Introduction
create_ae_summary_table() makes safety tables for
treatment-emergent adverse events (TEAEs).
Quick Safety Report
Generate a complete safety report in one call:
# One-line safety report with multiple tables
quick_safety_report(
data = adae,
adsl = adsl,
output = "safety_report.docx",
title = "Safety Analysis",
include_overview = TRUE, # AE overview table
include_soc = TRUE, # SOC table
include_soc_pt = FALSE, # Skip SOC/PT (large)
include_sae = TRUE # SAE table
)The report automatically includes: - Overview of TEAEs, related AEs, SAEs, discontinuations - AEs by System Organ Class - Serious Adverse Events - Formatted Word document with proper styling
For detailed control of individual tables, use the functions below.
Table Types
| Type | Description | Key Variables |
|---|---|---|
overview |
Summary of TEAEs, related AEs, SAEs, discontinuations |
TRTEMFL, AEREL, AESER,
AEACN
|
soc |
AEs by System Organ Class | AEBODSYS |
soc_pt |
AEs by SOC and Preferred Term (hierarchical) |
AEBODSYS, AEDECOD
|
pt |
AEs by Preferred Term only | AEDECOD |
common |
Most frequently reported AEs | AEDECOD |
severity |
AEs by maximum severity | AESEV |
relationship |
AEs by relationship to study drug | AEREL |
sae |
Serious Adverse Events | AESER |
discontinuation |
AEs leading to discontinuation | AEACN |
deaths |
Deaths summary | DTHFL |
comparison |
AE comparison with RD/RR |
TRTEMFL, AEBODSYS,
AEDECOD
|
Setup
library(pharmhand)
library(dplyr)
library(tidyr)
# Set flextable defaults for readable tables in light/dark mode
flextable::set_flextable_defaults(
font.color = "#000000",
background.color = "#FFFFFF"
)
# Load example data from pharmaverseadam
adsl <- pharmaverseadam::adsl
adae <- pharmaverseadam::adae
adlb <- pharmaverseadam::adlbAE Overview Tables
# Create AE overview table
overview_table <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "overview",
title = "Table 1: Overview of Treatment-Emergent Adverse Events"
)
# Display the table
overview_table@flextableTable 1: Overview of Treatment-Emergent Adverse Events | |||
|---|---|---|---|
Category |
Placebo |
Xanomeline High Dose |
Xanomeline Low Dose |
Subjects with at least one TEAE |
65 (75.6%) |
75 (89.3%) |
77 (91.7%) |
Subjects with at least one related TEAE |
43 (50.0%) |
69 (82.1%) |
72 (85.7%) |
Subjects with at least one SAE |
0 (0.0%) |
2 (2.4%) |
1 (1.2%) |
Deaths |
2 (2.3%) |
0 (0.0%) |
1 (1.2%) |
The overview table calculates: - Subjects with ≥1 TEAE
(TRTEMFL == "Y") - Related TEAEs (AEREL in
[“RELATED”, “PROBABLE”, “POSSIBLE”]) - Serious AEs
(AESER == "Y") - AEs leading to discontinuation
(AEACN == "DRUG WITHDRAWN") - Deaths
(AEOUT == "FATAL")
AE by SOC Tables
# Create SOC table
soc_table <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "soc",
title = "Table 2: Treatment-Emergent Adverse Events by System Organ Class"
)
# Display the table
soc_table@flextableTable 2: Treatment-Emergent Adverse Events by System Organ Class | |||
|---|---|---|---|
Body System or Organ Class |
Placebo |
Xanomeline High Dose |
Xanomeline Low Dose |
CARDIAC DISORDERS |
12 (14%) |
15 (17.9%) |
13 (15.5%) |
CONGENITAL, FAMILIAL AND GENETIC DISORDERS |
0 (0.0%) |
2 (2.4%) |
1 (1.2%) |
EAR AND LABYRINTH DISORDERS |
1 (1.2%) |
1 (1.2%) |
2 (2.4%) |
EYE DISORDERS |
2 (2.3%) |
1 (1.2%) |
2 (2.4%) |
GASTROINTESTINAL DISORDERS |
17 (19.8%) |
20 (23.8%) |
14 (16.7%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
21 (24.4%) |
40 (47.6%) |
47 (56%) |
HEPATOBILIARY DISORDERS |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
IMMUNE SYSTEM DISORDERS |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
INFECTIONS AND INFESTATIONS |
16 (18.6%) |
13 (15.5%) |
9 (10.7%) |
INJURY, POISONING AND PROCEDURAL COMPLICATIONS |
4 (4.7%) |
5 (6%) |
5 (6%) |
INVESTIGATIONS |
10 (11.6%) |
6 (7.1%) |
6 (7.1%) |
METABOLISM AND NUTRITION DISORDERS |
6 (7%) |
2 (2.4%) |
1 (1.2%) |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
4 (4.7%) |
7 (8.3%) |
7 (8.3%) |
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) |
0 (0.0%) |
1 (1.2%) |
2 (2.4%) |
NERVOUS SYSTEM DISORDERS |
8 (9.3%) |
25 (29.8%) |
20 (23.8%) |
PSYCHIATRIC DISORDERS |
10 (11.6%) |
8 (9.5%) |
10 (11.9%) |
RENAL AND URINARY DISORDERS |
4 (4.7%) |
3 (3.6%) |
3 (3.6%) |
REPRODUCTIVE SYSTEM AND BREAST DISORDERS |
2 (2.3%) |
1 (1.2%) |
0 (0.0%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
8 (9.3%) |
10 (11.9%) |
9 (10.7%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
20 (23.3%) |
39 (46.4%) |
39 (46.4%) |
SOCIAL CIRCUMSTANCES |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
SURGICAL AND MEDICAL PROCEDURES |
2 (2.3%) |
2 (2.4%) |
1 (1.2%) |
VASCULAR DISORDERS |
3 (3.5%) |
1 (1.2%) |
3 (3.6%) |
Safety Population | |||
n (%) = Number (percentage) of subjects with at least one event | |||
SOC/PT Analysis
Click to expand: SOC/PT Hierarchical Table
# Create hierarchical SOC/PT table
soc_pt_table <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "soc_pt",
title = "Table 3: TEAEs by System Organ Class and Preferred Term"
)
# Display the table
soc_pt_table@flextableTable 3: TEAEs by System Organ Class and Preferred Term | ||||
|---|---|---|---|---|
Body System or Organ Class |
Dictionary-Derived Term |
Placebo |
Xanomeline High Dose |
Xanomeline Low Dose |
CARDIAC DISORDERS |
ATRIAL FIBRILLATION |
1 (1.2%) |
3 (3.6%) |
1 (1.2%) |
CARDIAC DISORDERS |
ATRIAL FLUTTER |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
CARDIAC DISORDERS |
ATRIAL HYPERTROPHY |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
CARDIAC DISORDERS |
ATRIOVENTRICULAR BLOCK FIRST DEGREE |
1 (1.2%) |
0 (0.0%) |
1 (1.2%) |
CARDIAC DISORDERS |
ATRIOVENTRICULAR BLOCK SECOND DEGREE |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
CARDIAC DISORDERS |
BRADYCARDIA |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
CARDIAC DISORDERS |
BUNDLE BRANCH BLOCK LEFT |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
CARDIAC DISORDERS |
BUNDLE BRANCH BLOCK RIGHT |
1 (1.2%) |
0 (0.0%) |
1 (1.2%) |
CARDIAC DISORDERS |
CARDIAC DISORDER |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
CARDIAC DISORDERS |
CARDIAC FAILURE CONGESTIVE |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
CARDIAC DISORDERS |
MYOCARDIAL INFARCTION |
4 (4.7%) |
4 (4.8%) |
2 (2.4%) |
CARDIAC DISORDERS |
PALPITATIONS |
0 (0.0%) |
0 (0.0%) |
2 (2.4%) |
CARDIAC DISORDERS |
SINUS ARRHYTHMIA |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
CARDIAC DISORDERS |
SINUS BRADYCARDIA |
2 (2.3%) |
8 (9.5%) |
7 (8.3%) |
CARDIAC DISORDERS |
SUPRAVENTRICULAR EXTRASYSTOLES |
1 (1.2%) |
1 (1.2%) |
1 (1.2%) |
CARDIAC DISORDERS |
SUPRAVENTRICULAR TACHYCARDIA |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
CARDIAC DISORDERS |
TACHYCARDIA |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
CARDIAC DISORDERS |
VENTRICULAR EXTRASYSTOLES |
0 (0.0%) |
1 (1.2%) |
2 (2.4%) |
CARDIAC DISORDERS |
VENTRICULAR HYPERTROPHY |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
CARDIAC DISORDERS |
WOLFF-PARKINSON-WHITE SYNDROME |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
CONGENITAL, FAMILIAL AND GENETIC DISORDERS |
VENTRICULAR SEPTAL DEFECT |
0 (0.0%) |
2 (2.4%) |
1 (1.2%) |
EAR AND LABYRINTH DISORDERS |
CERUMEN IMPACTION |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
