TL Catalog
  1. Listings
  2. Adverse Events
  3. LSFAE06A
  • 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. Listings
  2. Adverse Events
  3. LSFAE06A

LSFAE06A

Selected Narrow / Broad OCMQs


Output

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Code
# Program Name:              lsfae06a.R

# Prep environment

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

# Define script level parameters

tblid <- "LSFAE06a"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map
popfl <- "SAFFL"
trtvar <- "TRT01A"
ocmqclass <- "Narrow"
key_cols <- c("COL0", "COL1", "COL2", "COL3")
disp_cols <- paste0("COL", 0:8)
concat_sep <- " / "
# Parameter to control whether time should be displayed
include_time <- TRUE

# Process data

adaeocmq <- pharmaverseadamjnj::adaeocmq |>
  filter(
    !!sym(popfl) == "Y" &
      !is.na(OCMQNAM) &
      OCMQCLSS == ocmqclass &
      TRTEMFL == "Y"
  )

lsting <- adaeocmq |>
  mutate(
    AGE = explicit_na(as.character(AGE), ""),
    SEX = explicit_na(SEX, ""),
    RACE_DECODE = explicit_na(RACE_DECODE, ""),
    AEDECOD = explicit_na(AEDECOD, ""),
    AETERM = ifelse(
      is.na(AETERM),
      "",
      string_to_title(gsub("\\$", "", AETERM))
    ),
    ASTDT = ifelse(
      nchar(as.character(ASTDT)) == 10,
      toupper(format(ASTDT, "%d%b%Y")),
      ""
    ),
    ASTTM = ifelse(
      include_time & !is.na(ASTDTM),
      substr(as.character(ASTDTM), 12, 16),
      ""
    ),
    ASTDYN = ifelse(!is.na(ASTDY), ASTDY, NA),
    ASTDY = ifelse(!is.na(ASTDY), ASTDY, ""),
    ASTDTFS = ifelse(!is.na(ASTDTF), "*", ""),
    AENDT = explicit_na(as.character(AENDT), ""),
    AENDT = ifelse(
      nchar(AENDT) == 10,
      toupper(format(as.Date(AENDT), "%d%b%Y")),
      ""
    ),
    AENTM = ifelse(
      include_time & !is.na(AENDTM),
      substr(as.character(AENDTM), 12, 16),
      ""
    ),
    AENDY = ifelse(!is.na(AENDY), AENDY, ""),
    AENDTFS = ifelse(!is.na(AENDTF), "*", ""),
    AEOUTC = explicit_na(AEOUT_DECODE, ""),
    AESEV = explicit_na(AESEV, ""),
    AESER_DECODE = explicit_na(AESER_DECODE, ""),
    COL0 = OCMQNAM,
    COL1 = explicit_na(.data[[trtvar]], ""),
    COL2 = explicit_na(USUBJID, ""),
    COL3 = paste(AGE, SEX, RACE_DECODE, sep = concat_sep),
    COL4 = paste(AEDECOD, AETERM, sep = concat_sep),
    COL5 = case_when(
      ASTDT == "" ~ "",
      include_time & ASTDT != "" & ASTTM != "" & ASTDY != "" & ASTDTFS != "" ~
        paste0(ASTDT, concat_sep, ASTTM, " (", ASTDY, ")", ASTDTFS),
      include_time & ASTDT != "" & ASTTM != "" & ASTDY != "" & ASTDTFS == "" ~
        paste0(ASTDT, concat_sep, ASTTM, " (", ASTDY, ")"),
      include_time & ASTDT != "" & ASTTM == "" & ASTDY != "" & ASTDTFS != "" ~
        paste0(ASTDT, concat_sep, "--:--", " (", ASTDY, ")", ASTDTFS),
      include_time & ASTDT != "" & ASTTM == "" & ASTDY != "" & ASTDTFS == "" ~
        paste0(ASTDT, concat_sep, "--:--", " (", ASTDY, ")"),
      ASTDT != "" & ASTDY != "" & ASTDTFS != "" ~
        paste0(ASTDT, " (", ASTDY, ")", ASTDTFS),
      ASTDT != "" & ASTDY != "" & ASTDTFS == "" ~
        paste0(ASTDT, " (", ASTDY, ")"),
    ),
    COL6 = case_when(
      AENDT == "" ~ "",
      include_time & AENDT != "" & AENTM != "" & AENDY != "" & AENDTFS != "" ~
        paste0(AENDT, concat_sep, AENTM, " (", AENDY, ")", AENDTFS),
      include_time & AENDT != "" & AENTM != "" & AENDY != "" & AENDTFS == "" ~
        paste0(AENDT, concat_sep, AENTM, " (", AENDY, ")"),
      include_time & AENDT != "" & AENTM == "" & AENDY != "" & AENDTFS != "" ~
        paste0(AENDT, concat_sep, "--:--", " (", AENDY, ")", AENDTFS),
      include_time & AENDT != "" & AENTM == "" & AENDY != "" & AENDTFS == "" ~
        paste0(AENDT, concat_sep, "--:--", " (", AENDY, ")"),
      AENDT != "" & AENDY != "" & AENDTFS != "" ~
        paste0(AENDT, " (", AENDY, ")", AENDTFS),
      AENDT != "" & AENDY != "" & AENDTFS == "" ~
        paste0(AENDT, " (", AENDY, ")"),
    ),
    COL7 = explicit_na(AEACN_DECODE, ""),
    COL8 = paste(AEOUTC, AESEV, AESER_DECODE, sep = concat_sep)
  ) |>
  arrange(
    COL0,
    COL1,
    COL2,
    !is.na(ASTDYN),
    ASTDYN,
    if (include_time) ASTDTM else ASTDT,
    AEDECOD,
    AETERM
  )

