TL Catalog
  1. Tables
  2. Adverse Events
  3. TSFAE13
  • 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. TSFAE13

TSFAE13

Exposure-adjusted Incidence Rate Analysis by Preferred Term


Output

  • Preview
Code
# Program Name:              tsfae13.R

# Prep environment:

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

# Define script level parameters:

tblid <- "TSFAE13"
fileid <- tblid
popfl <- "SAFFL"
trtvar <- "TRT01A"
ctrl_grp <- "Placebo"
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

# Process data:

adexsum <- pharmaverseadamjnj::adexsum %>%
  filter(!!rlang::sym(popfl) == "Y" & PARAMCD == "TRTDURY") %>%
  create_colspan_var(
    non_active_grp = ctrl_grp,
    non_active_grp_span_lbl = " ",
    active_grp_span_lbl = "Active Study Agent",
    colspan_var = "colspan_trt",
    trt_var = trtvar
  ) %>%
  mutate(
    rrisk_header = "Risk Difference (95% CI)",
    rrisk_label = paste(!!rlang::sym(trtvar), "vs", ctrl_grp),
    TRTDURY = AVAL
  ) %>%
  select(
    USUBJID,
    !!rlang::sym(trtvar),
    colspan_trt,
    rrisk_header,
    rrisk_label,
    TRTDURY
  )

adae <- pharmaverseadamjnj::adae %>%
  filter(TRTEMFL == "Y" & AOCCPFL == "Y") %>%
  select(USUBJID, AEDECOD, ASTDY, AOCCPFL)

#  join -- -- subjects without ae will be handled via alt_counts_df dataframe
aefup <- right_join(adae, adexsum, by = "USUBJID")

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

# Define layout and build table:

lyt <- basic_table(
  show_colcounts = TRUE,
  colcount_format = "N=xx",
  top_level_section_div = " "
) %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  ) %>%
  split_cols_by(trtvar) %>%
  split_cols_by("rrisk_header", nested = FALSE) %>%
  split_cols_by(
    trtvar,
    labels_var = "rrisk_label",
    split_fun = remove_split_levels(ctrl_grp)
  ) %>%
  analyze(
    "TRTDURY",
    nested = FALSE,
    show_labels = "hidden",
    afun = a_patyrs_j,
    extra_args = list(.labels = c(patyrs = "Subject years\u1D43"))
  ) %>%
  analyze(
    vars = "AEDECOD",
    nested = FALSE,
    afun = a_eair100_j,
    extra_args = list(
      fup_var = "TRTDURY",
      occ_var = "AOCCPFL",
      occ_dy = "ASTDY",
      ref_path = ref_path,
      drop_levels = TRUE
    )
  ) %>%
  append_topleft("Preferred Term, EAIR Per 100 SY")


result <- build_table(lyt, aefup, alt_counts_df = adexsum)

# Post-Processing:

result <- result %>%
  sort_at_path(
    path = c("AEDECOD"),
    scorefun = jj_complex_scorefun(colpath = "Xanomeline High Dose")
  )

result <- remove_col_count(result)

# 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")

TSFAE13: Exposure-adjusted Incidence Rate Analysis by Preferred Term; Safety Analysis Set (Study jjcs - core)

Active Study Agent

Risk Difference (95% CI)

Xanomeline High Dose

Xanomeline Low Dose

Placebo

Xanomeline High Dose vs Placebo

Xanomeline Low Dose vs Placebo

Preferred Term, EAIR Per 100 SY

N=53

N=73

N=59

Subject yearsᵃ

92.1

126.5

99.8

PRURITUS

30.4

13.9

6.7

23.77 (9.41, 38.12)

7.28 (-1.75, 16.31)

APPLICATION SITE PRURITUS

18.4

16.3

4.2

14.18 (3.39, 24.97)

12.09 (3.34, 20.84)

ERYTHEMA

16.0

7.3

6.6

9.31 (-1.16, 19.79)

0.68 (-6.67, 8.02)

APPLICATION SITE ERYTHEMA

13.1

10.0

2.1

11.06 (2.43, 19.68)