EAR AND LABYRINTH DISORDERS |
EAR PAIN |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
EAR AND LABYRINTH DISORDERS |
VERTIGO |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
EYE DISORDERS |
CONJUNCTIVAL HAEMORRHAGE |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
EYE DISORDERS |
CONJUNCTIVITIS |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
EYE DISORDERS |
EYE ALLERGY |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
EYE DISORDERS |
EYE PRURITUS |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
EYE DISORDERS |
EYE SWELLING |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
EYE DISORDERS |
VISION BLURRED |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
GASTROINTESTINAL DISORDERS |
ABDOMINAL DISCOMFORT |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
GASTROINTESTINAL DISORDERS |
ABDOMINAL PAIN |
1 (1.2%) |
1 (1.2%) |
3 (3.6%) |
GASTROINTESTINAL DISORDERS |
CONSTIPATION |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
GASTROINTESTINAL DISORDERS |
DIARRHOEA |
9 (10.5%) |
4 (4.8%) |
4 (4.8%) |
GASTROINTESTINAL DISORDERS |
DYSPEPSIA |
1 (1.2%) |
0 (0.0%) |
1 (1.2%) |
GASTROINTESTINAL DISORDERS |
DYSPHAGIA |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
GASTROINTESTINAL DISORDERS |
FLATULENCE |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
GASTROINTESTINAL DISORDERS |
GASTROINTESTINAL HAEMORRHAGE |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
GASTROINTESTINAL DISORDERS |
GASTROOESOPHAGEAL REFLUX DISEASE |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
GASTROINTESTINAL DISORDERS |
GLOSSITIS |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
GASTROINTESTINAL DISORDERS |
HIATUS HERNIA |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
GASTROINTESTINAL DISORDERS |
NAUSEA |
3 (3.5%) |
6 (7.1%) |
3 (3.6%) |
GASTROINTESTINAL DISORDERS |
RECTAL HAEMORRHAGE |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
GASTROINTESTINAL DISORDERS |
SALIVARY HYPERSECRETION |
0 (0.0%) |
4 (4.8%) |
0 (0.0%) |
GASTROINTESTINAL DISORDERS |
STOMACH DISCOMFORT |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
GASTROINTESTINAL DISORDERS |
VOMITING |
3 (3.5%) |
7 (8.3%) |
3 (3.6%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE BLEEDING |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE DERMATITIS |
5 (5.8%) |
7 (8.3%) |
9 (10.7%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE DESQUAMATION |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE DISCHARGE |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE DISCOLOURATION |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE ERYTHEMA |
3 (3.5%) |
15 (17.9%) |
12 (14.3%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE INDURATION |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE IRRITATION |
3 (3.5%) |
9 (10.7%) |
9 (10.7%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE PAIN |
0 (0.0%) |
2 (2.4%) |
0 (0.0%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE PERSPIRATION |
0 (0.0%) |
2 (2.4%) |
0 (0.0%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE PRURITUS |
6 (7%) |
22 (26.2%) |
22 (26.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE REACTION |
1 (1.2%) |
1 (1.2%) |
0 (0.0%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE SWELLING |
0 (0.0%) |
2 (2.4%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE URTICARIA |
0 (0.0%) |
1 (1.2%) |
2 (2.4%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE VESICLES |
1 (1.2%) |
6 (7.1%) |
4 (4.8%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE WARMTH |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
ASTHENIA |
1 (1.2%) |
1 (1.2%) |
0 (0.0%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
CHEST DISCOMFORT |
0 (0.0%) |
2 (2.4%) |
0 (0.0%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
CHEST PAIN |
0 (0.0%) |
2 (2.4%) |
0 (0.0%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
CHILLS |
1 (1.2%) |
1 (1.2%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
FATIGUE |
1 (1.2%) |
5 (6%) |
5 (6%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
FEELING ABNORMAL |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
FEELING COLD |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
INFLAMMATION |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
MALAISE |
0 (0.0%) |
2 (2.4%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
OEDEMA |
0 (0.0%) |
0 (0.0%) |
2 (2.4%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
OEDEMA PERIPHERAL |
2 (2.3%) |
2 (2.4%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
PAIN |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
PYREXIA |
2 (2.3%) |
1 (1.2%) |
0 (0.0%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
SECRETION DISCHARGE |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
SUDDEN DEATH |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
SWELLING |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
ULCER |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
HEPATOBILIARY DISORDERS |
HYPERBILIRUBINAEMIA |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
IMMUNE SYSTEM DISORDERS |
HYPERSENSITIVITY |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
INFECTIONS AND INFESTATIONS |
BRONCHITIS |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
INFECTIONS AND INFESTATIONS |
CELLULITIS |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
INFECTIONS AND INFESTATIONS |
CERVICITIS |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
INFECTIONS AND INFESTATIONS |
CYSTITIS |
1 (1.2%) |
1 (1.2%) |
0 (0.0%) |
INFECTIONS AND INFESTATIONS |
EAR INFECTION |
2 (2.3%) |
0 (0.0%) |
0 (0.0%) |
INFECTIONS AND INFESTATIONS |
GASTROENTERITIS VIRAL |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
INFECTIONS AND INFESTATIONS |
HORDEOLUM |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
INFECTIONS AND INFESTATIONS |
INFLUENZA |
1 (1.2%) |
1 (1.2%) |
1 (1.2%) |
INFECTIONS AND INFESTATIONS |
LOCALISED INFECTION |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
INFECTIONS AND INFESTATIONS |
LOWER RESPIRATORY TRACT INFECTION |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
INFECTIONS AND INFESTATIONS |
NASOPHARYNGITIS |
2 (2.3%) |
6 (7.1%) |
4 (4.8%) |
INFECTIONS AND INFESTATIONS |
PNEUMONIA |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
INFECTIONS AND INFESTATIONS |
RHINITIS |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
INFECTIONS AND INFESTATIONS |
UPPER RESPIRATORY TRACT INFECTION |
6 (7%) |
3 (3.6%) |
1 (1.2%) |
INFECTIONS AND INFESTATIONS |
URINARY TRACT INFECTION |
2 (2.3%) |
1 (1.2%) |
0 (0.0%) |
INFECTIONS AND INFESTATIONS |
VAGINAL MYCOSIS |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
INFECTIONS AND INFESTATIONS |
VIRAL INFECTION |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
INJURY, POISONING AND PROCEDURAL COMPLICATIONS |
CONTUSION |
1 (1.2%) |
2 (2.4%) |
1 (1.2%) |
INJURY, POISONING AND PROCEDURAL COMPLICATIONS |
EXCORIATION |
2 (2.3%) |
1 (1.2%) |
1 (1.2%) |
INJURY, POISONING AND PROCEDURAL COMPLICATIONS |
FACIAL BONES FRACTURE |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
INJURY, POISONING AND PROCEDURAL COMPLICATIONS |
FALL |
1 (1.2%) |
1 (1.2%) |
2 (2.4%) |
INJURY, POISONING AND PROCEDURAL COMPLICATIONS |
HIP FRACTURE |
1 (1.2%) |
