TL Catalog
  1. Tables
  2. Adverse Events
  3. TSFAE03A
  • 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. TSFAE03A

TSFAE03A

Subjects With Treatment-emergent Serious Adverse Events by System Organ Class, Preferred Term, and Subgroup


Output

  • Preview
Code
# Program Name:              tsfae03a.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSFAE03a"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map


trtvar <- "TRT01A"
popfl <- "SAFFL"

subgrpvar <- "AGEGR1"
subgrptxt <- "Age Group"
subgrpunit <- "years"

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") %>%
  mutate(
    subgrpdisplay = as.factor(paste0(
      subgrptxt,
      ": ",
      !!as.name(subgrpvar),
      " ",
      subgrpunit
    ))
  ) %>%
  select(
    STUDYID,
    USUBJID,
    all_of(trtvar),
    all_of(popfl),
    all_of(subgrpvar),
    subgrpdisplay
  )

adae <- pharmaverseadamjnj::adae %>%
  filter(TRTEMFL == "Y" & AESER == "Y") %>%
  select(USUBJID, TRTEMFL, 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 <- left_join(adsl, adae, by = c("USUBJID"))

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

# Define layout and build table:

ref_path <- c("colspan_trt", " ", "TRT01A", "Placebo")

extra_args_rr <- list(
  denom = "n_altdf",
  denom_by = "subgrpdisplay",
  riskdiff = FALSE,
  extrablankline = TRUE,
  .stats = c("n_altdf")
)

extra_args_rr2 <- list(
  denom = "n_altdf",
  denom_by = "subgrpdisplay",
  riskdiff = TRUE,
  ref_path = ref_path,
  method = "wald",
  .stats = c("count_unique_fraction")
)

lyt <- basic_table(
  top_level_section_div = " ",
  show_colcounts = TRUE,
  colcount_format = "N=xx"
) %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  )

if (combined_colspan_trt == TRUE) {
  lyt <- lyt %>%
    split_cols_by(trtvar, split_fun = mysplit)
} else {
  lyt <- lyt %>%
    split_cols_by(trtvar)
}

if (risk_diff == TRUE) {
  lyt <- lyt %>%
    split_cols_by("rrisk_header", nested = FALSE) %>%
    split_cols_by(
      trtvar,
      labels_var = "rrisk_label",
      split_fun = remove_split_levels("Placebo")
    )
}

lyt <- lyt %>%
  split_rows_by(
    "subgrpdisplay",
    split_label = "",
    split_fun = trim_levels_in_group("STUDYID"),
    indent_mod = -1L,
    section_div = c(" "),
    page_by = TRUE
  ) %>% # Set page_by = FALSE if you do not wish to start a new page after a new subgroup
  summarize_row_groups(
    "subgrpdisplay",
    cfun = a_freq_j,
    indent_mod = 0L,
    extra_args = extra_args_rr
  ) %>%
  split_rows_by(
    "TRTEMFL",
    split_fun = keep_split_levels("Y"),
    indent_mod = -1L,
    section_div = c(" ")
  ) %>%
  summarize_row_groups(
    "TRTEMFL",
    cfun = a_freq_j,
    indent_mod = 0L,
    extra_args = append(
      extra_args_rr2,
      list(label = "Subjects with >=1 SAE", extrablankline = TRUE)
    )
  ) %>%
  split_rows_by(
    "AEBODSYS",
    split_label = "System Organ Class",
    split_fun = trim_levels_in_group("AEDECOD"),
    label_pos = "topleft",
    indent_mod = 0L,
    section_div = c(" ")
  ) %>%
  summarize_row_groups(
    "AEBODSYS",
    cfun = a_freq_j,
    extra_args = extra_args_rr2
  ) %>%
  analyze("AEDECOD", afun = a_freq_j, extra_args = extra_args_rr2) %>%
  append_topleft("  Preferred Term, n (%)")

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

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

# Post-Processing step to sort by descending count on chosen active treatment columns.

if (length(adae$TRTEMFL) != 0) {
  result <- sort_at_path(
    result,
    c("subgrpdisplay", "*", "TRTEMFL", "*", "AEBODSYS"),
    scorefun = jj_complex_scorefun()
  )
  result <- sort_at_path(
    result,
    c("subgrpdisplay", "*", "TRTEMFL", "*", "AEBODSYS", "*", "AEDECOD"),
    scorefun = jj_complex_scorefun()
  )
}