lsting <- var_relabel(
  lsting,
  COL0 = "OCMQ",
  COL1 = "Treatment Group",
  COL2 = "Subject ID",
  COL3 = paste("Age (years)", "Sex", "Race", sep = concat_sep),
  COL4 = paste("Preferred Term", "Reported Term", sep = concat_sep),
  COL5 = if (include_time) {
    paste("Start Date", "Time (Study Day~[super a])", sep = concat_sep)
  } else {
    "Start Date (Study Day~[super a])"
  },
  COL6 = if (include_time) {
    paste("End Date", "Time (Study Day~[super a])", sep = concat_sep)
  } else {
    "End Date (Study Day~[super a])"
  },
  COL7 = "Action Taken With Study Treatment",
  COL8 = paste("Outcome", "Severity", "Serious", sep = concat_sep)
)

# Build listing

result <- rlistings::as_listing(
  df = lsting,
  key_cols = key_cols,
  disp_cols = disp_cols
)

# Add titles and footnotes:

result <- set_titles(result, tab_titles)

# Output listing

tt_to_tlgrtf(string_map = string_map, tt = head(result, 100), file = fileid, orientation = "landscape")

LSFAE06a: Selected [Narrow / Broad] FDA Medical Queries; Safety Analysis Set (Study jjcs - core)

OCMQ

Treatment Group

Subject ID

Age (years) / Sex / Race

Preferred Term / Reported Term

Start Date / Time (Study Daya)

End Date / Time (Study Daya)

Action Taken With Study Treatment

Outcome / Severity / Serious

Abdominal Pain

Xanomeline High Dose

01-701-1302

61 / M / Asian

STOMACH DISCOMFORT / Stomach Discomfort

30AUG2013 / 00:00 (2)

Dose Not Changed

Not Recovered/Not Resolved / Mild / Yes

01-704-1065

75 / M / Multiple

ABDOMINAL DISCOMFORT / Abdominal Discomfort

26OCT2013 / 00:00 (3)

Unknown

Not Recovered/Not Resolved / Mild / Yes

Xanomeline Low Dose

01-705-1393

84 / F / Native Hawaiian or other Pacific Islander

ABDOMINAL PAIN / Abdominal Pain

19SEP2012 / 00:00 (13)

24SEP2012 / 23:59 (18)

Unknown

Recovered/Resolved / Mild / No

01-716-1311

78 / M / Black or African American

ABDOMINAL PAIN / Abdominal Pain

22JUL2014 / 00:00 (70)

02AUG2014 / 23:59 (81)

Dose Rate Reduced

Recovered/Resolved / Moderate / Yes

Placebo

01-708-1286

80 / F / Unknown

ABDOMINAL PAIN / Abdominal Pain

18FEB2014 / 00:00 (162)

18FEB2014 / 23:59 (162)

Unknown

Recovered/Resolved / Mild / Yes

Abnormal Uterine Bleeding

Xanomeline High Dose

01-701-1034

77 / F / White

ABNORMAL UTERINE BLEEDING / Abnormal Uterine Bleeding

27AUG2014 / 00:00 (58)

Not Applicable

Not Recovered/Not Resolved / Mild / Yes

Acute Coronary Syndrome

Xanomeline High Dose

01-704-1017

77 / M / Asian

MYOCARDIAL INFARCTION / Myocardial Infarction

19OCT2013 / 00:00 (14)

Drug Withdrawn

Not Recovered/Not Resolved / Mild / Yes

01-710-1142

76 / F / Not reported

MYOCARDIAL INFARCTION / Myocardial Infarction

19OCT2012 / 00:00 (18)

19OCT2012 / 23:59 (18)

Not Applicable

Recovered/Resolved / Moderate / Yes

01-718-1101

82 / M / Asian

MYOCARDIAL INFARCTION / Myocardial Infarction

06JUL2013 / 00:00 (140)