7.96 (1.38, 14.55)

HYPERHIDROSIS

10.7

3.3

2.1

8.62 (0.67, 16.56)

1.19 (-3.11, 5.49)

APPLICATION SITE IRRITATION

10.3

6.2

2.1

8.21 (0.55, 15.87)

4.11 (-1.27, 9.50)

DIZZINESS

9.1

6.9

0.0

9.08 (2.35, 15.80)

6.88 (2.11, 11.65)

SINUS BRADYCARDIA

8.7

3.3

0.0

8.66 (2.24, 15.07)

3.35 (0.07, 6.63)

HEADACHE

6.2

2.5

2.1

4.12 (-2.00, 10.24)

0.40 (-3.58, 4.38)

VOMITING

6.1

1.6

0.0

6.12 (0.76, 11.48)

1.60 (-0.62, 3.81)

RASH

6.0

8.1

4.3

1.70 (-4.99, 8.39)

3.86 (-2.90, 10.61)

FATIGUE

5.9

4.3

0.0

5.93 (0.73, 11.12)

4.30 (0.53, 8.07)

NAUSEA

5.8

1.7

0.0

5.84 (0.72, 10.97)

1.65 (-0.64, 3.94)

SKIN IRRITATION

4.7

3.3

3.1

1.67 (-4.12, 7.47)

0.28 (-4.49, 5.05)

APPLICATION SITE DERMATITIS

4.7

6.0

5.5

-0.77 (-7.42, 5.89)

0.57 (-5.99, 7.13)

APPLICATION SITE VESICLES

4.6

3.3

0.0

4.58 (0.09, 9.07)

3.31 (0.07, 6.55)

SALIVARY HYPERSECRETION

4.4

0.0

0.0

4.42 (0.09, 8.76)

0.00 (0.00, 0.00)

NASAL CONGESTION

3.5

0.0

2.0

1.44 (-3.40, 6.28)

-2.04 (-4.86, 0.79)

MYOCARDIAL INFARCTION

3.4

0.8

3.1

0.30 (-4.94, 5.55)

-2.33 (-6.19, 1.53)

COUGH

3.4

3.4

1.0

2.38 (-1.94, 6.71)

2.35 (-1.49, 6.20)

NASOPHARYNGITIS

3.4

2.5

2.1

1.24 (-3.59, 6.07)

0.36 (-3.73, 4.44)

MALAISE

2.3

0.8

0.0

2.32 (-0.90, 5.55)

0.81 (-0.77, 2.38)

RASH PRURITIC

2.3

0.8

0.0

2.32 (-0.89, 5.53)

0.80 (-0.77, 2.37)

APPLICATION SITE PERSPIRATION

2.3

0.0

0.0

2.31 (-0.89, 5.51)

0.00 (0.00, 0.00)

BACK PAIN

2.3

0.8

1.0

1.28 (-2.45, 5.02)

-0.20 (-2.72, 2.33)

DIARRHOEA

2.3

2.4

3.1

-0.82 (-5.55, 3.90)

-0.66 (-5.13, 3.80)

CONTUSION

2.3

0.8

0.0

2.27 (-0.87, 5.40)

0.80 (-0.77, 2.36)

EPISTAXIS

2.3

0.0

0.0

2.26 (-0.87, 5.40)

0.00 (0.00, 0.00)

UPPER RESPIRATORY TRACT
 INFECTION

2.3

0.0

5.3

-3.01 (-8.59, 2.58)

-5.27 (-9.89, -0.65)

APPLICATION SITE PAIN

2.3

0.0

0.0

2.26 (-0.87, 5.38)

0.00 (0.00, 0.00)

APPLICATION SITE SWELLING

2.2

0.8

0.0

2.25 (-0.87, 5.37)

0.80 (-0.77, 2.36)

CHEST PAIN

2.2

0.0

0.0

2.22 (-0.86, 5.30)

0.00 (0.00, 0.00)

DELIRIUM

1.1

0.0

0.0

1.13 (-1.08, 3.33)

