Lowering your handicap with Stata

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Lowering your handicap with Stata

• Tim Collier
• Medical Statistics Department, LSHTM
• Leaside Golf Club, Edmonton

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The Inception
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The Inception
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(No Transcript)
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Golf
Stata
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Time


Golf
Stata
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Spare Time


Golf
Stata
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Spare Time


Golf
Stata
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Data Monitoring for Clinical Trials

• Double blind Randomised Controlled Trial
• New drug/treatment versus a control
• Previously tested in a small number of healthy
  volunteers or specially selected patients
• DSMB committee of independent clinical experts
  and a statistician
• Regularly produce routine reports safety and
  efficacy

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Typical Data Monitoring Report

• Baseline summary
• Recruitment and Patient status
• Adherence
• Safety adverse events
• Efficacy primary secondary endpoints
• Concomitant medications
• Laboratory values, vital signs

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Typical Data Monitoring Report

• Stata programming can save vast amounts of time
  particularly when repeating analyses and
  production of routine reports

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DemonstrationThe following tables were all
produced directly from Stata using relatively
simple user written Stata programs
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Adverse Event Table 1

Tab
le 1.1 SERIOUS ADVERSE EVENTS
Group A Group B

Sys
tem Organ Class
NP () NE NP ()
NE

Blood and lymphatic system disorders
34 (0.4) 35 32 (0.3) 32
Cardiac disorders
312 (3.3) 353 324 (3.4) 384
Congenital, familial and genetic disorders
13 (0.1) 13 13 (0.1) 13
Ear and labyrinth disorders
52 (0.5) 53 57 (0.6) 58
Endocrine disorders
9 (0.1) 9 7 (0.1) 7
Eye disorders
44 (0.5) 49 51 (0.5) 58
Gastrointestinal disorders
202 (2.1) 216 221 (2.3) 236
General disorders and administration site
conditions
134 (1.4) 134 128 (1.3) 132
Hepatobiliary disorders
48 (0.5) 52 51 (0.5) 55
Immune system disorders
9 (0.1) 9 8 (0.1) 8
Infections and infestations
373 (3.9) 443 343 (3.6) 404
Injury, poisoning and procedural complications
232 (2.4) 246 225 (2.4) 239
Investigations
29 (0.3) 31 39 (0.4) 41
Metabolism and nutrition disorders
83 (0.9) 88 98 (1.0) 104
Musculoskeletal and connective tissue disorders
128 (1.3) 145 173 (1.8) 177
Neoplasms benign, malignant and unspecified
(incl cysts and polyps)
171 (1.8) 175 167 (1.8) 171
Nervous system disorders
317 (3.3) 356 279 (2.9) 305
Psychiatric disorders
44 (0.5) 48 66 (0.7) 70
Renal and urinary disorders
76 (0.8) 78 58 (0.6) 60
Reproductive system and breast disorders
17 (0.2) 17 20 (0.2) 20
Respiratory, thoracic and mediastinal disorders
124 (1.3) 148 119 (1.3) 137
Skin and subcutaneous tissue disorders
10 (0.1) 11 11 (0.1) 11
Surgical and medical procedures
53 (0.6) 55 49 (0.5) 52
Vascular disorders
170 (1.8) 187 217 (2.3) 232

N
Pnos of patients with 1 events NE nos of
events plt0.05, plt0.01 and plt0.001
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Adverse Event Table 2

T
able 1.2 SERIOUS ADVERSE EVENTS
Group A Group B

S
ystem Organ Class
NP () NE Fatal NP () NE
Fatal

Blood and lymphatic system disorders
34 (0.4) 35 1 32 (0.3) 32
1 Cardiac disorders
312 (3.3) 353 11 324 (3.4) 384 10
Congenital, familial and genetic disorders
13 (0.1) 13 0 13 (0.1) 13 0
Ear and labyrinth disorders
52 (0.5) 53 0 57 (0.6) 58 0
Endocrine disorders
9 (0.1) 9 0 7 (0.1) 7 0
Eye disorders
44 (0.5) 49 0 51 (0.5) 58 0
Gastrointestinal disorders
202 (2.1) 216 5 221 (2.3) 236 4
General disorders and administration site
conditions
134 (1.4) 134 84 128 (1.3) 132 84
Hepatobiliary disorders
48 (0.5) 52 2 51 (0.5) 55 0
Immune system disorders
9 (0.1) 9 0 8 (0.1) 8 0
Infections and infestations
373 (3.9) 443 39 343 (3.6) 404 56
Injury, poisoning and procedural complications
232 (2.4) 246 6 225 (2.4) 239 4
Investigations
29 (0.3) 31 0 39 (0.4) 41 0
Metabolism and nutrition disorders
83 (0.9) 88 0 98 (1.0) 104 2
Musculoskeletal and connective tissue disorders
128 (1.3) 145 0 173 (1.8) 177 0
Neoplasms benign, malignant and unspecified
(incl cysts and polyps)
171 (1.8) 175 35 167 (1.8) 171 40
Nervous system disorders
317 (3.3) 356 4 279 (2.9) 305 1
Psychiatric disorders
44 (0.5) 48 4 66 (0.7) 70 8
Renal and urinary disorders
76 (0.8) 78 1 58 (0.6) 60 2
Reproductive system and breast disorders
17 (0.2) 17 0 20 (0.2) 20 0
Respiratory, thoracic and mediastinal disorders
124 (1.3) 148 25 119 (1.3) 137 21
Skin and subcutaneous tissue disorders
10 (0.1) 11 0 11 (0.1) 11 1
Surgical and medical procedures
53 (0.6) 55 0 49 (0.5) 52 0
Vascular disorders
170 (1.8) 187 1 217 (2.3) 232 0