# Add titles and footnotes:

result <- set_titles(result, tab_titles)

# Convert to tbl file and output table

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

TSFAE03a: Subjects With Treatment-emergent Serious Adverse Events by System Organ Class, Preferred Term, and [Subgroup]; 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

Age Group: ≥18 to <65 years

8

5

13

7

Subjects with ≥1 SAE

7 (87.5%)

4 (80.0%)

11 (84.6%)

3 (42.9%)

44.6 (1.4, 87.9)

37.1 (-13.6, 87.9)

General disorders and
 administration site conditions

6 (75.0%)

3 (60.0%)

9 (69.2%)

2 (28.6%)

46.4 (1.5, 91.4)

31.4 (-23.0, 85.9)

APPLICATION SITE PRURITUS

3 (37.5%)

3 (60.0%)

6 (46.2%)

1 (14.3%)

23.2 (-19.2, 65.6)

45.7 (-4.4, 95.9)

APPLICATION SITE ERYTHEMA

4 (50.0%)

1 (20.0%)

5 (38.5%)

0

50.0 (15.4, 84.6)

20.0 (-15.1, 55.1)

APPLICATION SITE IRRITATION

2 (25.0%)

1 (20.0%)

3 (23.1%)

1 (14.3%)

10.7 (-28.9, 50.4)

5.7 (-37.9, 49.3)

APPLICATION SITE SWELLING

1 (12.5%)

1 (20.0%)

2 (15.4%)

0

12.5 (-10.4, 35.4)

20.0 (-15.1, 55.1)

APPLICATION SITE VESICLES

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

FEELING ABNORMAL

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

MALAISE

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

ASTHENIA

0

0

0

1 (14.3%)

-14.3 (-40.2, 11.6)

-14.3 (-40.2, 11.6)

Respiratory, thoracic and
 mediastinal disorders

4 (50.0%)

0

4 (30.8%)

0

50.0 (15.4, 84.6)

0.0 (0.0, 0.0)

COUGH

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

EPISTAXIS

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

NASAL CONGESTION

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

PRODUCTIVE COUGH

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

RHINORRHOEA

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

Gastrointestinal disorders

3 (37.5%)

0

3 (23.1%)

1 (14.3%)

23.2 (-19.2, 65.6)

-14.3 (-40.2, 11.6)

SALIVARY HYPERSECRETION

2 (25.0%)

0

2 (15.4%)

0

25.0 (-5.0, 55.0)

0.0 (0.0, 0.0)

STOMACH DISCOMFORT

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

VOMITING

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

DYSPEPSIA

0

0

0

1 (14.3%)

-14.3 (-40.2, 11.6)

-14.3 (-40.2, 11.6)

GASTROOESOPHAGEAL REFLUX
 DISEASE

0

0

0

1 (14.3%)

-14.3 (-40.2, 11.6)

-14.3 (-40.2, 11.6)

Skin and subcutaneous tissue
 disorders

2 (25.0%)

1 (20.0%)

3 (23.1%)

2 (28.6%)

-3.6 (-48.5, 41.4)

-8.6 (-57.0, 39.9)

ERYTHEMA

2 (25.0%)

1 (20.0%)

3 (23.1%)

1 (14.3%)

10.7 (-28.9, 50.4)

5.7 (-37.9, 49.3)

PRURITUS

1 (12.5%)

1 (20.0%)

2 (15.4%)

0

12.5 (-10.4, 35.4)

20.0 (-15.1, 55.1)

DRUG ERUPTION

0

0

0

1 (14.3%)

-14.3 (-40.2, 11.6)

-14.3 (-40.2, 11.6)

RASH

0

0

0

1 (14.3%)

-14.3 (-40.2, 11.6)

-14.3 (-40.2, 11.6)

Infections and infestations

2 (25.0%)

0

2 (15.4%)

1 (14.3%)

10.7 (-28.9, 50.4)

-14.3 (-40.2, 11.6)

HORDEOLUM

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

RHINITIS

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

UPPER RESPIRATORY TRACT
 INFECTION

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

CERVICITIS

0

0

0

1 (14.3%)