0.00 (0.00, 0.00)

STOMACH DISCOMFORT

1.1

0.0

0.0

1.12 (-1.08, 3.33)

0.00 (0.00, 0.00)

PAIN

1.1

0.0

0.0

1.12 (-1.08, 3.33)

0.00 (0.00, 0.00)

URTICARIA

1.1

0.8

0.0

1.12 (-1.08, 3.33)

0.81 (-0.77, 2.39)

MYALGIA

1.1

0.0

0.0

1.12 (-1.08, 3.33)

0.00 (0.00, 0.00)

PHARYNGOLARYNGEAL PAIN

1.1

0.0

0.0

1.12 (-1.08, 3.33)

0.00 (0.00, 0.00)

PRODUCTIVE COUGH

1.1

0.0

0.0

1.12 (-1.08, 3.33)

0.00 (0.00, 0.00)

ABDOMINAL DISCOMFORT

1.1

0.0

0.0

1.12 (-1.08, 3.32)

0.00 (0.00, 0.00)

RESPIRATORY TRACT
 CONGESTION

1.1

0.0

0.0

1.12 (-1.08, 3.32)

0.00 (0.00, 0.00)

RHINITIS

1.1

0.0

0.0

1.12 (-1.08, 3.32)

0.00 (0.00, 0.00)

FEELING ABNORMAL

1.1

0.0

0.0

1.12 (-1.08, 3.32)

0.00 (0.00, 0.00)

LIBIDO DECREASED

1.1

0.0

0.0

1.12 (-1.08, 3.32)

0.00 (0.00, 0.00)

LISTLESS

1.1

0.0

0.0

1.12 (-1.08, 3.32)

0.00 (0.00, 0.00)

VISION BLURRED

1.1

0.8

0.0

1.12 (-1.08, 3.32)

0.79 (-0.76, 2.35)

COGNITIVE DISORDER

1.1

0.0

0.0

1.12 (-1.08, 3.32)

0.00 (0.00, 0.00)

INCREASED APPETITE

1.1

0.0

0.0

1.12 (-1.08, 3.32)

0.00 (0.00, 0.00)

CHILLS

1.1

0.0

0.0

1.12 (-1.08, 3.32)

0.00 (0.00, 0.00)

ABNORMAL UTERINE BLEEDING

1.1

0.0

0.0

1.12 (-1.08, 3.32)

0.00 (0.00, 0.00)

CONFUSIONAL STATE

1.1

2.5

2.1

-0.93 (-4.53, 2.66)

0.42 (-3.57, 4.41)

INSOMNIA

1.1

0.0

1.0

0.11 (-2.84, 3.07)

-1.01 (-2.99, 0.97)

SOMNOLENCE

1.1

1.6

1.0

0.09 (-2.89, 3.07)

0.58 (-2.43, 3.60)

PRURITUS GENERALISED

1.1

0.0

0.0

1.12 (-1.08, 3.32)

0.00 (0.00, 0.00)

BURNING SENSATION

1.1

0.0

0.0

1.12 (-1.07, 3.31)

0.00 (0.00, 0.00)

VENTRICULAR EXTRASYSTOLES

1.1

1.6

0.0

1.12 (-1.07, 3.31)

1.64 (-0.63, 3.91)

NIGHTMARE

1.1

0.0

0.0

1.12 (-1.07, 3.31)

0.00 (0.00, 0.00)

BIOPSY

1.1

0.0

0.0

1.12 (-1.07, 3.31)

0.00 (0.00, 0.00)

BLOOD CHOLESTEROL
 INCREASED

1.1

0.0

0.0

1.12 (-1.07, 3.31)

0.00 (0.00, 0.00)

ALLERGIC GRANULOMATOUS
 ANGIITIS

1.1

0.0

0.0

1.12 (-1.07, 3.31)

0.00 (0.00, 0.00)

FEELING COLD

1.1

0.0

0.0

1.12 (-1.07, 3.30)

0.00 (0.00, 0.00)

OEDEMA PERIPHERAL

1.1

0.8

1.0

0.10 (-2.86, 3.06)

