L1.

1
Biostatistics II
(PUBH5769)
TOPIC 1
UNIT OVERVIEW AND
INTRODUCTORY MATERIAL
1.1 UNIT OVERVIEW
This course covers biostatistical methods commonly used in
epidemiological and clinical research.
It focuses on modern regression (and a few classical) methods for
Quantitative outcomes
Binary outcomes
Count (number of events) outcomes
Time-to-event outcomes.
It considers and describes the application of these methods to data
from
cross-sectional,
case-control,
cohort and
clinical studies
The emphasis is on
How to intelligently use these methods
How to use SAS to do the calculations
How to interpret the results
And not on
The underlying statistical theory
Memorising formulae
L1.2
Assumed prior knowledge and experience
A knowledge of basic statistical methods and concepts
(as taught in introductory biostatistics/statistics courses
such as PUBH8753/4401 Biostatistics 1)
A basic familiarity with epidemiological/clinical study designs
(copy of a chapter from a book is on LMS)
Familiarity with hand-held calculators
You must have your own calculator and know how to use it.
Also, it must have an approved UWA sticker to take into exam.
Familiarity with computing in a Windows environment
Experience with at least one statistical analysis package
(such as SPSS).
SPSS
Learning outcomes
Understand and be able to apply standard biostatistical
methods commonly used in epidemiological and clinical
research including
ANOVA and multiple linear regression
2 x K frequency table methods, logistic regression
Incidence rates and Poisson regression
Kaplan-Meier survival curves and Cox regression
Be able to use the package SAS to carry out statistical
analyses of epidemiological/clinical data.
Understand the statistical content of articles in
epidemiological/clinical literature.
PUBH5769
Biostatistics II course
L1.3
Course Reader and textbooks
Biostatistics II Course Reader
Lecture notes (pages numbered Lx.x)
Problems, Computing and Answers (pages numbered Px.x)
Review articles (pages numbered Rx.x)
Introduction to SAS (pages numbered Cx.x)
Statistical Tables (pages numbered Tx.x)
Recommended reading
>Woodward M. Epidemiology: Study design and data analysis. Chapman and Hall.
>Le CT. Introductory Biostatistics. J ohn Wiley.
>Kahn, H.A. and Sempos, C.T. Statistical methods in epidemiology. Oxford
University Press.
>Dawson, B. and Trapp, R.G. Basic and clinical biostatistics. Prentice-Hall.
>Everitt, BS and Der, G. A handbook of statistical analyses using SAS.
Chapman and Hall
Lectures and Tutorials
Weekly class Wednesday 9.00 -11.50am includes
Tutorial (Starts 9am for 45 minutes)
Lecture (Starts at 10am for 1 hour and 50 minutes with
break around 11am)
The tutorial covers the topic of the previous weeks
lecture.
Bring your calculator to the tutorial!
The Course Reader includes a copy of the lecture
presentation (so read ahead!)
ALL LECTURES SHOULD BE RECORDED AND
AVAILABLE THROUGH LMS FOR PLAYBACK
ANYTIME.
L1.4
Computing and SAS
The statistics package is SAS.
The Course Reader contains a self-explanatory Introduction to SAS. Sign up for an
Introduction to SAS Session with Mark Divitini if you want help with getting
started.
The expectation is that you do the SAS computing activities on your own (or
preferably with a class mate) at a place and time that suits you. Some of the
Problems in the Course reader involve using SAS.
SAS is available on the computers in the
SPH Postgrad Computer Lab (Rm1.27, Clifton St Building) for SPH students only
SPH Main Computer Lab on the Nedlands Campus next to cafeteria (all students)
Bring a USB flash drive to save and keep your work!
If you use SAS elsewhere, download a copy of the files (datasets and programs) from
LMS or email Mark Divitini and he will send them to you.
UWA has a site license for SAS and all enrolled students can get a copy. See LMS
for more details and forms.
If you need help with SAS during the semester, email Mark Divitini with your
questions or to arrange a time to see him.
SAS
Assessment
Three assignments each 20% (Due Sept 4, Oct 9, Nov 1)
Final (written) examination 40% (Exam period Nov 9-23)
Assignments involve data analysis using hand-calculation as well as
SAS, providing written answers to questions that test understanding,
and reviewing articles from the literature.
Hand assignments (with cover sheet) to SPH Reception.
There is a penalty for (unapproved) late assignments.
The final exam involves providing written answers to problems. Many
will involve use of a hand-calculator. Some will include SAS output.
The exam is open book.
L1.5
LMS www.lms.uwa.edu.au
All supplementary unit materials are placed on LMS
(including assignments)
The recording of the lecture should be available soon after the
lecture has finished (same day).
All students enrolled for credit (i.e. doing assessment) are
automatically given permission to access the LMS unit materials.
Others who need access should contact lecturer (and provide an
email address).
Study plan and workload
Study each topic each week by reviewing the lecture notes, reading
appropriate sections of the books, doing the related SAS computing,
and doing the problems in the course reader.
Attempt the problems before coming to the tutorial.
Begin assignments early, dont leave until last few days.
You should spend about 9 hours per week on this course
Tutorial (1 hour)
Lecture (2 hours)
Computing (1-2 hours)
Private study and assignments (4-5 hours)
L1.6
Today
Class schedule
Week Date (Wed) Lecture topics
1 J uly 31 Topic 1: Course overview and introductory material
2 August 7 Topic 2: Quantitative outcome data (2.1 & 2.2)
3 August 14 Topic 2 (2.3 & 2.4)
4 August 21 Topic 2 (2.5, 2.6 & 2.7)
5 August 28 Review of published article
6 September 4 Topic 3: Binary outcome data (3.1)
7 September 11 Topic 3 (3.2)
8 September 18 Topic 3 (3.3 & 3.4)
9 September 25 Review of article
October 2 NON-TEACHING WEEK
10 October 9 Topic 4: Follow-up time outcome data (4.1 & 4.2)
11 October 16 Topic 4 (4.3)
12 October 23 Topic 4 (4.4)
13 October 30 Review of article & Topic 5: course wind-up
November 4-8 Pre-examination study period
November 9-23 Examination period