2 (2.4%) |
0 (0.0%) |
INJURY, POISONING AND PROCEDURAL COMPLICATIONS |
JOINT DISLOCATION |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
INJURY, POISONING AND PROCEDURAL COMPLICATIONS |
SKIN LACERATION |
1 (1.2%) |
0 (0.0%) |
2 (2.4%) |
INJURY, POISONING AND PROCEDURAL COMPLICATIONS |
WOUND |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
INVESTIGATIONS |
BIOPSY |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
INVESTIGATIONS |
BIOPSY PROSTATE |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
INVESTIGATIONS |
BLOOD ALKALINE PHOSPHATASE INCREASED |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
INVESTIGATIONS |
BLOOD CHOLESTEROL INCREASED |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
INVESTIGATIONS |
BLOOD CREATINE PHOSPHOKINASE INCREASED |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
INVESTIGATIONS |
BLOOD GLUCOSE INCREASED |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
INVESTIGATIONS |
BLOOD URINE PRESENT |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
INVESTIGATIONS |
BODY TEMPERATURE INCREASED |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
INVESTIGATIONS |
CYSTOSCOPY |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
INVESTIGATIONS |
ELECTROCARDIOGRAM ST SEGMENT DEPRESSION |
4 (4.7%) |
0 (0.0%) |
1 (1.2%) |
INVESTIGATIONS |
ELECTROCARDIOGRAM T WAVE AMPLITUDE DECREASED |
1 (1.2%) |
0 (0.0%) |
1 (1.2%) |
INVESTIGATIONS |
ELECTROCARDIOGRAM T WAVE INVERSION |
2 (2.3%) |
1 (1.2%) |
1 (1.2%) |
INVESTIGATIONS |
HEART RATE INCREASED |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
INVESTIGATIONS |
HEART RATE IRREGULAR |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
INVESTIGATIONS |
NASAL MUCOSA BIOPSY |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
INVESTIGATIONS |
WEIGHT DECREASED |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
METABOLISM AND NUTRITION DISORDERS |
DECREASED APPETITE |
1 (1.2%) |
1 (1.2%) |
0 (0.0%) |
METABOLISM AND NUTRITION DISORDERS |
DEHYDRATION |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
METABOLISM AND NUTRITION DISORDERS |
DIABETES MELLITUS |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
METABOLISM AND NUTRITION DISORDERS |
FOOD CRAVING |
1 (1.2%) |
0 (0.0%) |
1 (1.2%) |
METABOLISM AND NUTRITION DISORDERS |
HYPONATRAEMIA |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
METABOLISM AND NUTRITION DISORDERS |
INCREASED APPETITE |
1 (1.2%) |
1 (1.2%) |
0 (0.0%) |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
ARTHRALGIA |
1 (1.2%) |
1 (1.2%) |
2 (2.4%) |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
ARTHRITIS |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
BACK PAIN |
1 (1.2%) |
3 (3.6%) |
1 (1.2%) |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
FLANK PAIN |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
MUSCLE SPASMS |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
MUSCULAR WEAKNESS |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
MYALGIA |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
PAIN IN EXTREMITY |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
SHOULDER PAIN |
1 (1.2%) |
0 (0.0%) |
2 (2.4%) |
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) |
COLON CANCER |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) |
MALIGNANT FIBROUS HISTIOCYTOMA |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) |
PROSTATE CANCER |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
AMNESIA |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
BALANCE DISORDER |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
NERVOUS SYSTEM DISORDERS |
BURNING SENSATION |
0 (0.0%) |
2 (2.4%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
COGNITIVE DISORDER |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
COMPLEX PARTIAL SEIZURES |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
NERVOUS SYSTEM DISORDERS |
COORDINATION ABNORMAL |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
NERVOUS SYSTEM DISORDERS |
DIZZINESS |
2 (2.3%) |
11 (13.1%) |
8 (9.5%) |
NERVOUS SYSTEM DISORDERS |
HEADACHE |
3 (3.5%) |
5 (6%) |
3 (3.6%) |
NERVOUS SYSTEM DISORDERS |
HEMIANOPIA HOMONYMOUS |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
NERVOUS SYSTEM DISORDERS |
HYPERSOMNIA |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
LETHARGY |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
NERVOUS SYSTEM DISORDERS |
PARAESTHESIA |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
PARAESTHESIA ORAL |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
NERVOUS SYSTEM DISORDERS |
PARKINSON'S DISEASE |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
PAROSMIA |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
PARTIAL SEIZURES WITH SECONDARY GENERALISATION |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
PSYCHOMOTOR HYPERACTIVITY |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
SOMNOLENCE |
2 (2.3%) |
1 (1.2%) |
3 (3.6%) |
NERVOUS SYSTEM DISORDERS |
STUPOR |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
NERVOUS SYSTEM DISORDERS |
SYNCOPE |
0 (0.0%) |
3 (3.6%) |
4 (4.8%) |
NERVOUS SYSTEM DISORDERS |
SYNCOPE VASOVAGAL |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
TRANSIENT ISCHAEMIC ATTACK |
0 (0.0%) |
1 (1.2%) |
2 (2.4%) |
PSYCHIATRIC DISORDERS |
AGITATION |
2 (2.3%) |
1 (1.2%) |
2 (2.4%) |
PSYCHIATRIC DISORDERS |
ANXIETY |
0 (0.0%) |
0 (0.0%) |
3 (3.6%) |
PSYCHIATRIC DISORDERS |
COMPLETED SUICIDE |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
PSYCHIATRIC DISORDERS |
CONFUSIONAL STATE |
2 (2.3%) |
1 (1.2%) |
3 (3.6%) |
PSYCHIATRIC DISORDERS |
DELIRIUM |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
PSYCHIATRIC DISORDERS |
DELUSION |
1 (1.2%) |
1 (1.2%) |
0 (0.0%) |
PSYCHIATRIC DISORDERS |
DEPRESSED MOOD |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
PSYCHIATRIC DISORDERS |
DISORIENTATION |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
PSYCHIATRIC DISORDERS |
HALLUCINATION |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
PSYCHIATRIC DISORDERS |
HALLUCINATION, VISUAL |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
PSYCHIATRIC DISORDERS |
INSOMNIA |
2 (2.3%) |
2 (2.4%) |
0 (0.0%) |
PSYCHIATRIC DISORDERS |
IRRITABILITY |
1 (1.2%) |
0 (0.0%) |
1 (1.2%) |
PSYCHIATRIC DISORDERS |
LIBIDO DECREASED |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
PSYCHIATRIC DISORDERS |
LISTLESS |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
PSYCHIATRIC DISORDERS |
NIGHTMARE |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
PSYCHIATRIC DISORDERS |
RESTLESSNESS |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
RENAL AND URINARY DISORDERS |
CALCULUS URETHRAL |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
RENAL AND URINARY DISORDERS |
DYSURIA |
1 (1.2%) |
0 (0.0%) |
1 (1.2%) |
RENAL AND URINARY DISORDERS |
INCONTINENCE |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
RENAL AND URINARY DISORDERS |
MICTURITION URGENCY |
1 (1.2%) |
1 (1.2%) |
1 (1.2%) |
RENAL AND URINARY DISORDERS |
NEPHROLITHIASIS |
1 (1.2%) |
1 (1.2%) |
0 (0.0%) |
RENAL AND URINARY DISORDERS |
POLLAKIURIA |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
REPRODUCTIVE SYSTEM AND BREAST DISORDERS |
BENIGN PROSTATIC HYPERPLASIA |
1 (1.2%) |
1 (1.2%) |
0 (0.0%) |