-0.23 (-2.76, 2.30)

CHEST DISCOMFORT

1.1

0.8

0.0

1.11 (-1.07, 3.30)

0.79 (-0.76, 2.35)

WOUND HAEMORRHAGE

1.1

0.0

0.0

1.11 (-1.07, 3.30)

0.00 (0.00, 0.00)

HALLUCINATION, VISUAL

1.1

0.0

0.0

1.11 (-1.07, 3.29)

0.00 (0.00, 0.00)

PARTIAL SEIZURES WITH
 SECONDARY GENERALISATION

1.1

0.0

0.0

1.11 (-1.07, 3.29)

0.00 (0.00, 0.00)

BIOPSY PROSTATE

1.1

0.0

0.0

1.11 (-1.07, 3.29)

0.00 (0.00, 0.00)

BENIGN PROSTATIC HYPERPLASIA

1.1

0.0

1.0

0.08 (-2.88, 3.05)

-1.03 (-3.04, 0.98)

ELECTROCARDIOGRAM T WAVE
 INVERSION

1.1

0.8

2.1

-0.97 (-4.57, 2.63)

-1.28 (-4.55, 1.99)

VERTIGO

1.1

0.8

0.0

1.10 (-1.06, 3.27)

0.80 (-0.77, 2.38)

SKIN ODOUR ABNORMAL

1.1

0.0

0.0

1.10 (-1.06, 3.26)

0.00 (0.00, 0.00)

TRANSIENT ISCHAEMIC ATTACK

1.1

1.6

0.0

1.10 (-1.06, 3.26)

1.60 (-0.62, 3.81)

ARTHRALGIA

1.1

0.8

0.0

1.10 (-1.06, 3.26)

0.80 (-0.77, 2.37)

VENTRICULAR SEPTAL DEFECT

1.1

0.8

0.0

1.10 (-1.06, 3.26)

0.81 (-0.77, 2.39)

HORDEOLUM

1.1

0.0

0.0

1.10 (-1.06, 3.25)

0.00 (0.00, 0.00)

SYNCOPE VASOVAGAL

1.1

0.0

0.0

1.10 (-1.06, 3.25)

0.00 (0.00, 0.00)

CARDIAC DISORDER

1.1

0.0

0.0

1.10 (-1.06, 3.25)

0.00 (0.00, 0.00)

INFLUENZA

1.1

0.8

1.0

0.08 (-2.87, 3.02)

-0.21 (-2.77, 2.34)

NEPHROLITHIASIS

1.1

0.0

0.0

1.10 (-1.05, 3.25)

0.00 (0.00, 0.00)

URINARY TRACT INFECTION

1.1

0.0

2.1

-0.99 (-4.60, 2.62)

-2.09 (-4.99, 0.81)

LOWER RESPIRATORY TRACT
 INFECTION

1.1

0.0

0.0

1.10 (-1.05, 3.25)

0.00 (0.00, 0.00)

ACROCHORDON EXCISION

1.1

0.0

0.0

1.10 (-1.05, 3.24)

0.00 (0.00, 0.00)

FLANK PAIN

1.1

0.0

0.0

1.10 (-1.05, 3.24)

0.00 (0.00, 0.00)

HYPERSOMNIA

1.1

0.0

0.0

1.10 (-1.05, 3.24)

0.00 (0.00, 0.00)

CALCULUS URETHRAL

1.1

0.0

0.0

1.10 (-1.05, 3.24)

0.00 (0.00, 0.00)

SYNCOPE

1.1

2.4

0.0

1.09 (-1.05, 3.24)

2.42 (-0.32, 5.17)

FACIAL BONES FRACTURE

1.1

0.0

0.0

1.09 (-1.05, 3.24)

0.00 (0.00, 0.00)

FALL

1.1

1.6

1.0

0.09 (-2.83, 3.00)

0.60 (-2.38, 3.58)

ACTINIC KERATOSIS

1.1

0.0

0.0

1.09 (-1.05, 3.24)