-14.3 (-40.2, 11.6)

-14.3 (-40.2, 11.6)

VAGINAL MYCOSIS

0

0

0

1 (14.3%)

-14.3 (-40.2, 11.6)

-14.3 (-40.2, 11.6)

Nervous system disorders

2 (25.0%)

0

2 (15.4%)

0

25.0 (-5.0, 55.0)

0.0 (0.0, 0.0)

DIZZINESS

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

PAROSMIA

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

Musculoskeletal and connective
 tissue disorders

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

FLANK PAIN

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

Psychiatric disorders

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

LIBIDO DECREASED

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

LISTLESS

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

Renal and urinary disorders

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

CALCULUS URETHRAL

1 (12.5%)

0

1 (7.7%)

0

12.5 (-10.4, 35.4)

0.0 (0.0, 0.0)

Cardiac disorders

0

0

0

1 (14.3%)

-14.3 (-40.2, 11.6)

-14.3 (-40.2, 11.6)

ATRIOVENTRICULAR BLOCK
 SECOND DEGREE

0

0

0

1 (14.3%)

-14.3 (-40.2, 11.6)

-14.3 (-40.2, 11.6)

Reproductive system and breast
 disorders

0

0

0

2 (28.6%)

-28.6 (-62.0, 4.9)

-28.6 (-62.0, 4.9)

ERECTILE DYSFUNCTION

0

0

0

1 (14.3%)

-14.3 (-40.2, 11.6)

-14.3 (-40.2, 11.6)

PELVIC PAIN

0

0

0

1 (14.3%)

-14.3 (-40.2, 11.6)

-14.3 (-40.2, 11.6)

Age Group: ≥65 to <75 years

16

17

33

19

Subjects with ≥1 SAE

13 (81.2%)

14 (82.4%)

27 (81.8%)

11 (57.9%)

23.4 (-5.9, 52.7)

24.5 (-4.2, 53.1)

General disorders and
 administration site conditions

5 (31.2%)

9 (52.9%)

14 (42.4%)

5 (26.3%)

4.9 (-25.2, 35.1)

26.6 (-4.3, 57.5)

APPLICATION SITE PRURITUS

3 (18.8%)

3 (17.6%)

6 (18.2%)

0

18.8 (-0.4, 37.9)

17.6 (-0.5, 35.8)

APPLICATION SITE ERYTHEMA

2 (12.5%)

2 (11.8%)

4 (12.1%)

1 (5.3%)

7.2 (-11.8, 26.3)

6.5 (-11.8, 24.8)

APPLICATION SITE IRRITATION

1 (6.2%)

2 (11.8%)

3 (9.1%)

0

6.2 (-5.6, 18.1)

11.8 (-3.6, 27.1)

APPLICATION SITE VESICLES

1 (6.2%)

1 (5.9%)

2 (6.1%)

0

6.2 (-5.6, 18.1)

5.9 (-5.3, 17.1)

APPLICATION SITE DERMATITIS

1 (6.2%)

0

1 (3.0%)

3 (15.8%)

-9.5 (-29.8, 10.7)

-15.8 (-32.2, 0.6)

APPLICATION SITE URTICARIA

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

CHEST DISCOMFORT

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

FATIGUE

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

PYREXIA

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

OEDEMA PERIPHERAL

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

Skin and subcutaneous tissue
 disorders

8 (50.0%)

4 (23.5%)

12 (36.4%)

3 (15.8%)

34.2 (4.7, 63.7)

7.7 (-18.2, 33.7)

PRURITUS

5 (31.2%)

3 (17.6%)

8 (24.2%)

0

31.2 (8.5, 54.0)

17.6 (-0.5, 35.8)

HYPERHIDROSIS

2 (12.5%)

1 (5.9%)

3 (9.1%)

1 (5.3%)

7.2 (-11.8, 26.3)

0.6 (-14.4, 15.6)

ERYTHEMA

0

2 (11.8%)

2 (6.1%)

0

0.0 (0.0, 0.0)

11.8 (-3.6, 27.1)

RASH

1 (6.2%)

1 (5.9%)

2 (6.1%)

2 (10.5%)

