Specific adverse events table in gt format

Usage

gt_ae_specific(
  outdata,
  meddra_version,
  source,
  analysis,
  footnotes = NULL,
  title = c("analysis", "observation", "population")
)

Arguments

outdata: An outdata object created by prepare_ae_specific().
meddra_version: A character value of the MedDRA version for this dataset.
source: A character value of the data source.
analysis: One of analysis name existing at outdata$meta$analysis
footnotes: A character vector of table footnotes.
title: Term "analysis", "observation"and "population") for collecting title from metadata or a character vector of table titles.

Value

A gt_tbl object for an AE specific table.

Examples

library(gt)

# Define metadata
adsl <- forestly::forestly_adsl
adae <- forestly::forestly_adae

adsl$TRT01A <- factor(
  adsl$TRT01A,
  levels = c("Xanomeline Low Dose", "Placebo"),
  labels = c("Low Dose", "Placebo")
)
adae$TRTA <- factor(
  adae$TRTA,
  levels = c("Xanomeline Low Dose", "Placebo"),
  labels = c("Low Dose", "Placebo")
)

analysis_plan <- metalite::plan(
  analysis = "ae_specific",
  population = "apat",
  observation = "wk12",
  parameter = "rel"
)

meta <- metalite::meta_adam(observation = adae, population = adsl) |>
  metalite::define_plan(analysis_plan) |>
  metalite::define_population(
    name = "apat",
    var = c("USUBJID", "SAFFL", "TRT01A", "SITEID", "SEX", "RACE", "AGE"),
    group = "TRT01A",
    subset = SAFFL == "Y",
    label = "All Participants as Treated"
  ) |>
  metalite::define_observation(
    name = "wk12",
    var = c(
      "USUBJID", "SAFFL", "TRTA", "SEX", "AEDECOD", "AEBODSYS",
      "AEREL", "AESER", "AEOUT", "AEACN", "AESDTH", "ASTDT", "AENDT"
    ),
    group = "TRTA",
    subset = SAFFL == "Y",
    label = "Weeks 0 to 12"
  ) |>
  metalite::define_parameter(
    name = "rel",
    term1 = "Drug-Related",
    term2 = "",
    subset = AEREL %in% c("POSSIBLE", "PROBABLE"),
    var = "AEDECOD",
    soc = "AEBODSYS",
    label = "Drug-related AEs"
  ) |>
  metalite::define_analysis(
    name = "ae_specific",
    title = "Participants With Drug-Related Adverse Events"
  ) |>
  metalite::meta_build()

meta |>
  prepare_ae_specific(
    population = "apat",
    observation = "wk12",
    parameter = "rel"
  ) |>
  format_ae_specific() |>
  gt_ae_specific(
    meddra_version = "24.0",
    source = "Source:  [CDISCpilot: adam-adsl; adae]",
    analysis = "ae_specific"
  )


  Participants With Drug-Related Adverse Events

(Incidence > 0 % in One or More Treatment Groups)

Weeks 0 to 12

All Participants as Treated
    

      
        Low Dose
      
      
        Placebo
      
      
        Total
      
    
n
      (%)
      n
      (%)
      n
      (%)
    
Participants in population
84


86


170

with one or more drug-related adverse events
73
(86.9)
44
(51.2)
117
(68.8)
with no drug-related adverse events
11
(13.1)
42
(48.8)
53
(31.2)