0.00 (0.00, 0.00)

APPLICATION SITE REACTION

1.1

0.0

1.0

0.06 (-2.88, 3.01)

-1.03 (-3.05, 0.99)

ERECTILE DYSFUNCTION

1.1

0.0

1.0

0.07 (-2.86, 3.00)

-1.02 (-3.02, 0.98)

ATRIAL FLUTTER

1.1

0.8

0.0

1.09 (-1.05, 3.23)

0.81 (-0.77, 2.39)

ATRIAL FIBRILLATION

1.1

1.6

0.0

1.09 (-1.05, 3.23)

1.63 (-0.63, 3.90)

EXCORIATION

1.1

0.8

0.0

1.09 (-1.05, 3.23)

0.81 (-0.78, 2.39)

BLISTER

1.1

1.6

0.0

1.09 (-1.05, 3.23)

1.62 (-0.62, 3.86)

PARAESTHESIA

1.1

0.0

0.0

1.09 (-1.05, 3.23)

0.00 (0.00, 0.00)

DELUSION

1.1

0.0

1.0

0.08 (-2.84, 2.99)

-1.01 (-2.99, 0.97)

HALLUCINATION

1.1

0.0

0.0

1.09 (-1.05, 3.22)

0.00 (0.00, 0.00)

BLOOD GLUCOSE INCREASED

1.1

0.8

0.0

1.09 (-1.05, 3.22)

0.80 (-0.77, 2.37)

PROSTATE CANCER

1.1

0.0

0.0

1.09 (-1.04, 3.22)

0.00 (0.00, 0.00)

PAROSMIA

1.1

0.0

0.0

1.09 (-1.04, 3.21)

0.00 (0.00, 0.00)

RHINORRHOEA

1.1

0.8

0.0

1.08 (-1.04, 3.20)

0.81 (-0.78, 2.39)

ABDOMINAL PAIN

0.0

1.6

1.0

-1.03 (-3.04, 0.98)

0.58 (-2.42, 3.57)

AGITATION

0.0

1.6

1.0

-1.01 (-2.98, 0.97)

0.59 (-2.38, 3.56)

ALOPECIA

0.0

0.0

1.0

-1.00 (-2.97, 0.96)

-1.00 (-2.97, 0.96)

ANXIETY

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.81 (-0.78, 2.39)

APPLICATION SITE BLEEDING

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.76, 2.36)

APPLICATION SITE
 DESQUAMATION

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.76, 2.36)

APPLICATION SITE INDURATION

0.0

0.0

1.0

-1.01 (-2.99, 0.97)

-1.01 (-2.99, 0.97)

APPLICATION SITE URTICARIA

0.0

1.6

0.0

0.00 (0.00, 0.00)

1.64 (-0.63, 3.91)

ASTHENIA

0.0

0.8

1.0

-1.03 (-3.06, 0.99)

-0.23 (-2.79, 2.33)

ATRIOVENTRICULAR BLOCK FIRST
 DEGREE

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.81 (-0.77, 2.39)

ATRIOVENTRICULAR BLOCK
 SECOND DEGREE

0.0

0.0

1.0

-1.02 (-3.02, 0.98)

-1.02 (-3.02, 0.98)

BALANCE DISORDER

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.36)

BLEEDING ANOVULATORY

0.0

0.8

1.0

-1.01 (-2.98, 0.97)

-0.21 (-2.73, 2.31)

BLOOD ALKALINE PHOSPHATASE
 INCREASED

0.0

0.0

1.0

-1.01 (-3.00, 0.97)

-1.01 (-3.00, 0.97)

BLOOD CREATINE
 PHOSPHOKINASE INCREASED

0.0

0.0

1.0

-1.01 (-2.99, 0.97)

-1.01 (-2.99, 0.97)

BLOOD URINE PRESENT

0.0

0.0

1.0

-1.03 (-3.04, 0.98)

-1.03 (-3.04, 0.98)

BODY TEMPERATURE INCREASED

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.76, 2.36)

BRONCHITIS

0.0

0.0

1.0

-1.02 (-3.00, 0.97)