-4.3 (-22.5, 13.9)

-4.6 (-22.4, 13.1)

RASH MACULO-PAPULAR

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

RASH PRURITIC

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

SKIN IRRITATION

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

URTICARIA

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

Nervous system disorders

4 (25.0%)

1 (5.9%)

5 (15.2%)

2 (10.5%)

14.5 (-10.8, 39.8)

-4.6 (-22.4, 13.1)

DIZZINESS

1 (6.2%)

1 (5.9%)

2 (6.1%)

0

6.2 (-5.6, 18.1)

5.9 (-5.3, 17.1)

HEADACHE

1 (6.2%)

1 (5.9%)

2 (6.1%)

1 (5.3%)

1.0 (-14.6, 16.5)

0.6 (-14.4, 15.6)

COGNITIVE DISORDER

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

PARTIAL SEIZURES WITH
 SECONDARY
 GENERALISATION

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

STUPOR

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

TRANSIENT ISCHAEMIC
 ATTACK

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

PARKINSON'S DISEASE

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

Investigations

1 (6.2%)

1 (5.9%)

2 (6.1%)

3 (15.8%)

-9.5 (-29.8, 10.7)

-9.9 (-29.8, 9.9)

BLOOD CHOLESTEROL
 INCREASED

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

WEIGHT DECREASED

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

BLOOD CREATINE
 PHOSPHOKINASE INCREASED

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

ELECTROCARDIOGRAM ST
 SEGMENT DEPRESSION

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

ELECTROCARDIOGRAM T WAVE
 AMPLITUDE DECREASED

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

ELECTROCARDIOGRAM T WAVE
 INVERSION

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

Reproductive system and breast
 disorders

2 (12.5%)

0

2 (6.1%)

0

12.5 (-3.7, 28.7)

0.0 (0.0, 0.0)

BENIGN PROSTATIC
 HYPERPLASIA

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

ERECTILE DYSFUNCTION

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

Respiratory, thoracic and
 mediastinal disorders

1 (6.2%)

1 (5.9%)

2 (6.1%)

1 (5.3%)

1.0 (-14.6, 16.5)

0.6 (-14.4, 15.6)

ALLERGIC GRANULOMATOUS
 ANGIITIS

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

DYSPHONIA

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

POSTNASAL DRIP

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

Cardiac disorders

0

1 (5.9%)

1 (3.0%)

1 (5.3%)

-5.3 (-15.3, 4.8)

0.6 (-14.4, 15.6)

SINUS BRADYCARDIA

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

SINUS ARRHYTHMIA

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

Eye disorders

0

1 (5.9%)

1 (3.0%)

1 (5.3%)

-5.3 (-15.3, 4.8)

0.6 (-14.4, 15.6)

VISION BLURRED

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

CONJUNCTIVITIS

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

Gastrointestinal disorders

1 (6.2%)

0

1 (3.0%)

2 (10.5%)

-4.3 (-22.5, 13.9)

-10.5 (-24.3, 3.3)

VOMITING

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

DIARRHOEA

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

GLOSSITIS

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

Infections and infestations

0

1 (5.9%)

1 (3.0%)

1 (5.3%)

-5.3 (-15.3, 4.8)

0.6 (-14.4, 15.6)

NASOPHARYNGITIS

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

INFLUENZA

0

0

0

1 (5.3%)

-5.3 (-15.3, 4.8)

-5.3 (-15.3, 4.8)

Injury, poisoning and
 procedural complications

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

EXCORIATION

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

Psychiatric disorders

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

CONFUSIONAL STATE

0

1 (5.9%)

1 (3.0%)

0

0.0 (0.0, 0.0)

5.9 (-5.3, 17.1)

Vascular disorders

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

WOUND HAEMORRHAGE

1 (6.2%)

0

1 (3.0%)

0

6.2 (-5.6, 18.1)

0.0 (0.0, 0.0)

Age Group: ≥75 years

29

51

80

33

Subjects with ≥1 SAE

27 (93.1%)

36 (70.6%)

63 (78.8%)

23 (69.7%)

23.4 (5.2, 41.6)

0.9 (-19.2, 20.9)

Skin and subcutaneous tissue
 disorders

17 (58.6%)