NPnos of patients with 1 events NE nos of
events plt0.05, plt0.01 and
plt0.001 Fatal - nos of events with outcome
recorded as fatal
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Adverse Event Table Two levels 3 (edited)

Tab
le 1.5 SERIOUS ADVERSE EVENTS
Group A Group B

Sys
tem Organ Class/MedDRA Preferred term
NP () NE NP ()
NE

BLOOD AND LYMPHATIC SYSTEM DISORDERS
34 (0.4) 35 32 (0.3) 32


Anaemia
20 (0.2) 21 15 (0.2) 15
Iron deficiency anaemia 7
(0.1) 7 7 (0.1) 7
Microcytic anaemia 5
(0.1) 5 1 (lt0.1) 1
Thrombocytopenia 2
(lt0.1) 2 9 (0.1) 9

C
ARDIAC DISORDERS
312 (3.3) 353 324 (3.4) 384


Angina pectoris
26 (0.3) 26 30 (0.3) 32
EDITED EDITED

EAR AND LABYRINTH DISORDERS
52 (0.5) 53 57
(0.6) 58

Acute vestibular syndrome
6 (0.1) 7 5 (0.1)
5 Vertigo
21 (0.2) 21 19 (0.2)
19 Vertigo positional
8 (0.1) 8 17 (0.2)
17 Vestibular disorder
10 (0.1) 10 13 (0.1) 13
Vestibular neuronitis
7 (0.1) 7 4 (lt0.1) 4

E
NDOCRINE DISORDERS
9 (0.1) 9 7 (0.1) 7


Goitre
7 (0.1) 7 5 (0.1) 5
Hyperthyroidism 2
(lt0.1) 2 2 (lt0.1) 2

EY
E DISORDERS
44 (0.5) 49 51 (0.5) 58


Cataract
38 (0.4) 42 43 (0.5) 49

NP
nos of patients with 1 events N nos of
events plt0.05, plt0.01 and plt0.001
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Adverse Event Table Two levels 3 (edited)

Tab
le 1.5 SERIOUS ADVERSE EVENTS
Group A Group B

Sys
tem Organ Class/MedDRA Preferred term
NP () NE NP ()
NE

EYE DISORDERS (contd) Diabetic retinopathy
2 (lt0.1) 2
3 (lt0.1) 3 Retinal detachment
5 (0.1) 5 6
(0.1) 6

GASTROINTESTINAL DISORDERS
202 (2.1) 216 221 (2.3)
236

Abdominal hernia
2 (lt0.1) 2 4 (lt0.1)
4 Abdominal pain
5 (0.1) 5 4 (lt0.1) 4
Anal fissure
4 (lt0.1) 4 1 (lt0.1) 1
EDITED EDITED

GENERAL DISORDERS AND
ADMINISTRATION SITE CONDITIONS
134 (1.4) 134 128
(1.3) 132

Chest pain
24 (0.3) 24 20 (0.2)
21 Death
49 (0.5) 49 41 (0.4)
41 Drug intolerance
5 (0.1) 5 3 (lt0.1)
3 Gait disturbance
5 (0.1) 5 2 (lt0.1) 2
General physical health deterioration
11 (0.1) 11 7 (0.1) 7
Malaise
2 (lt0.1) 2 3 (lt0.1) 3
Non-cardiac chest pain
4 (lt0.1) 4 4 (lt0.1) 4
Oedema peripheral 1
(lt0.1) 1 4 (lt0.1) 4
Pyrexia 3
(lt0.1) 3 5 (0.1) 7
Sudden death 30
(0.3) 30 40 (0.4) 40

HE
PATOBILIARY DISORDERS
48 (0.5) 52 51 (0.5) 55


Bile duct stone
2 (lt0.1) 2 6 (0.1) 6

NP
nos of patients with 1 events N nos of
events plt0.05, plt0.01 and plt0.001
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Baseline Demographic Table (edited)

Table 11 Baseline
Demographics Group A Group B
(N485)
(N492)
GE
NDER-Nos.()

Male 264 (54.5)
271 (55.3) Female
220 (45.5) 219 (44.7) Missing
1
2
AGE AT
RANDOMISATION (yrs)

Number 484
490 Mean (SD)
59.4 (10.6) 59.7 (10.9) Median
(IQR) 59.7 (52.7 to 67.3)
60.5 (51.8 to 67.6) Range
23.5 to 83.7 29.0 to 86.6 AGE
CATEGORIES-Nos.() 18-49 yrs
89 (18.4) 91 (18.6) 50-59
yrs 156 (32.2)
145 (29.6) 60-69 yrs
156 (32.2) 166 (33.9) 70 yrs
83 (17.1) 88
(18.0) Missing
1 2

DURATION OF DIABETES (yrs)

Number
483 488 Median (IQR)
8.8 (4.3 to 13.7) 9.2 (4.9 to
13.8) Range 0.1
to 42.5 0.2 to 63.2 Missing
2
5

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SAE event listing (edited)

Patient number
XXX-XXX
A
ge/Gender 82 years/Female Treatm
ent group Group F Date of
Randomisation 16/Aug/2011 Date of SAE
Onset 23/Aug/2011 Date of SAE stop
25/Aug/2011 SAE Narrative Subject
presented to the ER c/o intractable nausea and
abdominal pain on 23Aug20 11. CT scan identified
left ovarian thrombus. On 24Aug2011 the patient
reported that the abdominal pain had
intensified. On the 26Aug2011 the patient
experienced a SAE Treatment Doctor requested
much longer string variables SAE Outcome
Recovered SAE Criteria
Hospitalization Relation to study drug
Definitely not related to study drug Action with
Study Drug None SAR Severity
Moderate