-1.02 (-3.00, 0.97)

BUNDLE BRANCH BLOCK LEFT

0.0

0.0

1.0

-1.00 (-2.97, 0.96)

-1.00 (-2.97, 0.96)

BUNDLE BRANCH BLOCK RIGHT

0.0

0.8

1.0

-1.02 (-3.01, 0.98)

-0.21 (-2.75, 2.33)

CATARACT OPERATION

0.0

0.0

1.0

-1.02 (-3.03, 0.98)

-1.02 (-3.03, 0.98)

CELLULITIS

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

CERUMEN IMPACTION

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

CERVICITIS

0.0

0.0

1.0

-1.03 (-3.05, 0.99)

-1.03 (-3.05, 0.99)

COLON CANCER

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.79 (-0.76, 2.35)

COMPLEX PARTIAL SEIZURES

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.76, 2.36)

CONJUNCTIVAL HAEMORRHAGE

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

CONJUNCTIVITIS

0.0

0.0

1.0

-1.01 (-2.98, 0.97)

-1.01 (-2.98, 0.97)

CONSTIPATION

0.0

0.0

1.0

-1.03 (-3.04, 0.98)

-1.03 (-3.04, 0.98)

COORDINATION ABNORMAL

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.76, 2.36)

CYSTOSCOPY

0.0

0.0

1.0

-1.03 (-3.04, 0.98)

-1.03 (-3.04, 0.98)

DECREASED APPETITE

0.0

0.0

1.0

-1.02 (-3.02, 0.98)

-1.02 (-3.02, 0.98)

DEHYDRATION

0.0

0.0

1.0

-1.02 (-3.03, 0.98)

-1.02 (-3.03, 0.98)

DEPRESSED MOOD

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

DISORIENTATION

0.0

0.0

1.0

-1.02 (-3.02, 0.98)

-1.02 (-3.02, 0.98)

DISTURBANCE IN SEXUAL
 AROUSAL

0.0

0.0

1.0

-1.00 (-2.96, 0.96)

-1.00 (-2.96, 0.96)

DRUG ERUPTION

0.0

0.0

1.0

-1.01 (-2.98, 0.97)

-1.01 (-2.98, 0.97)

DYSPEPSIA

0.0

0.8

1.0

-1.03 (-3.06, 0.99)

-0.22 (-2.80, 2.36)

DYSPHONIA

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

DYSPNOEA

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

DYSURIA

0.0

0.8

1.0

-1.03 (-3.06, 0.99)

-0.24 (-2.79, 2.30)

EAR INFECTION

0.0

0.0

2.0

-2.05 (-4.89, 0.79)

-2.05 (-4.89, 0.79)

EAR PAIN

0.0

0.0

1.0

-1.01 (-3.00, 0.97)

-1.01 (-3.00, 0.97)

ELECTROCARDIOGRAM ST
 SEGMENT DEPRESSION

0.0

0.8

3.1

-3.11 (-6.62, 0.41)

-2.30 (-6.16, 1.55)

ELECTROCARDIOGRAM T WAVE
 AMPLITUDE DECREASED

0.0

0.8

1.0

-1.02 (-3.02, 0.98)

-0.21 (-2.76, 2.33)

EMPHYSEMA

0.0

0.0

1.0

-1.03 (-3.04, 0.99)

-1.03 (-3.04, 0.99)

EYE ALLERGY

0.0

0.0

1.0

-1.01 (-3.00, 0.97)

-1.01 (-3.00, 0.97)

EYE LASER SURGERY

0.0

0.0

1.0

-1.03 (-3.06, 0.99)

-1.03 (-3.06, 0.99)

EYE PRURITUS

0.0

0.0

1.0

-1.01 (-2.99, 0.97)

-1.01 (-2.99, 0.97)

EYE SWELLING

0.0

0.0

1.0

-1.01 (-3.00, 0.97)

-1.01 (-3.00, 0.97)

GASTROENTERITIS VIRAL

0.0

0.0

1.0

-1.03 (-3.06, 0.99)