Dose Reduced

Not Recovered/Not Resolved / Mild / No

Xanomeline Low Dose

01-708-1348

79 / F / Multiple

MYOCARDIAL INFARCTION / Myocardial Infarction

18AUG2013 / 00:00 (14)

31AUG2013 / 23:59 (27)

Dose Rate Reduced

Not Recovered/Not Resolved / Mild / Yes

MYOCARDIAL INFARCTION / Myocardial Infarction

18AUG2013 / 00:00 (14)

31AUG2013 / 23:59 (27)

Dose Not Changed

Recovered/Resolved / Mild / Yes

Placebo

01-703-1299

81 / F / Black or African American

MYOCARDIAL INFARCTION / Myocardial Infarction

13MAR2013 / 00:00 (183)

Dose Reduced

Not Recovered/Not Resolved / Moderate / Yes

01-708-1286

80 / F / Unknown

MYOCARDIAL INFARCTION / Myocardial Infarction

23SEP2013 / 00:00 (14)

Drug Interrupted

Not Recovered/Not Resolved / Mild / No

01-710-1083

89 / F / White

MYOCARDIAL INFARCTION / Myocardial Infarction

02AUG2013 / 00:00 (12)

02AUG2013 / 23:59 (12)

Dose Rate Reduced

Fatal / Severe / Yes

Alopecia

Placebo

01-717-1201

85 / F / Native Hawaiian or other Pacific Islander

ALOPECIA / Alopecia

15JAN2014 / 00:00 (28)

Dose Not Changed

Not Recovered/Not Resolved / Mild / No

Anxiety

Xanomeline Low Dose

01-717-1004

80 / F / Not reported

ANXIETY / Anxiety

15JAN2014 / 00:00 (2)

Unknown

Not Recovered/Not Resolved / Mild / Yes

Arrhythmia

Xanomeline High Dose

01-704-1008

76 / F / White

SINUS BRADYCARDIA / Sinus Bradycardia

25FEB2013 / 00:00 (44)

Dose Rate Reduced

Not Recovered/Not Resolved / Moderate / Yes

01-704-1065

75 / M / Multiple

SINUS BRADYCARDIA / Sinus Bradycardia

24DEC2013 / 00:00 (62)

Unknown

Not Recovered/Not Resolved / Mild / No

01-704-1266

82 / M / Multiple

ATRIAL FLUTTER / Atrial Flutter

27OCT2013 / 00:00 (15)

08NOV2013 / 23:59 (27)

Dose Reduced

Not Recovered/Not Resolved / Mild / Yes

ATRIAL FLUTTER / Atrial Flutter

27OCT2013 / 00:00 (15)

08NOV2013 / 23:59 (27)

Dose Increased

Recovered/Resolved / Mild / Yes

ATRIAL FIBRILLATION / Atrial Fibrillation

08NOV2013 / 00:00 (27)

06DEC2013 / 23:59 (55)

Not Applicable

Not Recovered/Not Resolved / Mild / No

ATRIAL FIBRILLATION / Atrial Fibrillation

08NOV2013 / 00:00 (27)

06DEC2013 / 23:59 (55)

Not Applicable

Recovered/Resolved / Mild / No

01-710-1006

77 / M / Asian

SINUS BRADYCARDIA / Sinus Bradycardia

29JUN2013 / 00:00 (140)

04JUL2013 / 23:59 (145)

Dose Increased

Not Recovered/Not Resolved / Moderate / No

SINUS BRADYCARDIA / Sinus Bradycardia

29JUN2013 / 00:00 (140)

04JUL2013 / 23:59 (145)

Not Applicable

Recovered/Resolved / Moderate / Yes

01-714-1288

77 / M / Multiple

SINUS BRADYCARDIA / Sinus Bradycardia

27MAY2014 / 00:00 (175)

Drug Interrupted

Not Recovered/Not Resolved / Moderate / No

01-715-1319

65 / M / Multiple

SINUS BRADYCARDIA / Sinus Bradycardia

18MAR2013 / 00:00 (30)

18MAR2013 / 23:59 (30)

Drug Interrupted

Recovered/Resolved / Moderate / No

01-715-1321

75 / F / Native Hawaiian or other Pacific Islander

SINUS BRADYCARDIA / Sinus Bradycardia

22APR2014 / 00:00 (71)

Dose Rate Reduced

Not Recovered/Not Resolved / Mild / Yes

01-717-1109

84 / M / Asian

VENTRICULAR EXTRASYSTOLES / Ventricular Extrasystoles

18APR2014 / 00:00 (82)

Dose Increased

Not Recovered/Not Resolved / Mild / No

01-718-1101

82 / M / Asian

SINUS BRADYCARDIA / Sinus Bradycardia

13APR2013 / 00:00 (56)

12MAY2013 / 23:59 (85)

