4 (7.5%)

4 (5.5%)

8 (6.3%)

0

7.5 (0.4, 14.7)

5.5 (0.3, 10.7)

HEADACHE

3 (5.7%)

2 (2.7%)

5 (4.0%)

2 (3.4%)

2.3 (-5.5, 10.0)

-0.7 (-6.6, 5.3)

TRANSIENT ISCHAEMIC
 ATTACK

0

2 (2.7%)

2 (1.6%)

0

0.0 (0.0, 0.0)

2.7 (-1.0, 6.5)

BALANCE DISORDER

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

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)

HEMIANOPIA HOMONYMOUS

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

PARAESTHESIA ORAL

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

SOMNOLENCE

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

STUPOR

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)

Cardiac disorders

8 (15.1%)

9 (12.3%)

17 (13.5%)

6 (10.2%)

4.9 (-7.4, 17.3)

2.2 (-8.6, 12.9)

SINUS BRADYCARDIA

6 (11.3%)

1 (1.4%)

7 (5.6%)

0

11.3 (2.8, 19.9)

1.4 (-1.3, 4.0)

ATRIAL FIBRILLATION

0

2 (2.7%)

2 (1.6%)

0

0.0 (0.0, 0.0)

2.7 (-1.0, 6.5)

MYOCARDIAL INFARCTION

1 (1.9%)

1 (1.4%)

2 (1.6%)

3 (5.1%)

-3.2 (-9.9, 3.5)

-3.7 (-9.9, 2.5)

VENTRICULAR EXTRASYSTOLES

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

ATRIAL FLUTTER

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

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)

PALPITATIONS

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

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)

WOLFF-PARKINSON-WHITE
 SYNDROME

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

BUNDLE BRANCH BLOCK LEFT

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

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)

Gastrointestinal disorders

9 (17.0%)

4 (5.5%)

13 (10.3%)

4 (6.8%)

10.2 (-1.8, 22.2)

-1.3 (-9.6, 7.0)

NAUSEA

3 (5.7%)

2 (2.7%)

5 (4.0%)

0

5.7 (-0.6, 11.9)

2.7 (-1.0, 6.5)

VOMITING

4 (7.5%)

0

4 (3.2%)

0

7.5 (0.4, 14.7)

0.0 (0.0, 0.0)

DIARRHOEA

2 (3.8%)

1 (1.4%)

3 (2.4%)

2 (3.4%)

0.4 (-6.5, 7.3)

-2.0 (-7.4, 3.3)

SALIVARY HYPERSECRETION

3 (5.7%)

0

3 (2.4%)

0

5.7 (-0.6, 11.9)

0.0 (0.0, 0.0)

ABDOMINAL PAIN

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

CONSTIPATION

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

DYSPEPSIA

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

GASTROOESOPHAGEAL REFLUX
 DISEASE

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Infections and infestations

5 (9.4%)

5 (6.8%)

10 (7.9%)

7 (11.9%)

-2.4 (-13.8, 9.0)

-5.0 (-15.1, 5.1)

NASOPHARYNGITIS

2 (3.8%)

2 (2.7%)

4 (3.2%)

1 (1.7%)

2.1 (-4.0, 8.2)

1.0 (-3.9, 6.0)

UPPER RESPIRATORY TRACT
 INFECTION

2 (3.8%)

0

2 (1.6%)

3 (5.1%)

-1.3 (-8.9, 6.3)

-5.1 (-10.7, 0.5)

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)

INFLUENZA

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

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)

BRONCHITIS

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

CERVICITIS

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

EAR INFECTION

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)

URINARY TRACT INFECTION

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

VAGINAL MYCOSIS

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Psychiatric disorders

3 (5.7%)

6 (8.2%)

9 (7.1%)

4 (6.8%)

-1.1 (-10.1, 7.8)

1.4 (-7.6, 10.4)

CONFUSIONAL STATE

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%)

0

0.0 (0.0, 0.0)

2.7 (-1.0, 6.5)

DELUSION

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-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)

INSOMNIA

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

RESTLESSNESS

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

DISTURBANCE IN SEXUAL
 AROUSAL

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Respiratory, thoracic and
 mediastinal disorders

4 (7.5%)

4 (5.5%)

8 (6.3%)

3 (5.1%)

2.5 (-6.6, 11.5)

0.4 (-7.3, 8.1)

COUGH

1 (1.9%)

4 (5.5%)

5 (4.0%)

1 (1.7%)

0.2 (-4.7, 5.1)

3.8 (-2.4, 10.0)

NASAL CONGESTION

2 (3.8%)

0

2 (1.6%)

1 (1.7%)

2.1 (-4.0, 8.2)

-1.7 (-5.0, 1.6)

PRODUCTIVE COUGH

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

RHINORRHOEA

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

EMPHYSEMA

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Injury, poisoning and
 procedural complications

2 (3.8%)

5 (6.8%)

7 (5.6%)

2 (3.4%)

0.4 (-6.5, 7.3)