Cardiac disorders
7
 (8.3)
6
 (7.0)
13
 (7.6)
Atrial fibrillation
0
 (0.0)
1
 (1.2)
1
 (0.6)
Atrial flutter
1
 (1.2)
0
 (0.0)
1
 (0.6)
Atrioventricular block first degree
0
 (0.0)
1
 (1.2)
1
 (0.6)
Atrioventricular block second degree
0
 (0.0)
1
 (1.2)
1
 (0.6)
Bradycardia
0
 (0.0)
1
 (1.2)
1
 (0.6)
Bundle branch block right
1
 (1.2)
0
 (0.0)
1
 (0.6)
Cardiac failure congestive
0
 (0.0)
1
 (1.2)
1
 (0.6)
Myocardial infarction
1
 (1.2)
2
 (2.3)
3
 (1.8)
Palpitations
1
 (1.2)
0
 (0.0)
1
 (0.6)
Sinus arrhythmia
0
 (0.0)
1
 (1.2)
1
 (0.6)
Sinus bradycardia
2
 (2.4)
2
 (2.3)
4
 (2.4)
Supraventricular extrasystoles
1
 (1.2)
0
 (0.0)
1
 (0.6)
Ventricular extrasystoles
1
 (1.2)
0
 (0.0)
1
 (0.6)
Wolff-parkinson-white syndrome
1
 (1.2)
0
 (0.0)
1
 (0.6)
Congenital, familial and genetic disorders
1
 (1.2)
0
 (0.0)
1
 (0.6)
Ventricular septal defect
1
 (1.2)
0
 (0.0)
1
 (0.6)
Ear and labyrinth disorders
2
 (2.4)
0
 (0.0)
2
 (1.2)
Tinnitus
1
 (1.2)
0
 (0.0)
1
 (0.6)
Vertigo
1
 (1.2)
0
 (0.0)
1
 (0.6)
Eye disorders
1
 (1.2)
0
 (0.0)
1
 (0.6)
Vision blurred
1
 (1.2)
0
 (0.0)
1
 (0.6)
Gastrointestinal disorders
8
 (9.5)
4
 (4.7)
12
 (7.1)
Abdominal pain
1
 (1.2)
0
 (0.0)
1
 (0.6)
Diarrhoea
3
 (3.6)
3
 (3.5)
6
 (3.5)
Dyspepsia
1
 (1.2)
1
 (1.2)
2
 (1.2)
Gastrooesophageal reflux disease
0
 (0.0)
1
 (1.2)
1
 (0.6)
Nausea
3
 (3.6)
0
 (0.0)
3
 (1.8)
Vomiting
2
 (2.4)
0
 (0.0)
2
 (1.2)
General disorders and administration site conditions
43
(51.2)
18
(20.9)
61
(35.9)
Application site bleeding
1
 (1.2)
0
 (0.0)
1
 (0.6)
Application site dermatitis
9
(10.7)
5
 (5.8)
14
 (8.2)
Application site desquamation
1
 (1.2)
0
 (0.0)
1
 (0.6)
Application site discolouration
1
 (1.2)
0
 (0.0)
1
 (0.6)
Application site erythema
12
(14.3)
3
 (3.5)
15
 (8.8)
Application site induration
0
 (0.0)
1
 (1.2)
1
 (0.6)
Application site irritation
9
(10.7)
3
 (3.5)
12
 (7.1)
Application site pruritus
22
(26.2)
6
 (7.0)
28
(16.5)
Application site reaction
0
 (0.0)
1
 (1.2)
1
 (0.6)
Application site swelling
1
 (1.2)
0
 (0.0)
1
 (0.6)
Application site urticaria
2
 (2.4)
0
 (0.0)
2
 (1.2)
Application site vesicles
4
 (4.8)
1
 (1.2)
5
 (2.9)
Application site warmth
1
 (1.2)
0
 (0.0)
1
 (0.6)
Asthenia
0
 (0.0)
1
 (1.2)
1
 (0.6)
Chills
1
 (1.2)
1
 (1.2)
2
 (1.2)
Fatigue
2
 (2.4)
1
 (1.2)
3
 (1.8)
Malaise
1
 (1.2)
0
 (0.0)
1
 (0.6)
Oedema
2
 (2.4)
0
 (0.0)
2
 (1.2)
Pain
1
 (1.2)
0
 (0.0)
1
 (0.6)
Injury, poisoning and procedural complications
2
 (2.4)
0
 (0.0)
2
 (1.2)
Fall
1
 (1.2)
0
 (0.0)
1
 (0.6)
Skin laceration
1
 (1.2)
0
 (0.0)
1
 (0.6)
Wound
1
 (1.2)
0
 (0.0)
1
 (0.6)
Investigations
2
 (2.4)
4
 (4.7)
6
 (3.5)