Dose Rate Reduced

Not Recovered/Not Resolved / Mild / No

SINUS BRADYCARDIA / Sinus Bradycardia

13APR2013 / 00:00 (56)

12MAY2013 / 23:59 (85)

Dose Reduced

Recovered/Resolved / Mild / No

Xanomeline Low Dose

01-708-1213

76 / F / Unknown

ATRIAL FIBRILLATION / Atrial Fibrillation

22FEB2013 / 00:00 (14)

22FEB2013 / 23:59 (14)

Dose Increased

Not Recovered/Not Resolved / Mild / No

ATRIAL FIBRILLATION / Atrial Fibrillation

22FEB2013 / 00:00 (14)

22FEB2013 / 23:59 (14)

Drug Interrupted

Recovered/Resolved / Mild / No

01-708-1272

82 / M / Not reported

VENTRICULAR EXTRASYSTOLES / Ventricular Extrasystoles

21FEB2013 / 00:00 (16)

20MAR2013 / 23:59 (43)

Unknown

Not Recovered/Not Resolved / Mild / Yes

VENTRICULAR EXTRASYSTOLES / Ventricular Extrasystoles

21FEB2013 / 00:00 (16)

20MAR2013 / 23:59 (43)

Dose Increased

Recovered/Resolved / Mild / No

01-708-1297

61 / M / Not reported

SINUS BRADYCARDIA / Sinus Bradycardia

08MAY2013 / 00:00 (104)

Not Applicable

Not Recovered/Not Resolved / Mild / No

01-709-1285

87 / M / Native Hawaiian or other Pacific Islander

SINUS BRADYCARDIA / Sinus Bradycardia

19MAY2013 / 00:00 (57)

Not Applicable

Not Recovered/Not Resolved / Mild / Yes

01-710-1385

77 / M / Multiple

SUPRAVENTRICULAR TACHYCARDIA / Supraventricular Tachycardia

12NOV2012 / 00:00 (15)

13NOV2012 / 23:59 (16)

Drug Interrupted

Not Recovered/Not Resolved / Moderate / No

SUPRAVENTRICULAR TACHYCARDIA / Supraventricular Tachycardia

12NOV2012 / 00:00 (15)

13NOV2012 / 23:59 (16)

Dose Increased

Recovered/Resolved / Moderate / No

ATRIAL FIBRILLATION / Atrial Fibrillation

18FEB2013 / 00:00 (113)

Drug Interrupted

Not Recovered/Not Resolved / Moderate / No

01-711-1143

76 / F / Black or African American

SUPRAVENTRICULAR EXTRASYSTOLES / Supraventricular Extrasystoles

29APR2013 / 00:00 (27)

15MAY2013 / 23:59 (43)

Unknown

Not Recovered/Not Resolved / Mild / No

SUPRAVENTRICULAR EXTRASYSTOLES / Supraventricular Extrasystoles

29APR2013 / 00:00 (27)

15MAY2013 / 23:59 (43)

Drug Interrupted

Recovered/Resolved / Mild / No

VENTRICULAR EXTRASYSTOLES / Ventricular Extrasystoles

28MAY2013 / 00:00 (56)

01JUN2013 / 23:59 (60)

Dose Not Changed

Not Recovered/Not Resolved / Moderate / Yes

VENTRICULAR EXTRASYSTOLES / Ventricular Extrasystoles

28MAY2013 / 00:00 (56)

01JUN2013 / 23:59 (60)

Unknown

Recovered/Resolved / Moderate / Yes

01-715-1405

69 / M / Unknown

SINUS BRADYCARDIA / Sinus Bradycardia

13JUL2013 / 00:00 (8)

13JUL2013 / 23:59 (8)

Unknown

Not Recovered/Not Resolved / Moderate / Yes

SINUS BRADYCARDIA / Sinus Bradycardia

13JUL2013 / 00:00 (8)

13JUL2013 / 23:59 (8)

Dose Not Changed

Recovered/Resolved / Moderate / Yes

01-716-1094

82 / M / Black or African American

ATRIAL FLUTTER / Atrial Flutter

19JAN2013 / 00:00 (32)

Not Applicable

Not Recovered/Not Resolved / Moderate / Yes

01-717-1004

80 / F / Not reported

SINUS BRADYCARDIA / Sinus Bradycardia

08APR2014 / 00:00 (85)

Drug Interrupted

Not Recovered/Not Resolved / Mild / No

Placebo

01-703-1299

81 / F / Black or African American

TACHYCARDIA / Tachycardia

01MAR2013 / 00:00 (171)

Dose Increased

Not Recovered/Not Resolved / Mild / Yes

TACHYCARDIA / Tachycardia

01MAR2013 / 00:00 (171)

Dose Not Changed

Not Recovered/Not Resolved / Moderate / Yes

01-707-1206

65 / M / Native Hawaiian or other Pacific Islander

SINUS ARRHYTHMIA / Sinus Arrhythmia

25NOV2013 / 00:00 (29)