Please read the Unit Outline carefully for
full details and other information on how
the course is organised.
ANY QUESTIONS?
L1.7
1.2 INTRODUCTORY MATERIAL
TYPE OF OUTCOME VARIABLE
The type of outcome variable determines the method of
statistical analysis.
There are four main types:
Quantitative eg. blood pressure
Binary eg. disease / disease free
Number of events eg. number of deaths
for a group
Time to event eg. time to death (possibly censored)
The focus in this unit is on analysing data on these
outcome variables using modern regression modelling
methods.
However, a few classical methods (for proportions and
group incidence rates) that are still in common use are
also included.
The regression model for an outcome variable is based
on a particular summary measure and a measure of effect
L1.8
Quantitative outcome variable
Example: measured systolic blood pressure (SBP)
Summary measure: mean
Effect measure: difference in means
Regression method: linear regression
Examples of linear regression models
Mean (SBP) =o +|
1
Age
|
1
=Difference in mean (SBP) if Age increases by 1 year
Mean (SBP) =o +|
1
[if group=control] +|
2
[if group=treated]
|
1
- |
2
=Difference in mean (SBP) for control vs treated groups
Binary outcome variable
Example: disease / disease free
Summary measure: proportion
Effect measure: odds ratio
Regression method: Logistic regression
Prevalence and risk are proportions (p).

persons of number total
cases existing of number
Prevalence =
eg. Prevalence of diabetes in WA women aged 60-69 years in 1990 is 0.047 or 4.7%.

beginning at risk at persons of number total
time of period in cases new of number
Risk =
eg. Risk of 50 years old woman having a stroke in next 10 years is 0.02 or 2%.