Blood creatine phosphokinase increased
0
 (0.0)
1
 (1.2)
1
 (0.6)
Body temperature increased
1
 (1.2)
0
 (0.0)
1
 (0.6)
Electrocardiogram st segment depression
1
 (1.2)
1
 (1.2)
2
 (1.2)
Heart rate increased
0
 (0.0)
1
 (1.2)
1
 (0.6)
Heart rate irregular
0
 (0.0)
1
 (1.2)
1
 (0.6)
Metabolism and nutrition disorders
0
 (0.0)
3
 (3.5)
3
 (1.8)
Decreased appetite
0
 (0.0)
1
 (1.2)
1
 (0.6)
Food craving
0
 (0.0)
1
 (1.2)
1
 (0.6)
Increased appetite
0
 (0.0)
1
 (1.2)
1
 (0.6)
Musculoskeletal and connective tissue disorders
0
 (0.0)
1
 (1.2)
1
 (0.6)
Shoulder pain
0
 (0.0)
1
 (1.2)
1
 (0.6)
Nervous system disorders
12
(14.3)
5
 (5.8)
17
(10.0)
Balance disorder
1
 (1.2)
0
 (0.0)
1
 (0.6)
Complex partial seizures
1
 (1.2)
0
 (0.0)
1
 (0.6)
Coordination abnormal
1
 (1.2)
0
 (0.0)
1
 (0.6)
Dizziness
6
 (7.1)
2
 (2.3)
8
 (4.7)
Headache
1
 (1.2)
2
 (2.3)
3
 (1.8)
Lethargy
1
 (1.2)
0
 (0.0)
1
 (0.6)
Paraesthesia oral
1
 (1.2)
0
 (0.0)
1
 (0.6)
Somnolence
0
 (0.0)
1
 (1.2)
1
 (0.6)
Stupor
1
 (1.2)
0
 (0.0)
1
 (0.6)
Syncope
4
 (4.8)
0
 (0.0)
4
 (2.4)
Transient ischaemic attack
1
 (1.2)
0
 (0.0)
1
 (0.6)
Psychiatric disorders
9
(10.7)
2
 (2.3)
11
 (6.5)
Agitation
2
 (2.4)
0
 (0.0)
2
 (1.2)
Anxiety
3
 (3.6)
0
 (0.0)
3
 (1.8)
Confusional state
2
 (2.4)
1
 (1.2)
3
 (1.8)
Depressed mood
1
 (1.2)
0
 (0.0)
1
 (0.6)
Irritability
1
 (1.2)
1
 (1.2)
2
 (1.2)
Restlessness
1
 (1.2)
0
 (0.0)
1
 (0.6)
Renal and urinary disorders
1
 (1.2)
0
 (0.0)
1
 (0.6)
Enuresis
1
 (1.2)
0
 (0.0)
1
 (0.6)
Reproductive system and breast disorders
0
 (0.0)
1
 (1.2)
1
 (0.6)
Pelvic pain
0
 (0.0)
1
 (1.2)
1
 (0.6)
Respiratory, thoracic and mediastinal disorders
0
 (0.0)
2
 (2.3)
2
 (1.2)
Dyspnoea
0
 (0.0)
1
 (1.2)
1
 (0.6)
Emphysema
0
 (0.0)
1
 (1.2)
1
 (0.6)
Skin and subcutaneous tissue disorders
39
(46.4)
17
(19.8)
56
(32.9)
Blister
5
 (6.0)
0
 (0.0)
5
 (2.9)
Cold sweat
0
 (0.0)
1
 (1.2)
1
 (0.6)
Dermatitis contact
1
 (1.2)
0
 (0.0)
1
 (0.6)
Erythema
13
(15.5)
9
(10.5)
22
(12.9)
Hyperhidrosis
4
 (4.8)
1
 (1.2)
5
 (2.9)
Pruritus
21
(25.0)
7
 (8.1)
28
(16.5)
Pruritus generalised
1
 (1.2)
0
 (0.0)
1
 (0.6)
Rash
11
(13.1)
3
 (3.5)
14
 (8.2)
Rash erythematous
2
 (2.4)
0
 (0.0)
2
 (1.2)
Rash pruritic
1
 (1.2)
0
 (0.0)
1
 (0.6)
Skin exfoliation
1
 (1.2)
0
 (0.0)
1
 (0.6)
Skin irritation
6
 (7.1)
2
 (2.3)
8
 (4.7)
Skin ulcer
0
 (0.0)
1
 (1.2)
1
 (0.6)
Urticaria
1
 (1.2)
0
 (0.0)
1
 (0.6)
Vascular disorders
2
 (2.4)
1
 (1.2)
3
 (1.8)
Hypertension
1
 (1.2)
0
 (0.0)
1
 (0.6)
Hypotension
1
 (1.2)
1
 (1.2)
2
 (1.2)
Orthostatic hypotension
0
 (0.0)
1
 (1.2)
1
 (0.6)
Every participant is counted a single time for each applicable row and column.
    