REPRODUCTIVE SYSTEM AND BREAST DISORDERS |
PELVIC PAIN |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
ALLERGIC GRANULOMATOUS ANGIITIS |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
COUGH |
1 (1.2%) |
5 (6%) |
5 (6%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
DYSPHONIA |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
DYSPNOEA |
1 (1.2%) |
1 (1.2%) |
1 (1.2%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
EMPHYSEMA |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
EPISTAXIS |
0 (0.0%) |
2 (2.4%) |
1 (1.2%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
HAEMOPTYSIS |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
NASAL CONGESTION |
3 (3.5%) |
3 (3.6%) |
1 (1.2%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
PHARYNGEAL ERYTHEMA |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
PHARYNGOLARYNGEAL PAIN |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
POSTNASAL DRIP |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
PRODUCTIVE COUGH |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
RALES |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
RESPIRATORY TRACT CONGESTION |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
RHINORRHOEA |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
ACTINIC KERATOSIS |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
ALOPECIA |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
BLISTER |
0 (0.0%) |
1 (1.2%) |
5 (6%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
COLD SWEAT |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
DERMATITIS CONTACT |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
DRUG ERUPTION |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
ERYTHEMA |
8 (9.3%) |
14 (16.7%) |
14 (16.7%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
HYPERHIDROSIS |
2 (2.3%) |
8 (9.5%) |
4 (4.8%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
PRURITUS |
8 (9.3%) |
25 (29.8%) |
21 (25%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
PRURITUS GENERALISED |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
RASH |
5 (5.8%) |
8 (9.5%) |
13 (15.5%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
RASH ERYTHEMATOUS |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
RASH MACULO-PAPULAR |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
RASH PRURITIC |
0 (0.0%) |
2 (2.4%) |
1 (1.2%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
SKIN EXFOLIATION |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
SKIN IRRITATION |
3 (3.5%) |
5 (6%) |
6 (7.1%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
SKIN ODOUR ABNORMAL |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
SKIN ULCER |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
URTICARIA |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
SOCIAL CIRCUMSTANCES |
ALCOHOL USE |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
SURGICAL AND MEDICAL PROCEDURES |
ACROCHORDON EXCISION |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
SURGICAL AND MEDICAL PROCEDURES |
CATARACT OPERATION |
1 (1.2%) |
0 (0.0%) |
1 (1.2%) |
SURGICAL AND MEDICAL PROCEDURES |
EYE LASER SURGERY |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
SURGICAL AND MEDICAL PROCEDURES |
SKIN LESION EXCISION |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
VASCULAR DISORDERS |
HOT FLUSH |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
VASCULAR DISORDERS |
HYPERTENSION |
1 (1.2%) |
0 (0.0%) |
1 (1.2%) |
VASCULAR DISORDERS |
HYPOTENSION |
2 (2.3%) |
0 (0.0%) |
1 (1.2%) |
VASCULAR DISORDERS |
ORTHOSTATIC HYPOTENSION |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
VASCULAR DISORDERS |
WOUND HAEMORRHAGE |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
Safety Population | ||||
n (%) = Number (percentage) of subjects with at least one event | ||||
Most Common AEs
# Create table of most common AEs (top 10)
common_table <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "common",
n_top = 10,
title = "Table 4: Most Common Treatment-Emergent Adverse Events (Top 10)"
)
# Display the table
common_table@flextableTable 4: Most Common Treatment-Emergent Adverse Events (Top 10) | ||||
|---|---|---|---|---|
Body System or Organ Class |
Dictionary-Derived Term |
Placebo |
Xanomeline High Dose |
Xanomeline Low Dose |
CARDIAC DISORDERS |
SINUS BRADYCARDIA |
2 (2.3%) |
8 (9.5%) |
7 (8.3%) |
GASTROINTESTINAL DISORDERS |
DIARRHOEA |
9 (10.5%) |
4 (4.8%) |
4 (4.8%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE DERMATITIS |
5 (5.8%) |
7 (8.3%) |
9 (10.7%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE ERYTHEMA |
3 (3.5%) |
15 (17.9%) |
12 (14.3%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE IRRITATION |
3 (3.5%) |
9 (10.7%) |
9 (10.7%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE PRURITUS |
6 (7%) |
22 (26.2%) |
22 (26.2%) |
NERVOUS SYSTEM DISORDERS |
DIZZINESS |
2 (2.3%) |
11 (13.1%) |
8 (9.5%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
ERYTHEMA |
8 (9.3%) |
14 (16.7%) |
14 (16.7%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
PRURITUS |
8 (9.3%) |
25 (29.8%) |
21 (25%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
RASH |
5 (5.8%) |
8 (9.5%) |
13 (15.5%) |
Safety Population | ||||
Showing top 10 most frequently reported Preferred Terms | ||||
Severity Analysis
# Create severity table
severity_table <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "severity",
title = "Table 5: Subjects by Maximum Adverse Event Severity"
)
# Display the table
severity_table@flextableTable 5: Subjects by Maximum Adverse Event Severity | |||
|---|---|---|---|
Maximum Severity |
Placebo |
Xanomeline High Dose |
Xanomeline Low Dose |
MILD |
36 (41.9%) |
22 (26.2%) |
19 (22.6%) |
MODERATE |
24 (27.9%) |
45 (53.6%) |
42 (50%) |
SEVERE |
5 (5.8%) |
8 (9.5%) |
16 (19%) |
Safety Population | |||
Maximum severity across all TEAEs per subject | |||
Severity categories order as: MILD → MODERATE → SEVERE.
Relationship Analysis
# Create relationship table
relationship_table <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "relationship",
title = "Table 6: Treatment-Emergent AEs by Relationship to Study Drug"
)
# Display the table
relationship_table@flextableTable 6: Treatment-Emergent AEs by Relationship to Study Drug | |||
|---|---|---|---|
Causality |
Placebo |
Xanomeline High Dose |
Xanomeline Low Dose |
PROBABLE |
23 (26.7%) |
50 (59.5%) |
49 (58.3%) |
REMOTE |
28 (32.6%) |
21 (25%) |
23 (27.4%) |
POSSIBLE |
25 (29.1%) |
47 (56%) |
44 (52.4%) |
NONE |
33 (38.4%) |
41 (48.8%) |
29 (34.5%) |
-- |
0 (0.0%) |
0 (0.0%) |
2 (2.4%) |
Safety Population | |||
Subjects counted once per relationship category | |||
SAE Tables
# Create SAE table
sae_table <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "sae",
title = "Table 7: Serious Adverse Events"
)
# Display the table
sae_table@flextableTable 7: Serious Adverse Events | |||
|---|---|---|---|
Body System or Organ Class |
Dictionary-Derived Term |
Xanomeline High Dose |
Xanomeline Low Dose |
NERVOUS SYSTEM DISORDERS |
PARTIAL SEIZURES WITH SECONDARY GENERALISATION |
1 (1.2%) |
0 (0.0%) |
NERVOUS SYSTEM DISORDERS |
SYNCOPE |
1 (1.2%) |
1 (1.2%) |
Safety Population | |||
SAE = Serious Adverse Event (AESER = 'Y') | |||
Shows message if no SAEs reported.