-1.03 (-3.06, 0.99)

GASTROOESOPHAGEAL REFLUX
 DISEASE

0.0

0.0

1.0

-1.03 (-3.06, 0.99)

-1.03 (-3.06, 0.99)

GLOSSITIS

0.0

0.0

1.0

-1.01 (-2.98, 0.97)

-1.01 (-2.98, 0.97)

HEMIANOPIA HOMONYMOUS

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.81 (-0.78, 2.39)

HIATUS HERNIA

0.0

0.0

1.0

-1.00 (-2.97, 0.96)

-1.00 (-2.97, 0.96)

HIP FRACTURE

0.0

0.0

1.0

-1.01 (-3.00, 0.97)

-1.01 (-3.00, 0.97)

HOT FLUSH

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.81 (-0.78, 2.40)

HYPERTENSION

0.0

0.8

1.0

-1.03 (-3.04, 0.99)

-0.23 (-2.78, 2.32)

HYPOTENSION

0.0

0.8

2.1

-2.07 (-4.93, 0.80)

-1.26 (-4.53, 2.00)

INCONTINENCE

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.38)

IRRITABILITY

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.81 (-0.78, 2.39)

JOINT DISLOCATION

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.38)

LETHARGY

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.38)

LOCALISED INFECTION

0.0

0.0

1.0

-1.03 (-3.04, 0.99)

-1.03 (-3.04, 0.99)

MICTURITION URGENCY

0.0

0.8

1.0

-1.02 (-3.03, 0.98)

-0.22 (-2.77, 2.32)

MUSCLE SPASMS

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.81 (-0.78, 2.40)

MUSCULAR WEAKNESS

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

NASAL MUCOSA BIOPSY

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

OEDEMA

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.81 (-0.78, 2.40)

ORTHOSTATIC HYPOTENSION

0.0

0.0

1.0

-1.02 (-3.03, 0.98)

-1.02 (-3.03, 0.98)

PALPITATIONS

0.0

1.6

0.0

0.00 (0.00, 0.00)

1.62 (-0.62, 3.86)

PARAESTHESIA ORAL

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

PARKINSON'S DISEASE

0.0

0.0

1.0

-1.03 (-3.05, 0.99)

-1.03 (-3.05, 0.99)

PELVIC PAIN

0.0

0.0

1.0

-1.03 (-3.06, 0.99)

-1.03 (-3.06, 0.99)

PNEUMONIA

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

POSTNASAL DRIP

0.0

0.0

1.0

-1.01 (-2.99, 0.97)

-1.01 (-2.99, 0.97)

PSYCHOMOTOR HYPERACTIVITY

0.0

0.0

1.0

-1.01 (-2.99, 0.97)

-1.01 (-2.99, 0.97)

PYREXIA

0.0

0.8

2.1

-2.07 (-4.95, 0.80)

-1.27 (-4.55, 2.01)

RASH ERYTHEMATOUS

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.36)

RECTAL HAEMORRHAGE

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

RESTLESSNESS

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.38)

SECRETION DISCHARGE

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

SHOULDER PAIN

0.0

0.8

1.0

-1.01 (-2.99, 0.97)

-0.21 (-2.74, 2.32)

SINUS ARRHYTHMIA

0.0

0.0

1.0

-1.01 (-2.99, 0.97)

-1.01 (-2.99, 0.97)

SKIN LACERATION

0.0

1.6

0.0

0.00 (0.00, 0.00)

1.62 (-0.62, 3.86)

SKIN ULCER

0.0

0.0

1.0

-1.03 (-3.06, 0.99)

-1.03 (-3.06, 0.99)

STUPOR

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.79 (-0.76, 2.35)

SUDDEN DEATH

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.37)

SUPRAVENTRICULAR
 EXTRASYSTOLES

0.0

0.8

1.0

-1.02 (-3.01, 0.98)

-0.22 (-2.75, 2.32)

SUPRAVENTRICULAR
 TACHYCARDIA

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.81 (-0.77, 2.39)