A system organ class or specific adverse event appears on this report only if its incidence in one or more of the columns meets the incidence criterion in the report title, after rounding.
    
Adverse event terms are from MedDRA Version 24.0.
    
Source:  [CDISCpilot: adam-adsl; adae]

	Low Dose		Placebo		Total
Participants With Drug-Related Adverse Events (Incidence > 0 % in One or More Treatment Groups) Weeks 0 to 12 All Participants as Treated
	n	(%)	n	(%)	n	(%)
Participants in population	84		86		170
with one or more drug-related adverse events	73	(86.9)	44	(51.2)	117	(68.8)
with no drug-related adverse events	11	(13.1)	42	(48.8)	53	(31.2)

Cardiac disorders	7	(8.3)	6	(7.0)	13	(7.6)
Atrial fibrillation	0	(0.0)	1	(1.2)	1	(0.6)
Atrial flutter	1	(1.2)	0	(0.0)	1	(0.6)
Atrioventricular block first degree	0	(0.0)	1	(1.2)	1	(0.6)
Atrioventricular block second degree	0	(0.0)	1	(1.2)	1	(0.6)
Bradycardia	0	(0.0)	1	(1.2)	1	(0.6)
Bundle branch block right	1	(1.2)	0	(0.0)	1	(0.6)
Cardiac failure congestive	0	(0.0)	1	(1.2)	1	(0.6)
Myocardial infarction	1	(1.2)	2	(2.3)	3	(1.8)
Palpitations	1	(1.2)	0	(0.0)	1	(0.6)
Sinus arrhythmia	0	(0.0)	1	(1.2)	1	(0.6)
Sinus bradycardia	2	(2.4)	2	(2.3)	4	(2.4)
Supraventricular extrasystoles	1	(1.2)	0	(0.0)	1	(0.6)
Ventricular extrasystoles	1	(1.2)	0	(0.0)	1	(0.6)
Wolff-parkinson-white syndrome	1	(1.2)	0	(0.0)	1	(0.6)
Congenital, familial and genetic disorders	1	(1.2)	0	(0.0)	1	(0.6)
Ventricular septal defect	1	(1.2)	0	(0.0)	1	(0.6)
Ear and labyrinth disorders	2	(2.4)	0	(0.0)	2	(1.2)
Tinnitus	1	(1.2)	0	(0.0)	1	(0.6)
Vertigo	1	(1.2)	0	(0.0)	1	(0.6)
Eye disorders	1	(1.2)	0	(0.0)	1	(0.6)
Vision blurred	1	(1.2)	0	(0.0)	1	(0.6)
Gastrointestinal disorders	8	(9.5)	4	(4.7)	12	(7.1)
Abdominal pain	1	(1.2)	0	(0.0)	1	(0.6)
Diarrhoea	3	(3.6)	3	(3.5)	6	(3.5)
Dyspepsia	1	(1.2)	1	(1.2)	2	(1.2)
Gastrooesophageal reflux disease	0	(0.0)	1	(1.2)	1	(0.6)
Nausea	3	(3.6)	0	(0.0)	3	(1.8)
Vomiting	2	(2.4)	0	(0.0)	2	(1.2)
General disorders and administration site conditions	43	(51.2)	18	(20.9)	61	(35.9)
Application site bleeding	1	(1.2)	0	(0.0)	1	(0.6)
Application site dermatitis	9	(10.7)	5	(5.8)	14	(8.2)
Application site desquamation	1	(1.2)	0	(0.0)	1	(0.6)
Application site discolouration	1	(1.2)	0	(0.0)	1	(0.6)
Application site erythema	12	(14.3)	3	(3.5)	15	(8.8)
Application site induration	0	(0.0)	1	(1.2)	1	(0.6)
Application site irritation	9	(10.7)	3	(3.5)	12	(7.1)
Application site pruritus	22	(26.2)	6	(7.0)	28	(16.5)
Application site reaction	0	(0.0)	1	(1.2)	1	(0.6)
Application site swelling	1	(1.2)	0	(0.0)	1	(0.6)
Application site urticaria	2	(2.4)	0	(0.0)	2	(1.2)
Application site vesicles	4	(4.8)	1	(1.2)	5	(2.9)
Application site warmth	1	(1.2)	0	(0.0)	1	(0.6)
Asthenia	0	(0.0)	1	(1.2)	1	(0.6)
Chills	1	(1.2)	1	(1.2)	2	(1.2)
Fatigue	2	(2.4)	1	(1.2)	3	(1.8)
Malaise	1	(1.2)	0	(0.0)	1	(0.6)
Oedema	2	(2.4)	0	(0.0)	2	(1.2)
Pain	1	(1.2)	0	(0.0)	1	(0.6)