Deaths and Discontinuations
Discontinuation
# Create discontinuation table
disc_table <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "discontinuation",
title = "Table 8: AEs Leading to Study Drug Discontinuation"
)
# Display the table
disc_table@flextableTable 8: AEs Leading to Study Drug Discontinuation |
|---|
Message |
No adverse events leading to study drug discontinuation |
Safety Population |
AEACN = 'DRUG WITHDRAWN' |
Deaths Summary
# Create deaths summary table
deaths_table <- create_ae_summary_table(
data = NULL, # Not needed for deaths
adsl = adsl,
type = "deaths",
title = "Table 9: Deaths Summary"
)
# Display the table
deaths_table@flextableTable 9: Deaths Summary | |||
|---|---|---|---|
Statistic |
Placebo |
Xanomeline High Dose |
Xanomeline Low Dose |
Safety Population (N) |
86 |
84 |
84 |
Deaths n (%) |
2 (2.3%) |
0 (0%) |
1 (1.2%) |
Safety Population | |||
DTHFL = 'Y' | |||
Lab Shift Tables
Click to expand: Lab Shift Table
# Example of lab shift analysis
trt_n <- adsl |>
dplyr::group_by(TRT01P) |>
dplyr::summarise(N = dplyr::n(), .groups = "drop")
lab_shift_table <- create_lab_shift_table(
data = adlb,
title = "Table 10: Lab Shift from Baseline to Max Post-Baseline"
)
# Display the table
lab_shift_table@flextableTable 10: Lab Shift from Baseline to Max Post-Baseline | ||||
|---|---|---|---|---|
Planned Treatment for Period 01 |
Baseline Reference Range Indicator |
NORMAL |
HIGH |
LOW |
Placebo |
NORMAL |
51 |
2 |
1 |
Xanomeline High Dose |
NORMAL |
28 |
0 |
0 |
Xanomeline Low Dose |
NORMAL |
24 |
2 |
0 |
Xanomeline High Dose |
HIGH |
2 |
0 |
0 |
Placebo |
HIGH |
3 |
0 |
0 |
Safety Population | ||||
Shift from baseline normal range indicator | ||||
Customization
Treatment Variable
# Use different treatment variable
overview_trtp <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "overview",
trt_var = "TRT01P", # Planned treatment
title = "Overview by Planned Treatment"
)
# Display the table
overview_trtp@flextableOverview by Planned Treatment | |||
|---|---|---|---|
Category |
Placebo |
Xanomeline High Dose |
Xanomeline Low Dose |
Subjects with at least one TEAE |
65 (75.6%) |
75 (89.3%) |
77 (91.7%) |
Subjects with at least one related TEAE |
43 (50.0%) |
69 (82.1%) |
72 (85.7%) |
Subjects with at least one SAE |
0 (0.0%) |
2 (2.4%) |
1 (1.2%) |
Deaths |
2 (2.3%) |
0 (0.0%) |
1 (1.2%) |
Top AEs
# Show top 5 instead of default 15
common_top5 <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "common",
n_top = 5,
title = "Top 5 Most Common AEs"
)
# Display the table
common_top5@flextableTop 5 Most Common AEs | ||||
|---|---|---|---|---|
Body System or Organ Class |
Dictionary-Derived Term |
Placebo |
Xanomeline High Dose |
Xanomeline Low Dose |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE ERYTHEMA |
3 (3.5%) |
15 (17.9%) |
12 (14.3%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
APPLICATION SITE PRURITUS |
6 (7%) |
22 (26.2%) |
22 (26.2%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
ERYTHEMA |
8 (9.3%) |
14 (16.7%) |
14 (16.7%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
PRURITUS |
8 (9.3%) |
25 (29.8%) |
21 (25%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
RASH |
5 (5.8%) |
8 (9.5%) |
13 (15.5%) |
Safety Population | ||||
Showing top 5 most frequently reported Preferred Terms | ||||
SOC Analysis
# Analyze only skin and subcutaneous tissue disorders
rash_table <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "pt",
soc = "SKIN AND SUBCUTANEOUS TISSUE DISORDERS",
title = "Table: Skin and Subcutaneous Tissue Disorders by Preferred Term"
)
# Display the table
rash_table@flextableTable: Skin and Subcutaneous Tissue Disorders by Preferred Term | |||
|---|---|---|---|
Dictionary-Derived Term |
Placebo |
Xanomeline Low Dose |
Xanomeline High Dose |
ACTINIC KERATOSIS |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
ALOPECIA |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
BLISTER |
0 (0.0%) |
5 (6%) |
1 (1.2%) |
COLD SWEAT |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
DERMATITIS CONTACT |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
DRUG ERUPTION |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
ERYTHEMA |
8 (9.3%) |
14 (16.7%) |
14 (16.7%) |
HYPERHIDROSIS |
2 (2.3%) |
4 (4.8%) |
8 (9.5%) |
PRURITUS |
8 (9.3%) |
21 (25%) |
25 (29.8%) |
PRURITUS GENERALISED |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
RASH |
5 (5.8%) |
13 (15.5%) |
8 (9.5%) |
RASH ERYTHEMATOUS |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
RASH MACULO-PAPULAR |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
RASH PRURITIC |
0 (0.0%) |
1 (1.2%) |
2 (2.4%) |
SKIN EXFOLIATION |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
SKIN IRRITATION |
3 (3.5%) |
6 (7.1%) |
5 (6%) |
SKIN ODOUR ABNORMAL |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
SKIN ULCER |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
URTICARIA |
0 (0.0%) |
1 (1.2%) |
1 (1.2%) |
Table Formatting
# Create table without autofit (for custom formatting)
soc_manual <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "soc",
autofit = FALSE,
title = "Manual Format Example"
)
# Access the underlying flextable for custom formatting
soc_ft <- soc_manual@flextable
# Display the table
soc_ftManual Format Example | |||
|---|---|---|---|
Body System or Organ Class |
Placebo |
Xanomeline High Dose |
Xanomeline Low Dose |
CARDIAC DISORDERS |
12 (14%) |
15 (17.9%) |
13 (15.5%) |
CONGENITAL, FAMILIAL AND GENETIC DISORDERS |
0 (0.0%) |
2 (2.4%) |
1 (1.2%) |
EAR AND LABYRINTH DISORDERS |
1 (1.2%) |
1 (1.2%) |
2 (2.4%) |
EYE DISORDERS |
2 (2.3%) |
1 (1.2%) |
2 (2.4%) |
GASTROINTESTINAL DISORDERS |
17 (19.8%) |
20 (23.8%) |
14 (16.7%) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
21 (24.4%) |
40 (47.6%) |
47 (56%) |
HEPATOBILIARY DISORDERS |
1 (1.2%) |
0 (0.0%) |
0 (0.0%) |
IMMUNE SYSTEM DISORDERS |
0 (0.0%) |
0 (0.0%) |
1 (1.2%) |
INFECTIONS AND INFESTATIONS |
16 (18.6%) |
13 (15.5%) |
9 (10.7%) |
INJURY, POISONING AND PROCEDURAL COMPLICATIONS |
4 (4.7%) |
5 (6%) |
5 (6%) |
INVESTIGATIONS |
10 (11.6%) |
6 (7.1%) |
6 (7.1%) |
METABOLISM AND NUTRITION DISORDERS |
6 (7%) |
2 (2.4%) |
1 (1.2%) |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
4 (4.7%) |
7 (8.3%) |
7 (8.3%) |
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) |
0 (0.0%) |
1 (1.2%) |
2 (2.4%) |
NERVOUS SYSTEM DISORDERS |
8 (9.3%) |
25 (29.8%) |
20 (23.8%) |
PSYCHIATRIC DISORDERS |
10 (11.6%) |
8 (9.5%) |
10 (11.9%) |
RENAL AND URINARY DISORDERS |
4 (4.7%) |
3 (3.6%) |
3 (3.6%) |
REPRODUCTIVE SYSTEM AND BREAST DISORDERS |
2 (2.3%) |
1 (1.2%) |
0 (0.0%) |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
8 (9.3%) |
10 (11.9%) |
9 (10.7%) |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
20 (23.3%) |
39 (46.4%) |
39 (46.4%) |
SOCIAL CIRCUMSTANCES |
0 (0.0%) |
1 (1.2%) |
0 (0.0%) |
SURGICAL AND MEDICAL PROCEDURES |
2 (2.3%) |
2 (2.4%) |
1 (1.2%) |
VASCULAR DISORDERS |
3 (3.5%) |
1 (1.2%) |
3 (3.6%) |
Safety Population | |||
n (%) = Number (percentage) of subjects with at least one event | |||
Export to Word
# Create multiple safety tables
safety_tables <- list(
overview = create_ae_summary_table(data = adae, adsl = adsl, type = "overview"),
soc = create_ae_summary_table(data = adae, adsl = adsl, type = "soc"),
common = create_ae_summary_table(data = adae, adsl = adsl, type = "common", n_top = 10),
sae = create_ae_summary_table(data = adae, adsl = adsl, type = "sae")
)
# Create report sections
safety_sections <- lapply(names(safety_tables), function(table_name) {
ReportSection(
title = paste("Safety Analysis:", table_name),
section_type = "safety",
content = list(safety_tables[[table_name]])
)
})
# Create clinical report
safety_report <- ClinicalReport(
study_id = "CDISCPILOT01",
study_title = "Safety Analysis Report",
sections = safety_sections
)
# Export to Word
# generate_word(safety_report, path = "safety_report.docx")
cat("Safety report structure created with", length(safety_tables), "tables.")