16 (31.4%)

33 (41.2%)

8 (24.2%)

34.4 (11.2, 57.5)

7.1 (-12.3, 26.5)

PRURITUS

6 (20.7%)

6 (11.8%)

12 (15.0%)

3 (9.1%)

11.6 (-6.1, 29.3)

2.7 (-10.5, 15.9)

ERYTHEMA

7 (24.1%)

3 (5.9%)

10 (12.5%)

3 (9.1%)

15.0 (-3.4, 33.5)

-3.2 (-15.0, 8.5)

HYPERHIDROSIS

3 (10.3%)

3 (5.9%)

6 (7.5%)

1 (3.0%)

7.3 (-5.2, 19.8)

2.9 (-5.9, 11.6)

SKIN IRRITATION

2 (6.9%)

3 (5.9%)

5 (6.2%)

3 (9.1%)

-2.2 (-15.7, 11.3)

-3.2 (-15.0, 8.5)

RASH

1 (3.4%)

3 (5.9%)

4 (5.0%)

1 (3.0%)

0.4 (-8.4, 9.3)

2.9 (-5.9, 11.6)

RASH PRURITIC

1 (3.4%)

1 (2.0%)

2 (2.5%)

0

3.4 (-3.2, 10.1)

2.0 (-1.8, 5.8)

BLISTER

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

PRURITUS GENERALISED

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

URTICARIA

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

SKIN ULCER

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

General disorders and
 administration site conditions

10 (34.5%)

16 (31.4%)

26 (32.5%)

4 (12.1%)

22.4 (1.8, 42.9)

19.3 (2.3, 36.2)

APPLICATION SITE ERYTHEMA

2 (6.9%)

5 (9.8%)

7 (8.8%)

0

6.9 (-2.3, 16.1)

9.8 (1.6, 18.0)

APPLICATION SITE PRURITUS

3 (10.3%)

4 (7.8%)

7 (8.8%)

2 (6.1%)

4.3 (-9.5, 18.0)

1.8 (-9.2, 12.8)

APPLICATION SITE DERMATITIS

2 (6.9%)

4 (7.8%)

6 (7.5%)

1 (3.0%)

3.9 (-7.1, 14.8)

4.8 (-4.6, 14.2)

APPLICATION SITE IRRITATION

2 (6.9%)

2 (3.9%)

4 (5.0%)

1 (3.0%)

3.9 (-7.1, 14.8)

0.9 (-7.0, 8.8)

FATIGUE

2 (6.9%)

2 (3.9%)

4 (5.0%)

0

6.9 (-2.3, 16.1)

3.9 (-1.4, 9.2)

APPLICATION SITE VESICLES

2 (6.9%)

0

2 (2.5%)

0

6.9 (-2.3, 16.1)

0.0 (0.0, 0.0)

OEDEMA PERIPHERAL

1 (3.4%)

1 (2.0%)

2 (2.5%)

1 (3.0%)

0.4 (-8.4, 9.3)

-1.1 (-8.0, 5.9)

APPLICATION SITE BLEEDING

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

APPLICATION SITE
 DESQUAMATION

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

APPLICATION SITE PAIN

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

APPLICATION SITE REACTION

1 (3.4%)

0

1 (1.2%)

1 (3.0%)

0.4 (-8.4, 9.3)

-3.0 (-8.9, 2.8)

CHEST PAIN

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

CHILLS

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

MALAISE

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

SUDDEN DEATH

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

ULCER

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

Nervous system disorders

5 (17.2%)

9 (17.6%)

14 (17.5%)

1 (3.0%)

14.2 (-0.7, 29.2)

14.6 (2.6, 26.6)

DIZZINESS

2 (6.9%)

2 (3.9%)

4 (5.0%)

0

6.9 (-2.3, 16.1)

3.9 (-1.4, 9.2)

HEADACHE

1 (3.4%)

2 (3.9%)

3 (3.8%)

0

3.4 (-3.2, 10.1)

3.9 (-1.4, 9.2)

SOMNOLENCE

0

2 (3.9%)

2 (2.5%)

1 (3.0%)

-3.0 (-8.9, 2.8)

0.9 (-7.0, 8.8)