Injury, poisoning and procedural complications	2	(2.4)	0	(0.0)	2	(1.2)
Fall	1	(1.2)	0	(0.0)	1	(0.6)
Skin laceration	1	(1.2)	0	(0.0)	1	(0.6)
Wound	1	(1.2)	0	(0.0)	1	(0.6)
Investigations	2	(2.4)	4	(4.7)	6	(3.5)
Blood creatine phosphokinase increased	0	(0.0)	1	(1.2)	1	(0.6)
Body temperature increased	1	(1.2)	0	(0.0)	1	(0.6)
Electrocardiogram st segment depression	1	(1.2)	1	(1.2)	2	(1.2)
Heart rate increased	0	(0.0)	1	(1.2)	1	(0.6)
Heart rate irregular	0	(0.0)	1	(1.2)	1	(0.6)
Metabolism and nutrition disorders	0	(0.0)	3	(3.5)	3	(1.8)
Decreased appetite	0	(0.0)	1	(1.2)	1	(0.6)
Food craving	0	(0.0)	1	(1.2)	1	(0.6)
Increased appetite	0	(0.0)	1	(1.2)	1	(0.6)
Musculoskeletal and connective tissue disorders	0	(0.0)	1	(1.2)	1	(0.6)
Shoulder pain	0	(0.0)	1	(1.2)	1	(0.6)
Nervous system disorders	12	(14.3)	5	(5.8)	17	(10.0)
Balance disorder	1	(1.2)	0	(0.0)	1	(0.6)
Complex partial seizures	1	(1.2)	0	(0.0)	1	(0.6)
Coordination abnormal	1	(1.2)	0	(0.0)	1	(0.6)
Dizziness	6	(7.1)	2	(2.3)	8	(4.7)
Headache	1	(1.2)	2	(2.3)	3	(1.8)
Lethargy	1	(1.2)	0	(0.0)	1	(0.6)
Paraesthesia oral	1	(1.2)	0	(0.0)	1	(0.6)
Somnolence	0	(0.0)	1	(1.2)	1	(0.6)
Stupor	1	(1.2)	0	(0.0)	1	(0.6)
Syncope	4	(4.8)	0	(0.0)	4	(2.4)
Transient ischaemic attack	1	(1.2)	0	(0.0)	1	(0.6)
Psychiatric disorders	9	(10.7)	2	(2.3)	11	(6.5)
Agitation	2	(2.4)	0	(0.0)	2	(1.2)
Anxiety	3	(3.6)	0	(0.0)	3	(1.8)
Confusional state	2	(2.4)	1	(1.2)	3	(1.8)
Depressed mood	1	(1.2)	0	(0.0)	1	(0.6)
Irritability	1	(1.2)	1	(1.2)	2	(1.2)
Restlessness	1	(1.2)	0	(0.0)	1	(0.6)
Renal and urinary disorders	1	(1.2)	0	(0.0)	1	(0.6)
Enuresis	1	(1.2)	0	(0.0)	1	(0.6)
Reproductive system and breast disorders	0	(0.0)	1	(1.2)	1	(0.6)
Pelvic pain	0	(0.0)	1	(1.2)	1	(0.6)
Respiratory, thoracic and mediastinal disorders	0	(0.0)	2	(2.3)	2	(1.2)
Dyspnoea	0	(0.0)	1	(1.2)	1	(0.6)
Emphysema	0	(0.0)	1	(1.2)	1	(0.6)
Skin and subcutaneous tissue disorders	39	(46.4)	17	(19.8)	56	(32.9)
Blister	5	(6.0)	0	(0.0)	5	(2.9)
Cold sweat	0	(0.0)	1	(1.2)	1	(0.6)
Dermatitis contact	1	(1.2)	0	(0.0)	1	(0.6)
Erythema	13	(15.5)	9	(10.5)	22	(12.9)
Hyperhidrosis	4	(4.8)	1	(1.2)	5	(2.9)
Pruritus	21	(25.0)	7	(8.1)	28	(16.5)
Pruritus generalised	1	(1.2)	0	(0.0)	1	(0.6)
Rash	11	(13.1)	3	(3.5)	14	(8.2)
Rash erythematous	2	(2.4)	0	(0.0)	2	(1.2)
Rash pruritic	1	(1.2)	0	(0.0)	1	(0.6)
Skin exfoliation	1	(1.2)	0	(0.0)	1	(0.6)
Skin irritation	6	(7.1)	2	(2.3)	8	(4.7)
Skin ulcer	0	(0.0)	1	(1.2)	1	(0.6)
Urticaria	1	(1.2)	0	(0.0)	1	(0.6)
Vascular disorders	2	(2.4)	1	(1.2)	3	(1.8)
Hypertension	1	(1.2)	0	(0.0)	1	(0.6)
Hypotension	1	(1.2)	1	(1.2)	2	(1.2)
Orthostatic hypotension	0	(0.0)	1	(1.2)	1	(0.6)
Every participant is counted a single time for each applicable row and column.
A system organ class or specific adverse event appears on this report only if its incidence in one or more of the columns meets the incidence criterion in the report title, after rounding.
Adverse event terms are from MedDRA Version 24.0.
Source: [CDISCpilot: adam-adsl; adae]