3.5 (-3.9, 10.9)

EXCORIATION

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

FALL

1 (1.9%)

1 (1.4%)

2 (1.6%)

1 (1.7%)

0.2 (-4.7, 5.1)

-0.3 (-4.6, 3.9)

CONTUSION

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

FACIAL BONES FRACTURE

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

JOINT DISLOCATION

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

SKIN LACERATION

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

WOUND

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

HIP FRACTURE

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Investigations

3 (5.7%)

3 (4.1%)

6 (4.8%)

3 (5.1%)

0.6 (-7.8, 8.9)

-1.0 (-8.2, 6.2)

ELECTROCARDIOGRAM T WAVE
 INVERSION

1 (1.9%)

1 (1.4%)

2 (1.6%)

1 (1.7%)

0.2 (-4.7, 5.1)

-0.3 (-4.6, 3.9)

BIOPSY

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

BIOPSY PROSTATE

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

BODY TEMPERATURE
 INCREASED

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

NASAL MUCOSA BIOPSY

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

BLOOD ALKALINE
 PHOSPHATASE INCREASED

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

ELECTROCARDIOGRAM ST
 SEGMENT DEPRESSION

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Musculoskeletal and connective
 tissue disorders

3 (5.7%)

3 (4.1%)

6 (4.8%)

2 (3.4%)

2.3 (-5.5, 10.0)

0.7 (-5.8, 7.2)

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)

ARTHRALGIA

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

MUSCULAR WEAKNESS

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

MYALGIA

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

SHOULDER PAIN

0

1 (1.4%)

1 (0.8%)

1 (1.7%)

-1.7 (-5.0, 1.6)

-0.3 (-4.6, 3.9)

Eye disorders

1 (1.9%)

2 (2.7%)

3 (2.4%)

2 (3.4%)

-1.5 (-7.4, 4.4)

-0.7 (-6.6, 5.3)

VISION BLURRED

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

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)

CONJUNCTIVITIS

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)

Congenital, familial and genetic
 disorders

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

VENTRICULAR SEPTAL DEFECT

1 (1.9%)

1 (1.4%)

2 (1.6%)

0

1.9 (-1.8, 5.5)

1.4 (-1.3, 4.0)

Ear and labyrinth disorders

0

2 (2.7%)

2 (1.6%)

0

0.0 (0.0, 0.0)

2.7 (-1.0, 6.5)

CERUMEN IMPACTION

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

VERTIGO

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Vascular disorders

0

2 (2.7%)

2 (1.6%)

2 (3.4%)

-3.4 (-8.0, 1.2)

-0.7 (-6.6, 5.3)

HOT FLUSH

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)

Endocrine disorders

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

BLEEDING ANOVULATORY

0

1 (1.4%)

1 (0.8%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

Metabolism and nutrition
 disorders

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

INCREASED APPETITE

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

DEHYDRATION

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Renal and urinary disorders

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%)

0

0.0 (0.0, 0.0)

1.4 (-1.3, 4.0)

MICTURITION URGENCY

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Reproductive system and breast
 disorders

1 (1.9%)

0

1 (0.8%)

1 (1.7%)

0.2 (-4.7, 5.1)

-1.7 (-5.0, 1.6)

BENIGN PROSTATIC
 HYPERPLASIA

1 (1.9%)

0

1 (0.8%)

0

1.9 (-1.8, 5.5)

0.0 (0.0, 0.0)

PELVIC PAIN

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Surgical and medical
 procedures

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

EYE LASER SURGERY

0

0

0

1 (1.7%)

-1.7 (-5.0, 1.6)

-1.7 (-5.0, 1.6)

Note: Subjects are counted only once for any given event, regardless of the number of times they actually experienced the event.

Note: Adverse events are coded using MedDRA version 26.0.

Download RTF file

TSFAE11
TSFAE13
Source Code
---
title: TSFAE12
subtitle: Subjects With Treatment-emergent Adverse Events Leading to Dose Modification of Study Treatment 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:              tsfae12.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSFAE12"
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
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::adae %>%
  filter(
    TRTEMFL == "Y" &
      !(AEACN %in%
        c(
          "",
          NA_character_,
          "DRUG WITHDRAWN",
          "DOSE NOT CHANGED",
          "UNKNOWN",
          "NOT APPLICABLE"
        ))
  ) %>%
  select(USUBJID, TRTEMFL, AEACN, AEBODSYS, 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", " ", trtvar, ctrl_grp)
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 %>%
  analyze(
    "TRTEMFL",
    afun = a_freq_j,
    show_labels = "hidden",
    extra_args = append(
      extra_args_rr,
      list(label = "Subjects with >=1 AE", NULL)
    )
  ) %>%
  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 = 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)

# 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()
  )
}

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

# If there is no data remove top row and display "No data to display" text
if (length(adae$TRTEMFL) == 0) {
  result <- safe_prune_table(
    result,
    prune_func = remove_rows(removerowtext = "Subjects with >=1 AE")
  )
}

# 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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