23DEC2013 / 23:59 (57)

Dose Rate Reduced

Not Recovered/Not Resolved / Mild / No

SINUS ARRHYTHMIA / Sinus Arrhythmia

25NOV2013 / 00:00 (29)

23DEC2013 / 23:59 (57)

Dose Reduced

Recovered/Resolved / Mild / Yes

01-714-1035

88 / F / Black or African American

SUPRAVENTRICULAR EXTRASYSTOLES / Supraventricular Extrasystoles

04JUN2014 / 00:00 (49)

17JUN2014 / 23:59 (62)

Dose Increased

Not Recovered/Not Resolved / Mild / Yes

SUPRAVENTRICULAR EXTRASYSTOLES / Supraventricular Extrasystoles

04JUN2014 / 00:00 (49)

17JUN2014 / 23:59 (62)

Drug Interrupted

Recovered/Resolved / Mild / Yes

Arthralgia

Xanomeline High Dose

01-714-1288

77 / M / Multiple

ARTHRALGIA / Arthralgia

08MAR2014 / 00:00 (95)

Dose Rate Reduced

Not Recovered/Not Resolved / Moderate / Yes

Xanomeline Low Dose

01-701-1111

81 / F / White

ARTHRALGIA / Arthralgia

13SEP2012 / 00:00 (7)

Unknown

Not Recovered/Not Resolved / Moderate / No

Back Pain

Xanomeline High Dose

01-701-1148

57 / M / Not reported

FLANK PAIN / Flank Pain

15DEC2013 / 00:00 (115)

17DEC2013 / 23:59 (117)

Unknown

Recovered/Resolved / Moderate / Yes

01-713-1141

79 / M / White

BACK PAIN / Back Pain

30JUN2013 / 00:00 (31)

Drug Interrupted

Not Recovered/Not Resolved / Moderate / Yes

01-714-1288

77 / M / Multiple

BACK PAIN / Back Pain

24FEB2014 / 00:00 (83)

08APR2014 / 23:59 (126)

Dose Increased

Not Recovered/Not Resolved / Mild / No

BACK PAIN / Back Pain

24FEB2014 / 00:00 (83)

08APR2014 / 23:59 (126)

Dose Not Changed

Recovered/Resolved / Mild / Yes

Xanomeline Low Dose

01-717-1004

80 / F / Not reported

BACK PAIN / Back Pain

21MAY2014 / 00:00 (128)

Dose Rate Reduced

Not Recovered/Not Resolved / Moderate / No

Placebo

01-701-1363

81 / F / White

BACK PAIN / Back Pain

13OCT2013 / 00:00 (137)

15OCT2013 / 23:59 (139)

Drug Interrupted

Not Recovered/Not Resolved / Mild / No

BACK PAIN / Back Pain

13OCT2013 / 00:00 (137)

15OCT2013 / 23:59 (139)

Dose Not Changed

Recovered/Resolved / Mild / No

Bacterial Infection

Xanomeline High Dose

01-701-1239

56 / M / White

HORDEOLUM / Hordeolum

01APR2014 / 00:00 (81)*

Drug Interrupted

Not Recovered/Not Resolved / Mild / Yes

01-710-1006

77 / M / Asian

URINARY TRACT INFECTION / Urinary Tract Infection

17APR2013 / 00:00 (67)

19APR2013 / 23:59 (69)

Dose Not Changed

Recovered/Resolved / Mild / No

Xanomeline Low Dose

01-701-1111

81 / F / White

CELLULITIS / Cellulitis

13SEP2012 / 00:00 (7)

Drug Interrupted

Not Recovered/Not Resolved / Moderate / Yes

Placebo

01-701-1130

84 / M / Other

URINARY TRACT INFECTION / Urinary Tract Infection

09MAR2014 / 00:00 (23)

16MAR2014 / 23:59 (30)

Drug Withdrawn

Not Recovered/Not Resolved / Mild / Yes

URINARY TRACT INFECTION / Urinary Tract Infection

09MAR2014 / 00:00 (23)

16MAR2014 / 23:59 (30)

Drug Withdrawn

Recovered/Resolved / Mild / No

01-713-1179

64 / F / American Indian or Alaska Native

URINARY TRACT INFECTION / Urinary Tract Infection

28AUG2013 / 00:00 (20)

08SEP2013 / 23:59 (31)

Dose Increased

Not Recovered/Not Resolved / Mild / No

URINARY TRACT INFECTION / Urinary Tract Infection

28AUG2013 / 00:00 (20)

08SEP2013 / 23:59 (31)

Unknown

Recovered/Resolved / Mild / No

Cardiac Conduction Disturbance

Xanomeline Low Dose

01-704-1025

81 / F / Asian

WOLFF-PARKINSON-WHITE SYNDROME / Wolff-parkinson-white Syndrome

25OCT2013 / 00:00 (29)