#> Safety report structure created with 4 tables.
cat("\nUse generate_word() to export to Word.")
#>
#> Use generate_word() to export to Word.Time-to-Event Analysis
# Calculate time-to-event data for a specific SOC
tte_data <- calculate_ae_tte_data(
adsl = adsl,
adae = adae,
soc = "Skin and subcutaneous tissue disorders"
)
# Preview TTE data structure
head(tte_data, 3)
#> # A tibble: 3 × 57
#> STUDYID USUBJID SUBJID RFSTDTC RFENDTC RFXSTDTC RFXENDTC RFICDTC RFPENDTC
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 CDISCPILOT01 01-701… 1015 2014-0… 2014-0… 2014-01… 2014-07… NA 2014-07…
#> 2 CDISCPILOT01 01-701… 1023 2012-0… 2012-0… 2012-08… 2012-09… NA 2013-02…
#> 3 CDISCPILOT01 01-701… 1028 2013-0… 2014-0… 2013-07… 2014-01… NA 2014-01…
#> # ℹ 48 more variables: DTHDTC <chr>, DTHFL <chr>, SITEID <chr>, AGE <dbl>,
#> # AGEU <chr>, SEX <chr>, RACE <chr>, ETHNIC <chr>, ARMCD <chr>, ARM <chr>,
#> # ACTARMCD <chr>, ACTARM <chr>, COUNTRY <chr>, DMDTC <chr>, DMDY <dbl>,
#> # TRT01P <chr>, TRT01A <chr>, TRTSDTM <dttm>, TRTSTMF <chr>, TRTEDTM <dttm>,
#> # TRTETMF <chr>, TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, SCRFDT <date>,
#> # EOSDT <date>, EOSSTT <chr>, FRVDT <date>, RANDDT <date>, DTHDT <date>,
#> # DTHDTF <chr>, DTHADY <dbl>, LDDTHELD <dbl>, DTHCAUS <chr>, DTHDOM <chr>, …
# Create KM plot
km_plot <- create_ae_km_plot_for_soc(
adsl = adsl,
adae = adae,
soc = "Skin and subcutaneous tissue disorders"
)
print(km_plot@plot)
AE Statistical Comparisons (Risk Difference)
For GBA/AMNOG dossiers, comparing adverse event rates between
treatment groups with risk differences and risk ratios is essential. The
create_ae_comparison_table() function provides these
statistics.
Basic Comparison Table
# Create AE comparison table with risk differences
comparison_table <- create_ae_summary_table(
data = adae,
adsl = adsl,
type = "comparison",
ref_group = "Placebo",
by = "soc",
title = "Table: AE Comparison by System Organ Class"
)
# Display the table
comparison_table@flextableTable: AE Comparison by System Organ Class | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Body System or Organ Class |
Placebo |
Xanomeline High Dose |
RD Xanomeline High Dose vs Placebo |
NNH Xanomeline High Dose vs Placebo |
RR Xanomeline High Dose vs Placebo |
P-value (Xanomeline High Dose vs Placebo) |
Xanomeline Low Dose |
RD Xanomeline Low Dose vs Placebo |
NNH Xanomeline Low Dose vs Placebo |
RR Xanomeline Low Dose vs Placebo |
P-value (Xanomeline Low Dose vs Placebo) |
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS |
21/86 (24.4%) |
40/84 (47.6%) |
23.2% (9.2%, 37.2%) |
4.3 (2.7, 10.9) |
1.95 (1.26, 3.01) |
0.002 |
47/84 (56.0%) |
31.5% (17.6%, 45.5%) |
3.2 (2.2, 5.7) |
2.29 (1.51, 3.48) |
<0.001 |
SKIN AND SUBCUTANEOUS TISSUE DISORDERS |
20/86 (23.3%) |
39/84 (46.4%) |
23.2% (9.3%, 37.1%) |
4.3 (2.7, 10.8) |
2.00 (1.28, 3.12) |
0.002 |
39/84 (46.4%) |
23.2% (9.3%, 37.1%) |
4.3 (2.7, 10.8) |
2.00 (1.28, 3.12) |
0.002 |
NERVOUS SYSTEM DISORDERS |
8/86 (9.3%) |
25/84 (29.8%) |
20.5% (8.9%, 32.0%) |
4.9 (3.1, 11.2) |
3.20 (1.53, 6.69) |
<0.001 |
20/84 (23.8%) |
14.5% (3.5%, 25.5%) |
6.9 (3.9, 28.4) |
2.56 (1.19, 5.49) |
0.011 |
GASTROINTESTINAL DISORDERS |
17/86 (19.8%) |
20/84 (23.8%) |
4.0% (-8.4%, 16.4%) |
NE |
1.20 (0.68, 2.13) |
0.523 |
14/84 (16.7%) |
-3.1% (-14.7%, 8.5%) |
NE |
0.84 (0.44, 1.60) |
0.601 |
INFECTIONS AND INFESTATIONS |
16/86 (18.6%) |
13/84 (15.5%) |
-3.1% (-14.4%, 8.2%) |
NE |
0.83 (0.43, 1.62) |
0.588 |
9/84 (10.7%) |
-7.9% (-18.4%, 2.7%) |
NE |
0.58 (0.27, 1.23) |
0.146 |
CARDIAC DISORDERS |
12/86 (14.0%) |
15/84 (17.9%) |
3.9% (-7.1%, 14.9%) |
NE |
1.28 (0.64, 2.57) |
0.486 |
13/84 (15.5%) |
1.5% (-9.1%, 12.2%) |
NE |
1.11 (0.54, 2.29) |
0.779 |
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS |
8/86 (9.3%) |
10/84 (11.9%) |
2.6% (-6.7%, 11.9%) |
NE |
1.28 (0.53, 3.08) |
0.581 |
9/84 (10.7%) |
1.4% (-7.6%, 10.4%) |
NE |
1.15 (0.47, 2.84) |
0.759 |
PSYCHIATRIC DISORDERS |
10/86 (11.6%) |
8/84 (9.5%) |
-2.1% (-11.3%, 7.1%) |
NE |
0.82 (0.34, 1.97) |
0.656 |
10/84 (11.9%) |
0.3% (-9.4%, 10.0%) |
NE |
1.02 (0.45, 2.33) |
0.955 |
INVESTIGATIONS |
10/86 (11.6%) |
6/84 (7.1%) |
-4.5% (-13.2%, 4.2%) |
NE |
0.61 (0.23, 1.61) |
0.317 |
6/84 (7.1%) |
-4.5% (-13.2%, 4.2%) |
NE |
0.61 (0.23, 1.61) |
0.317 |
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS |
4/86 (4.7%) |
7/84 (8.3%) |
3.7% (-3.7%, 11.1%) |
NE |
1.79 (0.54, 5.90) |
0.367 |
7/84 (8.3%) |
3.7% (-3.7%, 11.1%) |
NE |
1.79 (0.54, 5.90) |
0.367 |
METABOLISM AND NUTRITION DISORDERS |
6/86 (7.0%) |
2/84 (2.4%) |
-4.6% (-10.9%, 1.7%) |
NE |
0.34 (0.07, 1.64) |
0.278 |
1/84 (1.2%) |
-5.8% (-11.6%, 0.1%) |
NE |
0.17 (0.02, 1.39) |
0.117 |
INJURY, POISONING AND PROCEDURAL COMPLICATIONS |
4/86 (4.7%) |
5/84 (6.0%) |
1.3% (-5.4%, 8.0%) |
NE |
1.28 (0.36, 4.60) |