BURNING SENSATION

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

COORDINATION ABNORMAL

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

HEMIANOPIA HOMONYMOUS

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

LETHARGY

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

SYNCOPE

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

TRANSIENT ISCHAEMIC
 ATTACK

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

Cardiac disorders

6 (20.7%)

6 (11.8%)

12 (15.0%)

3 (9.1%)

11.6 (-6.1, 29.3)

2.7 (-10.5, 15.9)

SINUS BRADYCARDIA

3 (10.3%)

1 (2.0%)

4 (5.0%)

0

10.3 (-0.7, 21.4)

2.0 (-1.8, 5.8)

MYOCARDIAL INFARCTION

2 (6.9%)

1 (2.0%)

3 (3.8%)

2 (6.1%)

0.8 (-11.5, 13.1)

-4.1 (-13.1, 4.9)

ATRIAL FLUTTER

1 (3.4%)

1 (2.0%)

2 (2.5%)

0

3.4 (-3.2, 10.1)

2.0 (-1.8, 5.8)

VENTRICULAR EXTRASYSTOLES

0

2 (3.9%)

2 (2.5%)

0

0.0 (0.0, 0.0)

3.9 (-1.4, 9.2)

BUNDLE BRANCH BLOCK RIGHT

0

1 (2.0%)

1 (1.2%)

1 (3.0%)

-3.0 (-8.9, 2.8)

-1.1 (-8.0, 5.9)

WOLFF-PARKINSON-WHITE
 SYNDROME

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

SUPRAVENTRICULAR
 EXTRASYSTOLES

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

TACHYCARDIA

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

Gastrointestinal disorders

6 (20.7%)

5 (9.8%)

11 (13.8%)

1 (3.0%)

17.7 (1.8, 33.5)

6.8 (-3.3, 16.8)

DIARRHOEA

2 (6.9%)

2 (3.9%)

4 (5.0%)

0

6.9 (-2.3, 16.1)

3.9 (-1.4, 9.2)

NAUSEA

2 (6.9%)

0

2 (2.5%)

0

6.9 (-2.3, 16.1)

0.0 (0.0, 0.0)

ABDOMINAL DISCOMFORT

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

ABDOMINAL PAIN

0

1 (2.0%)

1 (1.2%)

1 (3.0%)

-3.0 (-8.9, 2.8)

-1.1 (-8.0, 5.9)

DYSPEPSIA

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

RECTAL HAEMORRHAGE

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

SALIVARY HYPERSECRETION

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

VOMITING

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

CONSTIPATION

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

Infections and infestations

3 (10.3%)

4 (7.8%)

7 (8.8%)

8 (24.2%)

-13.9 (-32.2, 4.5)

-16.4 (-32.8, -0.0)

NASOPHARYNGITIS

2 (6.9%)

2 (3.9%)

4 (5.0%)

2 (6.1%)

0.8 (-11.5, 13.1)

-2.1 (-11.9, 7.6)

CELLULITIS

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

INFLUENZA

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

PNEUMONIA

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

BRONCHITIS

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

LOCALISED INFECTION

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

UPPER RESPIRATORY TRACT
 INFECTION

0

0

0

3 (9.1%)

-9.1 (-18.9, 0.7)

-9.1 (-18.9, 0.7)

URINARY TRACT INFECTION

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

Injury, poisoning and
 procedural complications

1 (3.4%)

4 (7.8%)

5 (6.2%)

1 (3.0%)

0.4 (-8.4, 9.3)

4.8 (-4.6, 14.2)

FALL

1 (3.4%)

2 (3.9%)

3 (3.8%)

0

3.4 (-3.2, 10.1)

3.9 (-1.4, 9.2)

SKIN LACERATION

0

2 (3.9%)

2 (2.5%)

0

0.0 (0.0, 0.0)

3.9 (-1.4, 9.2)

CONTUSION

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

FACIAL BONES FRACTURE

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

WOUND

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

HIP FRACTURE

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

Investigations

1 (3.4%)

3 (5.9%)

4 (5.0%)

4 (12.1%)

-8.7 (-21.6, 4.3)

-6.2 (-19.1, 6.6)

BLOOD GLUCOSE INCREASED

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

BODY TEMPERATURE
 INCREASED

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

ELECTROCARDIOGRAM ST
 SEGMENT DEPRESSION

0

1 (2.0%)