29NOV2013 / 23:59 (64)

Drug Interrupted

Not Recovered/Not Resolved / Mild / Yes

WOLFF-PARKINSON-WHITE SYNDROME / Wolff-parkinson-white Syndrome

25OCT2013 / 00:00 (29)

29NOV2013 / 23:59 (64)

Not Applicable

Recovered/Resolved / Mild / No

01-710-1385

77 / M / Multiple

ATRIOVENTRICULAR BLOCK FIRST DEGREE / Atrioventricular Block First Degree

26NOV2012 / 00:00 (29)

Not Applicable

Not Recovered/Not Resolved / Mild / No

01-716-1094

82 / M / Black or African American

BUNDLE BRANCH BLOCK RIGHT / Bundle Branch Block Right

19JAN2013 / 00:00 (32)

Dose Reduced

Not Recovered/Not Resolved / Moderate / Yes

Placebo

01-701-1023

64 / M / Black or African American

ATRIOVENTRICULAR BLOCK SECOND DEGREE / Atrioventricular Block Second Degree

26AUG2012 / 00:00 (22)

Dose Not Changed

Not Recovered/Not Resolved / Mild / Yes

01-701-1047

85 / F / Native Hawaiian or other Pacific Islander

BUNDLE BRANCH BLOCK LEFT / Bundle Branch Block Left

10MAR2013 / 00:00 (27)

Dose Reduced

Not Recovered/Not Resolved / Mild / No

01-714-1035

88 / F / Black or African American

BUNDLE BRANCH BLOCK RIGHT / Bundle Branch Block Right

26MAY2014 / 00:00 (40)

04JUN2014 / 23:59 (49)

Dose Increased

Not Recovered/Not Resolved / Mild / Yes

BUNDLE BRANCH BLOCK RIGHT / Bundle Branch Block Right

26MAY2014 / 00:00 (40)

04JUN2014 / 23:59 (49)

Dose Reduced

Recovered/Resolved / Mild / No

Confusional State

Xanomeline High Dose

01-713-1141

79 / M / White

DELIRIUM / Delirium

01JUL2013 / 00:00 (32)

15JUL2013 / 23:59 (46)

Drug Withdrawn

Recovered/Resolved / Moderate / No

01-717-1109

84 / M / Asian

CONFUSIONAL STATE / Confusional State

20FEB2014 / 00:00 (25)

Dose Not Changed

Not Recovered/Not Resolved / Mild / Yes

Xanomeline Low Dose

01-701-1211

76 / F / Other

CONFUSIONAL STATE / Confusional State

11JAN2013 / 00:00 (58)

Drug Interrupted

Not Recovered/Not Resolved / Moderate / No

01-715-1405

69 / M / Unknown

CONFUSIONAL STATE / Confusional State

08JUL2013 / 00:00 (3)

08JUL2013 / 23:59 (3)

Dose Rate Reduced

Recovered/Resolved / Moderate / No

01-718-1079

67 / F / White

CONFUSIONAL STATE / Confusional State

05OCT2012 / 00:00 (17)

Drug Interrupted

Not Recovered/Not Resolved / Moderate / Yes

Placebo

01-703-1210

72 / F / Not reported

DISORIENTATION / Disorientation

02APR2013 / 00:00 (18)

Drug Withdrawn

Not Recovered/Not Resolved / Mild / No

01-716-1044

74 / M / Not reported

CONFUSIONAL STATE / Confusional State

15OCT2013 / 00:00 (172)

Dose Increased

Not Recovered/Not Resolved / Mild / No

01-718-1355

79 / M / Native Hawaiian or other Pacific Islander

CONFUSIONAL STATE / Confusional State

17APR2013 / 00:00 (49)

Dose Not Changed

Not Recovered/Not Resolved / Moderate / Yes

Constipation

Placebo

01-708-1286

80 / F / Unknown

CONSTIPATION / Constipation

18FEB2014 / 00:00 (162)

18FEB2014 / 23:59 (162)

Dose Reduced

Recovered/Resolved / Mild / Yes

Cough

Xanomeline High Dose

01-701-1275

61 / M / White

COUGH / Cough

12MAR2014 / 00:00 (34)

27MAR2014 / 23:59 (49)

Not Applicable

Not Recovered/Not Resolved / Mild / Yes

COUGH / Cough

12MAR2014 / 00:00 (34)

27MAR2014 / 23:59 (49)

Not Applicable

Recovered/Resolved / Mild / Yes

01-701-1302

61 / M / Asian

PRODUCTIVE COUGH / Productive Cough

02SEP2013 / 00:00 (5)