0.745 |
5/84 (6.0%) |
1.3% (-5.4%, 8.0%) |
NE |
1.28 (0.36, 4.60) |
0.745 |
RENAL AND URINARY DISORDERS |
4/86 (4.7%) |
3/84 (3.6%) |
-1.1% (-7.0%, 4.9%) |
NE |
0.77 (0.18, 3.33) |
1.000 |
3/84 (3.6%) |
-1.1% (-7.0%, 4.9%) |
NE |
0.77 (0.18, 3.33) |
1.000 |
VASCULAR DISORDERS |
3/86 (3.5%) |
1/84 (1.2%) |
-2.3% (-6.8%, 2.2%) |
NE |
0.34 (0.04, 3.22) |
0.621 |
3/84 (3.6%) |
0.1% (-5.5%, 5.6%) |
NE |
1.02 (0.21, 4.93) |
1.000 |
EYE DISORDERS |
2/86 (2.3%) |
1/84 (1.2%) |
-1.1% (-5.1%, 2.8%) |
NE |
0.51 (0.05, 5.54) |
1.000 |
2/84 (2.4%) |
0.1% (-4.5%, 4.6%) |
NE |
1.02 (0.15, 7.10) |
1.000 |
SURGICAL AND MEDICAL PROCEDURES |
2/86 (2.3%) |
2/84 (2.4%) |
0.1% (-4.5%, 4.6%) |
NE |
1.02 (0.15, 7.10) |
1.000 |
1/84 (1.2%) |
-1.1% (-5.1%, 2.8%) |
NE |
0.51 (0.05, 5.54) |
1.000 |
CONGENITAL, FAMILIAL AND GENETIC DISORDERS |
0/86 (0.0%) |
2/84 (2.4%) |
2.4% (-0.9%, 5.6%) |
NE |
5.12 (0.24, 106.90) |
0.243 |
1/84 (1.2%) |
1.2% (-1.1%, 3.5%) |
NE |
3.07 (0.12, 75.72) |
0.494 |
EAR AND LABYRINTH DISORDERS |
1/86 (1.2%) |
1/84 (1.2%) |
0.0% (-3.2%, 3.3%) |
NE |
1.02 (0.07, 16.10) |
1.000 |
2/84 (2.4%) |
1.2% (-2.8%, 5.2%) |
NE |
2.05 (0.19, 22.16) |
0.618 |
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) |
0/86 (0.0%) |
1/84 (1.2%) |
1.2% (-1.1%, 3.5%) |
NE |
3.07 (0.12, 75.72) |
0.494 |
2/84 (2.4%) |
2.4% (-0.9%, 5.6%) |
NE |
5.12 (0.24, 106.90) |
0.243 |
REPRODUCTIVE SYSTEM AND BREAST DISORDERS |
2/86 (2.3%) |
1/84 (1.2%) |
-1.1% (-5.1%, 2.8%) |
NE |
0.51 (0.05, 5.54) |
1.000 |
0/84 (0.0%) |
-2.3% (-5.5%, 0.9%) |
NE |
0.20 (0.01, 4.28) |
0.497 |
SOCIAL CIRCUMSTANCES |
0/86 (0.0%) |
1/84 (1.2%) |
1.2% (-1.1%, 3.5%) |
NE |
3.07 (0.12, 75.72) |
0.494 |
0/84 (0.0%) |
0.0% (0.0%, 0.0%) |
Inf (Inf, Inf) |
NA (NA, NA) |
1.000 |
IMMUNE SYSTEM DISORDERS |
0/86 (0.0%) |
0/84 (0.0%) |
0.0% (0.0%, 0.0%) |
Inf (Inf, Inf) |
NA (NA, NA) |
1.000 |
1/84 (1.2%) |
1.2% (-1.1%, 3.5%) |
NE |
3.07 (0.12, 75.72) |
0.494 |
HEPATOBILIARY DISORDERS |
1/86 (1.2%) |
0/84 (0.0%) |
-1.2% (-3.4%, 1.1%) |
NE |
0.34 (0.01, 8.42) |
1.000 |
0/84 (0.0%) |
-1.2% (-3.4%, 1.1%) |
NE |
0.34 (0.01, 8.42) |
1.000 |
Safety Population | |||||||||||
RD = Risk Difference, NNH = Number Needed to Harm, RR = Risk Ratio, CI = 95% Confidence Interval | |||||||||||
Reference group: Placebo | |||||||||||
P-values from Chi-square (or Fisher's exact when expected count < 5) | |||||||||||
NNH = 1/|RD|; NE = not estimable when CI crosses zero | |||||||||||
Note:
create_ae_summary_table(type = "comparison")is a convenience wrapper aroundcreate_ae_comparison_table(). Both functions produce identical results—use whichever entry point you prefer.
The comparison table includes: - n/N (%) for each treatment group - Risk Difference (RD) with 95% CI - Risk Ratio (RR) with 95% CI - P-value (Chi-square or Fisher’s exact test)
Preferred Term Level Comparison
# Compare at preferred term level with threshold
pt_comparison <- create_ae_comparison_table(
data = adae,
adsl = adsl,
ref_group = "Placebo",
by = "pt",
threshold = 5, # Only events with ≥5% incidence
sort_by = "rd", # Sort by risk difference
title = "AEs with ≥5% Incidence - Sorted by Risk Difference"
)
# Display the table
pt_comparison@flextableAEs with ≥5% Incidence - Sorted by Risk Difference | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Dictionary-Derived Term |
Placebo |
Xanomeline High Dose |
RD Xanomeline High Dose vs Placebo |
NNH Xanomeline High Dose vs Placebo |
RR Xanomeline High Dose vs Placebo |
P-value (Xanomeline High Dose vs Placebo) |
Xanomeline Low Dose |
RD Xanomeline Low Dose vs Placebo |
NNH Xanomeline Low Dose vs Placebo |
RR Xanomeline Low Dose vs Placebo |
P-value (Xanomeline Low Dose vs Placebo) |
PRURITUS |
8/86 (9.3%) |
25/84 (29.8%) |
20.5% (8.9%, 32.0%) |
4.9 (3.1, 11.2) |
3.20 (1.53, 6.69) |
<0.001 |
21/84 (25.0%) |
15.7% (4.6%, 26.8%) |
6.4 (3.7, 21.8) |
2.69 (1.26, 5.73) |
0.007 |
APPLICATION SITE PRURITUS |
6/86 (7.0%) |
22/84 (26.2%) |
19.2% (8.4%, 30.0%) |
5.2 (3.3, 11.9) |
3.75 (1.60, 8.79) |
<0.001 |
22/84 (26.2%) |
19.2% (8.4%, 30.0%) |
5.2 (3.3, 11.9) |
3.75 (1.60, 8.79) |
<0.001 |
APPLICATION SITE ERYTHEMA |
3/86 (3.5%) |
15/84 (17.9%) |
14.4% (5.3%, 23.4%) |
7.0 (4.3, 18.8) |
5.12 (1.54, 17.04) |
0.002 |
12/84 (14.3%) |
10.8% (2.4%, 19.2%) |
9.3 (5.2, 42.2) |
4.10 (1.20, 14.00) |
0.015 |
DIZZINESS |
2/86 (2.3%) |
11/84 (13.1%) |
10.8% (2.9%, 18.7%) |
9.3 (5.4, 34.7) |
5.63 (1.29, 24.65) |
0.009 |
8/84 (9.5%) |
7.2% (0.2%, 14.2%) |
13.9 (7.0, 629.4) |
4.10 (0.90, 18.73) |
0.056 |
ERYTHEMA |
8/86 (9.3%) |
14/84 (16.7%) |
7.4% (-2.7%, 17.4%) |
NE |
1.79 (0.79, 4.05) |
0.153 |
14/84 (16.7%) |
7.4% (-2.7%, 17.4%) |
NE |
1.79 (0.79, 4.05) |
0.153 |
APPLICATION SITE IRRITATION |
3/86 (3.5%) |
9/84 (10.7%) |
7.2% (-0.4%, 14.9%) |
NE |
3.07 (0.86, 10.95) |
0.078 |
9/84 (10.7%) |
7.2% (-0.4%, 14.9%) |