1 (1.2%)

2 (6.1%)

-6.1 (-14.2, 2.1)

-4.1 (-13.1, 4.9)

ELECTROCARDIOGRAM T WAVE
 AMPLITUDE DECREASED

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

BLOOD ALKALINE
 PHOSPHATASE INCREASED

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

BLOOD URINE PRESENT

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

Musculoskeletal and connective
 tissue disorders

2 (6.9%)

2 (3.9%)

4 (5.0%)

0

6.9 (-2.3, 16.1)

3.9 (-1.4, 9.2)

BACK PAIN

2 (6.9%)

0

2 (2.5%)

0

6.9 (-2.3, 16.1)

0.0 (0.0, 0.0)

ARTHRALGIA

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

MUSCLE SPASMS

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

MUSCULAR WEAKNESS

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

Psychiatric disorders

1 (3.4%)

2 (3.9%)

3 (3.8%)

4 (12.1%)

-8.7 (-21.6, 4.3)

-8.2 (-20.5, 4.1)

ANXIETY

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

CONFUSIONAL STATE

1 (3.4%)

0

1 (1.2%)

1 (3.0%)

0.4 (-8.4, 9.3)

-3.0 (-8.9, 2.8)

INSOMNIA

1 (3.4%)

0

1 (1.2%)

1 (3.0%)

0.4 (-8.4, 9.3)

-3.0 (-8.9, 2.8)

RESTLESSNESS

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

AGITATION

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

DELUSION

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

Respiratory, thoracic and
 mediastinal disorders

1 (3.4%)

2 (3.9%)

3 (3.8%)

0

3.4 (-3.2, 10.1)

3.9 (-1.4, 9.2)

COUGH

1 (3.4%)

1 (2.0%)

2 (2.5%)

0

3.4 (-3.2, 10.1)

2.0 (-1.8, 5.8)

RHINORRHOEA

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

Ear and labyrinth disorders

0

2 (3.9%)

2 (2.5%)

0

0.0 (0.0, 0.0)

3.9 (-1.4, 9.2)

CERUMEN IMPACTION

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

VERTIGO

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

Renal and urinary disorders

0

2 (3.9%)

2 (2.5%)

1 (3.0%)

-3.0 (-8.9, 2.8)

0.9 (-7.0, 8.8)

DYSURIA

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

INCONTINENCE

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

MICTURITION URGENCY

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

Endocrine disorders

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

BLEEDING ANOVULATORY

0

1 (2.0%)

1 (1.2%)

0

0.0 (0.0, 0.0)

2.0 (-1.8, 5.8)

Eye disorders

1 (3.4%)

0

1 (1.2%)

1 (3.0%)

0.4 (-8.4, 9.3)

-3.0 (-8.9, 2.8)

VISION BLURRED

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

EYE PRURITUS

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

Metabolism and nutrition
 disorders

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

INCREASED APPETITE

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

Reproductive system and breast
 disorders

1 (3.4%)

0

1 (1.2%)

1 (3.0%)

0.4 (-8.4, 9.3)

-3.0 (-8.9, 2.8)

ABNORMAL UTERINE BLEEDING

1 (3.4%)

0

1 (1.2%)

0

3.4 (-3.2, 10.1)

0.0 (0.0, 0.0)

BENIGN PROSTATIC
 HYPERPLASIA

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

Surgical and medical
 procedures

0

0

0

2 (6.1%)

-6.1 (-14.2, 2.1)

-6.1 (-14.2, 2.1)

CATARACT OPERATION

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

EYE LASER SURGERY

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

Vascular disorders

0

0

0

2 (6.1%)

-6.1 (-14.2, 2.1)

-6.1 (-14.2, 2.1)

HYPOTENSION

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

ORTHOSTATIC HYPOTENSION

0

0

0

1 (3.0%)

-3.0 (-8.9, 2.8)

-3.0 (-8.9, 2.8)

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

TSFAE03
TSFAE04
Source Code
---
title: TSFAE03A
subtitle: Subjects With Treatment-emergent Serious Adverse Events by System Organ Class, Preferred Term, and Subgroup
---