Drug Interrupted

Not Recovered/Not Resolved / Mild / Yes

01-701-1383

72 / F / Native Hawaiian or other Pacific Islander

COUGH / Cough

17JUL2013 / 00:00 (164)

26JUL2013 / 23:59 (173)

Dose Increased

Recovered/Resolved / Moderate / No

01-714-1288

77 / M / Multiple

COUGH / Cough

22JAN2014 / 00:00 (50)

25JAN2014 / 23:59 (53)

Dose Not Changed

Recovered/Resolved / Mild / Yes

Xanomeline Low Dose

01-708-1272

82 / M / Not reported

COUGH / Cough

01MAR2013 / 00:00 (24)

07MAR2013 / 23:59 (30)

Unknown

Not Recovered/Not Resolved / Mild / Yes

COUGH / Cough

01MAR2013 / 00:00 (24)

07MAR2013 / 23:59 (30)

Dose Reduced

Recovered/Resolved / Mild / No

01-709-1217

77 / M / American Indian or Alaska Native

COUGH / Cough

20MAR2013 / 00:00 (17)

Dose Reduced

Not Recovered/Not Resolved / Mild / No

01-709-1326

75 / F / Other

COUGH / Cough

12JUL2013 / 00:00 (99)

Dose Increased

Not Recovered/Not Resolved / Mild / No

01-717-1004

80 / F / Not reported

COUGH / Cough

15JAN2014 / 00:00 (2)

18FEB2014 / 23:59 (36)

Dose Not Changed

Not Recovered/Not Resolved / Moderate / No

COUGH / Cough

15JAN2014 / 00:00 (2)

18FEB2014 / 23:59 (36)

Dose Rate Reduced

Recovered/Resolved / Moderate / No

Placebo

01-713-1269

73 / M / White

COUGH / Cough

18APR2014 / 00:00 (82)

Dose Reduced

Not Recovered/Not Resolved / Mild / No

Decreased Appetite

Placebo

01-703-1210

72 / F / Not reported

DECREASED APPETITE / Decreased Appetite

04MAY2013 / 00:00 (50)

Unknown

Not Recovered/Not Resolved / Mild / No

DECREASED APPETITE / Decreased Appetite

04MAY2013 / 00:00 (50)

Drug Withdrawn

Not Recovered/Not Resolved / Moderate / No

Key: FMQ=FDA Medical Query

a Study day is relative to [the start of [study treatment]].

Note: Adverse events are coded using MedDRA version 26.0.

[lsfae06a.docx][/usr/lib/rstudio-server/bin/quarto/share/rmd/rmd.R] 12JAN2026, 16:09

Download RTF file

LSFAE05
LSFAE06B
Source Code
---
title: LSFAE06A
subtitle: Selected Narrow / Broad OCMQs
---

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

{{< 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:              lsfae06a.R

# Prep environment

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

# Define script level parameters

tblid <- "LSFAE06a"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map
popfl <- "SAFFL"
trtvar <- "TRT01A"
ocmqclass <- "Narrow"
key_cols <- c("COL0", "COL1", "COL2", "COL3")
disp_cols <- paste0("COL", 0:8)
concat_sep <- " / "
# Parameter to control whether time should be displayed
include_time <- TRUE

# Process data

adaeocmq <- pharmaverseadamjnj::adaeocmq |>
  filter(
    !!sym(popfl) == "Y" &
      !is.na(OCMQNAM) &
      OCMQCLSS == ocmqclass &
      TRTEMFL == "Y"
  )