TACHYCARDIA

0.0

0.0

1.0

-1.01 (-2.99, 0.97)

-1.01 (-2.99, 0.97)

ULCER

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.76, 2.35)

VAGINAL MYCOSIS

0.0

0.0

1.0

-1.03 (-3.05, 0.99)

-1.03 (-3.05, 0.99)

WEIGHT DECREASED

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.79 (-0.76, 2.35)

WOLFF-PARKINSON-WHITE
 SYNDROME

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.80 (-0.77, 2.38)

WOUND

0.0

0.8

0.0

0.00 (0.00, 0.00)

0.81 (-0.77, 2.39)

Key: EAIR=exposure-adjusted incidence rate, SY=subject years

a Subject years is the sum of all exposures per treatment group.

Note: EAIR is defined for each event as the number or subjects with an event divided by the sum of the at-risk exposure time. At-risk exposure time is calculated from [Day 1 to first onset of a specified event; for subjects with no event, it is the time from Day 1 to treatment discontinuation /completion date].

Note: Adverse events are coded using MedDRA version 26.0.

Download RTF file

TSFAE12
TSFAE14
Source Code
---
title: TSFAE13
subtitle: Exposure-adjusted Incidence Rate Analysis by 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:              tsfae13.R

# Prep environment:

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

# Define script level parameters:

tblid <- "TSFAE13"
fileid <- tblid
popfl <- "SAFFL"
trtvar <- "TRT01A"
ctrl_grp <- "Placebo"
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

# Process data:

adexsum <- pharmaverseadamjnj::adexsum %>%
  filter(!!rlang::sym(popfl) == "Y" & PARAMCD == "TRTDURY") %>%
  create_colspan_var(
    non_active_grp = ctrl_grp,
    non_active_grp_span_lbl = " ",
    active_grp_span_lbl = "Active Study Agent",
    colspan_var = "colspan_trt",
    trt_var = trtvar
  ) %>%
  mutate(
    rrisk_header = "Risk Difference (95% CI)",
    rrisk_label = paste(!!rlang::sym(trtvar), "vs", ctrl_grp),
    TRTDURY = AVAL
  ) %>%
  select(
    USUBJID,
    !!rlang::sym(trtvar),
    colspan_trt,
    rrisk_header,
    rrisk_label,
    TRTDURY
  )

adae <- pharmaverseadamjnj::adae %>%
  filter(TRTEMFL == "Y" & AOCCPFL == "Y") %>%
  select(USUBJID, AEDECOD, ASTDY, AOCCPFL)

#  join -- -- subjects without ae will be handled via alt_counts_df dataframe
aefup <- right_join(adae, adexsum, by = "USUBJID")

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

# Define layout and build table:

lyt <- basic_table(
  show_colcounts = TRUE,
  colcount_format = "N=xx",
  top_level_section_div = " "
) %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  ) %>%
  split_cols_by(trtvar) %>%
  split_cols_by("rrisk_header", nested = FALSE) %>%
  split_cols_by(
    trtvar,
    labels_var = "rrisk_label",
    split_fun = remove_split_levels(ctrl_grp)
  ) %>%
  analyze(
    "TRTDURY",
    nested = FALSE,
    show_labels = "hidden",
    afun = a_patyrs_j,
    extra_args = list(.labels = c(patyrs = "Subject years\u1D43"))
  ) %>%
  analyze(
    vars = "AEDECOD",
    nested = FALSE,
    afun = a_eair100_j,
    extra_args = list(
      fup_var = "TRTDURY",
      occ_var = "AOCCPFL",
      occ_dy = "ASTDY",
      ref_path = ref_path,
      drop_levels = TRUE
    )
  ) %>%
  append_topleft("Preferred Term, EAIR Per 100 SY")


result <- build_table(lyt, aefup, alt_counts_df = adexsum)

# Post-Processing:

result <- result %>%
  sort_at_path(
    path = c("AEDECOD"),
    scorefun = jj_complex_scorefun(colpath = "Xanomeline High Dose")
  )

result <- remove_col_count(result)

# 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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