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

{{< 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:              tsfae03a.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSFAE03a"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map


trtvar <- "TRT01A"
popfl <- "SAFFL"

subgrpvar <- "AGEGR1"
subgrptxt <- "Age Group"
subgrpunit <- "years"

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") %>%
  mutate(
    subgrpdisplay = as.factor(paste0(
      subgrptxt,
      ": ",
      !!as.name(subgrpvar),
      " ",
      subgrpunit
    ))
  ) %>%
  select(
    STUDYID,
    USUBJID,
    all_of(trtvar),
    all_of(popfl),
    all_of(subgrpvar),
    subgrpdisplay
  )

adae <- pharmaverseadamjnj::adae %>%
  filter(TRTEMFL == "Y" & AESER == "Y") %>%
  select(USUBJID, TRTEMFL, 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 <- left_join(adsl, adae, by = c("USUBJID"))

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

# Define layout and build table:

ref_path <- c("colspan_trt", " ", "TRT01A", "Placebo")

extra_args_rr <- list(
  denom = "n_altdf",
  denom_by = "subgrpdisplay",
  riskdiff = FALSE,
  extrablankline = TRUE,
  .stats = c("n_altdf")
)

extra_args_rr2 <- list(
  denom = "n_altdf",
  denom_by = "subgrpdisplay",
  riskdiff = TRUE,
  ref_path = ref_path,
  method = "wald",
  .stats = c("count_unique_fraction")
)

lyt <- basic_table(
  top_level_section_div = " ",
  show_colcounts = TRUE,
  colcount_format = "N=xx"
) %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  )

if (combined_colspan_trt == TRUE) {
  lyt <- lyt %>%
    split_cols_by(trtvar, split_fun = mysplit)
} else {
  lyt <- lyt %>%
    split_cols_by(trtvar)
}

if (risk_diff == TRUE) {
  lyt <- lyt %>%
    split_cols_by("rrisk_header", nested = FALSE) %>%
    split_cols_by(
      trtvar,
      labels_var = "rrisk_label",
      split_fun = remove_split_levels("Placebo")
    )
}

lyt <- lyt %>%
  split_rows_by(
    "subgrpdisplay",
    split_label = "",
    split_fun = trim_levels_in_group("STUDYID"),
    indent_mod = -1L,
    section_div = c(" "),
    page_by = TRUE
  ) %>% # Set page_by = FALSE if you do not wish to start a new page after a new subgroup
  summarize_row_groups(
    "subgrpdisplay",
    cfun = a_freq_j,
    indent_mod = 0L,
    extra_args = extra_args_rr
  ) %>%
  split_rows_by(
    "TRTEMFL",
    split_fun = keep_split_levels("Y"),
    indent_mod = -1L,
    section_div = c(" ")
  ) %>%
  summarize_row_groups(
    "TRTEMFL",
    cfun = a_freq_j,
    indent_mod = 0L,
    extra_args = append(
      extra_args_rr2,
      list(label = "Subjects with >=1 SAE", extrablankline = TRUE)
    )
  ) %>%
  split_rows_by(
    "AEBODSYS",
    split_label = "System Organ Class",
    split_fun = trim_levels_in_group("AEDECOD"),
    label_pos = "topleft",
    indent_mod = 0L,
    section_div = c(" ")
  ) %>%
  summarize_row_groups(
    "AEBODSYS",
    cfun = a_freq_j,
    extra_args = extra_args_rr2
  ) %>%
  analyze("AEDECOD", afun = a_freq_j, extra_args = extra_args_rr2) %>%
  append_topleft("  Preferred Term, n (%)")

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

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

# Post-Processing step to sort by descending count on chosen active treatment columns.

if (length(adae$TRTEMFL) != 0) {
  result <- sort_at_path(
    result,
    c("subgrpdisplay", "*", "TRTEMFL", "*", "AEBODSYS"),
    scorefun = jj_complex_scorefun()
  )
  result <- sort_at_path(
    result,
    c("subgrpdisplay", "*", "TRTEMFL", "*", "AEBODSYS", "*", "AEDECOD"),
    scorefun = jj_complex_scorefun()
  )
}

# Add titles and footnotes:

result <- set_titles(result, tab_titles)

# Convert to tbl file and output table

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

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

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