lsting <- adaeocmq |>
  mutate(
    AGE = explicit_na(as.character(AGE), ""),
    SEX = explicit_na(SEX, ""),
    RACE_DECODE = explicit_na(RACE_DECODE, ""),
    AEDECOD = explicit_na(AEDECOD, ""),
    AETERM = ifelse(
      is.na(AETERM),
      "",
      string_to_title(gsub("\\$", "", AETERM))
    ),
    ASTDT = ifelse(
      nchar(as.character(ASTDT)) == 10,
      toupper(format(ASTDT, "%d%b%Y")),
      ""
    ),
    ASTTM = ifelse(
      include_time & !is.na(ASTDTM),
      substr(as.character(ASTDTM), 12, 16),
      ""
    ),
    ASTDYN = ifelse(!is.na(ASTDY), ASTDY, NA),
    ASTDY = ifelse(!is.na(ASTDY), ASTDY, ""),
    ASTDTFS = ifelse(!is.na(ASTDTF), "*", ""),
    AENDT = explicit_na(as.character(AENDT), ""),
    AENDT = ifelse(
      nchar(AENDT) == 10,
      toupper(format(as.Date(AENDT), "%d%b%Y")),
      ""
    ),
    AENTM = ifelse(
      include_time & !is.na(AENDTM),
      substr(as.character(AENDTM), 12, 16),
      ""
    ),
    AENDY = ifelse(!is.na(AENDY), AENDY, ""),
    AENDTFS = ifelse(!is.na(AENDTF), "*", ""),
    AEOUTC = explicit_na(AEOUT_DECODE, ""),
    AESEV = explicit_na(AESEV, ""),
    AESER_DECODE = explicit_na(AESER_DECODE, ""),
    COL0 = OCMQNAM,
    COL1 = explicit_na(.data[[trtvar]], ""),
    COL2 = explicit_na(USUBJID, ""),
    COL3 = paste(AGE, SEX, RACE_DECODE, sep = concat_sep),
    COL4 = paste(AEDECOD, AETERM, sep = concat_sep),
    COL5 = case_when(
      ASTDT == "" ~ "",
      include_time & ASTDT != "" & ASTTM != "" & ASTDY != "" & ASTDTFS != "" ~
        paste0(ASTDT, concat_sep, ASTTM, " (", ASTDY, ")", ASTDTFS),
      include_time & ASTDT != "" & ASTTM != "" & ASTDY != "" & ASTDTFS == "" ~
        paste0(ASTDT, concat_sep, ASTTM, " (", ASTDY, ")"),
      include_time & ASTDT != "" & ASTTM == "" & ASTDY != "" & ASTDTFS != "" ~
        paste0(ASTDT, concat_sep, "--:--", " (", ASTDY, ")", ASTDTFS),
      include_time & ASTDT != "" & ASTTM == "" & ASTDY != "" & ASTDTFS == "" ~
        paste0(ASTDT, concat_sep, "--:--", " (", ASTDY, ")"),
      ASTDT != "" & ASTDY != "" & ASTDTFS != "" ~
        paste0(ASTDT, " (", ASTDY, ")", ASTDTFS),
      ASTDT != "" & ASTDY != "" & ASTDTFS == "" ~
        paste0(ASTDT, " (", ASTDY, ")"),
    ),
    COL6 = case_when(
      AENDT == "" ~ "",
      include_time & AENDT != "" & AENTM != "" & AENDY != "" & AENDTFS != "" ~
        paste0(AENDT, concat_sep, AENTM, " (", AENDY, ")", AENDTFS),
      include_time & AENDT != "" & AENTM != "" & AENDY != "" & AENDTFS == "" ~
        paste0(AENDT, concat_sep, AENTM, " (", AENDY, ")"),
      include_time & AENDT != "" & AENTM == "" & AENDY != "" & AENDTFS != "" ~
        paste0(AENDT, concat_sep, "--:--", " (", AENDY, ")", AENDTFS),
      include_time & AENDT != "" & AENTM == "" & AENDY != "" & AENDTFS == "" ~
        paste0(AENDT, concat_sep, "--:--", " (", AENDY, ")"),
      AENDT != "" & AENDY != "" & AENDTFS != "" ~
        paste0(AENDT, " (", AENDY, ")", AENDTFS),
      AENDT != "" & AENDY != "" & AENDTFS == "" ~
        paste0(AENDT, " (", AENDY, ")"),
    ),
    COL7 = explicit_na(AEACN_DECODE, ""),
    COL8 = paste(AEOUTC, AESEV, AESER_DECODE, sep = concat_sep)
  ) |>
  arrange(
    COL0,
    COL1,
    COL2,
    !is.na(ASTDYN),
    ASTDYN,
    if (include_time) ASTDTM else ASTDT,
    AEDECOD,
    AETERM
  )

lsting <- var_relabel(
  lsting,
  COL0 = "OCMQ",
  COL1 = "Treatment Group",
  COL2 = "Subject ID",
  COL3 = paste("Age (years)", "Sex", "Race", sep = concat_sep),
  COL4 = paste("Preferred Term", "Reported Term", sep = concat_sep),
  COL5 = if (include_time) {
    paste("Start Date", "Time (Study Day~[super a])", sep = concat_sep)
  } else {
    "Start Date (Study Day~[super a])"
  },
  COL6 = if (include_time) {
    paste("End Date", "Time (Study Day~[super a])", sep = concat_sep)
  } else {
    "End Date (Study Day~[super a])"
  },
  COL7 = "Action Taken With Study Treatment",
  COL8 = paste("Outcome", "Severity", "Serious", sep = concat_sep)
)

# Build listing

result <- rlistings::as_listing(
  df = lsting,
  key_cols = key_cols,
  disp_cols = disp_cols
)

# Add titles and footnotes:

result <- set_titles(result, tab_titles)

# Output listing

tt_to_tlgrtf(string_map = string_map, tt = head(result, 100), file = fileid, orientation = "landscape")
```
```{r result1, echo=FALSE, message=FALSE, warning=FALSE, test = list(result_v1 = "result")}
tt_to_flextable_j(head(result,100), tblid, string_map = string_map)
```

[Download RTF file](`r paste0(tolower(tblid), '.rtf')`)
::::

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