NE |
3.07 (0.86, 10.95) |
0.078 |
HYPERHIDROSIS |
2/86 (2.3%) |
8/84 (9.5%) |
7.2% (0.2%, 14.2%) |
13.9 (7.0, 629.4) |
4.10 (0.90, 18.73) |
0.056 |
4/84 (4.8%) |
2.4% (-3.1%, 8.0%) |
NE |
2.05 (0.39, 10.88) |
0.441 |
SINUS BRADYCARDIA |
2/86 (2.3%) |
8/84 (9.5%) |
7.2% (0.2%, 14.2%) |
13.9 (7.0, 629.4) |
4.10 (0.90, 18.73) |
0.056 |
7/84 (8.3%) |
6.0% (-0.7%, 12.7%) |
NE |
3.58 (0.77, 16.76) |
0.097 |
APPLICATION SITE VESICLES |
1/86 (1.2%) |
6/84 (7.1%) |
6.0% (0.0%, 11.9%) |
16.7 (8.4, 4040.4) |
6.14 (0.76, 49.94) |
0.062 |
4/84 (4.8%) |
3.6% (-1.5%, 8.7%) |
NE |
4.10 (0.47, 35.89) |
0.208 |
DIARRHOEA |
9/86 (10.5%) |
4/84 (4.8%) |
-5.7% (-13.6%, 2.2%) |
NE |
0.46 (0.15, 1.42) |
0.248 |
4/84 (4.8%) |
-5.7% (-13.6%, 2.2%) |
NE |
0.46 (0.15, 1.42) |
0.248 |
VOMITING |
3/86 (3.5%) |
7/84 (8.3%) |
4.8% (-2.2%, 11.9%) |
NE |
2.39 (0.64, 8.93) |
0.208 |
3/84 (3.6%) |
0.1% (-5.5%, 5.6%) |
NE |
1.02 (0.21, 4.93) |
1.000 |
NASOPHARYNGITIS |
2/86 (2.3%) |
6/84 (7.1%) |
4.8% (-1.5%, 11.2%) |
NE |
3.07 (0.64, 14.79) |
0.166 |
4/84 (4.8%) |
2.4% (-3.1%, 8.0%) |
NE |
2.05 (0.39, 10.88) |
0.441 |
FATIGUE |
1/86 (1.2%) |
5/84 (6.0%) |
4.8% (-0.8%, 10.3%) |
NE |
5.12 (0.61, 42.90) |
0.115 |
5/84 (6.0%) |
4.8% (-0.8%, 10.3%) |
NE |
5.12 (0.61, 42.90) |
0.115 |
COUGH |
1/86 (1.2%) |
5/84 (6.0%) |
4.8% (-0.8%, 10.3%) |
NE |
5.12 (0.61, 42.90) |
0.115 |
5/84 (6.0%) |
4.8% (-0.8%, 10.3%) |
NE |
5.12 (0.61, 42.90) |
0.115 |
RASH |
5/86 (5.8%) |
8/84 (9.5%) |
3.7% (-4.3%, 11.7%) |
NE |
1.64 (0.56, 4.81) |
0.363 |
13/84 (15.5%) |
9.7% (0.5%, 18.8%) |
10.3 (5.3, 207.6) |
2.66 (0.99, 7.14) |
0.041 |
NAUSEA |
3/86 (3.5%) |
6/84 (7.1%) |
3.7% (-3.1%, 10.4%) |
NE |
2.05 (0.53, 7.92) |
0.326 |
3/84 (3.6%) |
0.1% (-5.5%, 5.6%) |
NE |
1.02 (0.21, 4.93) |
1.000 |
UPPER RESPIRATORY TRACT INFECTION |
6/86 (7.0%) |
3/84 (3.6%) |
-3.4% (-10.1%, 3.3%) |
NE |
0.51 (0.13, 1.98) |
0.496 |
1/84 (1.2%) |
-5.8% (-11.6%, 0.1%) |
NE |
0.17 (0.02, 1.39) |
0.117 |
APPLICATION SITE DERMATITIS |
5/86 (5.8%) |
7/84 (8.3%) |
2.5% (-5.2%, 10.2%) |
NE |
1.43 (0.47, 4.34) |
0.521 |
9/84 (10.7%) |
4.9% (-3.4%, 13.2%) |
NE |
1.84 (0.64, 5.27) |
0.245 |
HEADACHE |
3/86 (3.5%) |
5/84 (6.0%) |
2.5% (-3.9%, 8.8%) |
NE |
1.71 (0.42, 6.92) |
0.493 |
3/84 (3.6%) |
0.1% (-5.5%, 5.6%) |
NE |
1.02 (0.21, 4.93) |
1.000 |
SKIN IRRITATION |
3/86 (3.5%) |
5/84 (6.0%) |
2.5% (-3.9%, 8.8%) |
NE |
1.71 (0.42, 6.92) |
0.493 |
6/84 (7.1%) |
3.7% (-3.1%, 10.4%) |
NE |
2.05 (0.53, 7.92) |
0.326 |
BLISTER |
0/86 (0.0%) |
1/84 (1.2%) |
1.2% (-1.1%, 3.5%) |
NE |
3.07 (0.12, 75.72) |
0.494 |
5/84 (6.0%) |
6.0% (0.9%, 11.0%) |
16.8 (9.1, 112.0) |
11.26 (0.62, 203.87) |
0.028 |
Safety Population | |||||||||||
RD = Risk Difference, NNH = Number Needed to Harm, RR = Risk Ratio, CI = 95% Confidence Interval | |||||||||||
Reference group: Placebo | |||||||||||
P-values from Chi-square (or Fisher's exact when expected count < 5) | |||||||||||
NNH = 1/|RD|; NE = not estimable when CI crosses zero | |||||||||||
Events with incidence >= 5.0% in any group | |||||||||||
Overall AE Summary Comparison
# Overall comparison (any TEAE)
overall_comparison <- create_ae_comparison_table(
data = adae,
adsl = adsl,
ref_group = "Placebo",
by = "overall",
title = "Overall TEAE Comparison"
)
# Display the table
overall_comparison@flextableOverall TEAE Comparison | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Term |
Placebo |
Xanomeline High Dose |
RD Xanomeline High Dose vs Placebo |
NNH Xanomeline High Dose vs Placebo |
RR Xanomeline High Dose vs Placebo |
P-value (Xanomeline High Dose vs Placebo) |
Xanomeline Low Dose |
RD Xanomeline Low Dose vs Placebo |
NNH Xanomeline Low Dose vs Placebo |
RR Xanomeline Low Dose vs Placebo |
P-value (Xanomeline Low Dose vs Placebo) |
Any TEAE |
65/86 (75.6%) |
75/84 (89.3%) |
13.7% (2.5%, 24.9%) |
7.3 (4.0, 40.5) |
1.18 (1.03, 1.36) |
0.019 |
77/84 (91.7%) |
16.1% (5.3%, 26.9%) |
6.2 (3.7, 19.0) |
1.21 (1.06, 1.39) |
0.005 |
Safety Population | |||||||||||
RD = Risk Difference, NNH = Number Needed to Harm, RR = Risk Ratio, CI = 95% Confidence Interval | |||||||||||
Reference group: Placebo | |||||||||||
P-values from Chi-square (or Fisher's exact when expected count < 5) | |||||||||||
NNH = 1/|RD|; NE = not estimable when CI crosses zero | |||||||||||
Interpreting Results
- Risk Difference > 0: Higher incidence in treatment vs reference
- Risk Ratio > 1: Higher relative risk in treatment vs reference
- P-value < 0.05: Statistically significant difference (unadjusted)
For GBA submissions, the risk difference is often the primary measure as it reflects the absolute impact on patients.
Related Functions
-
create_hta_table()- Underlying function for table formatting -
create_km_plot()- Kaplan-Meier plot creation -
ClinicalReport()- Report assembly -
generate_word()- Word document generation