Odds =p/(1-p) and Odds ratio
) p - (1 p
) p - (1 p
OR
2 2
1 1
=

L1.9
Binary outcome variable (ctd)
Example: disease / disease free
Summary measure: proportion
Effect measure: odds ratio
Regression method: Logistic regression
Examples of logistic regression models
log (odds of disease) =o +|
1
Age
|
1
=Difference in log (odds of disease) if Age increases by 1 year

=ratio of odds of disease if Age increases by 1 year

=1.05 ie odds of disease increases by 5% each year of age
log (odds of disease) =o +|
1
[if group=control] +|
2
[if group=treated]
|
1
|
2
=Difference in log(odds of disease) for control vs treated groups

=ratio of odds of disease for control vs treated groups

=2.0 ie odds of disease is twice as big in control vs treated
Numbers of events outcome variable
Example: number of deaths during follow-up of group
Summary measure: incidence rate
Effect measure: incidence rate ratio
Regression method: Poisson regression
For grouped data from follow-up studies, a common summary
statistic is the incidence rate.

risk at time - person total
up - follow during events new of number
rate Incidence =

eg. Incidence rate for stroke in women aged 50-59 years is 0.002 per
person per year or 2 per 1000 persons per year.

rate ratio
2 rate
1 rate
RR =

L1.10
Numbers of events outcome variable (ctd)
Example: number of deaths during follow-up of group
Summary measure: incidence rate
Effect measure: incidence rate ratio
Regression method: Poisson regression
Examples of Poisson regression models
log (rate) =o +|
1
Age
|
1
=Difference in log (rate) if Age increases by 1 year

=ratio of rates if Age increases by 1 year

=1.05 ie rate increases by 5% each year of age
log (rate) =o +|
1
[if group=control] +|
2
[if group=treated]
|
1
|
2
=Difference in log(rate) for control vs treated groups

=ratio of rates for control vs treated groups

=2.0 ie rate is twice as big in control vs treated
Time to event outcome variable
Example: time to death (possibly censored)
Summary measure: survival curve
Effect measure: hazard rate ratio
Regression method: Cox regression
A common summary of the time-to-event data for a group is the survival
curve.

S(t) =the proportion who have not had event by time t.

However, the comparison and modelling of survival curves is usually based
on the analysis of the magnitude of hazard ratios.

h(t) =hazard at time t is the risk of having event over the next instant given
event-free up to time t.
Hazard ratio
(t) h
(t) h
HR
2
1
= is the 'effect' size
and it is commonly assumed this does not change with time t (called
proportional hazards assumption).
L1.11
Time to event outcome variable (ctd)
Example: time to death (possibly censored)
Summary measure: survival curve
Effect measure: hazard rate ratio
Regression method: Cox regression
Examples of Cox regression models
log (hazard at t) =o(t) +|
1
Age
|
1
=Difference in log (hazard) if Age increases by 1 year

=ratio of hazards if Age increases by 1 year

=1.05 ie hazard increases by 5% each year of age
log (hazard at t) =o(t) +|
1
[if group=control] +|
2
[if group=treated]
|
1
|
2
=Difference in log(hazard) for control vs treated groups

=ratio of hazards for control vs treated groups

=2.0 ie hazard is twice as big in control vs treated
Study designs
Observational studies
cross-sectional (point in time)
case-control (retrospective)
cohort (prospective)
Intervention studies (experiments)
health promotion / disease prevention trial
therapeutic clinical trial
Cross-sectional study prevalence, mean
Case-control study odds ratio
prevalent cases odds of being diseased
incident cases odds of developing disease
Cohort and intervention studies risk, rate, mean
L1.12
Statistical inference
) (statistic
sample
statistical inference
) (parameter
population

value) - p statistic, test , hypothesis (null testing hypothesis

CI) SE, estimate, ( estimation

inference
l statistica


CIs and p-values are calculated from the sampling distributions of the
estimator and test statistic.
The 95% CI indicates how well we have estimated a population
parameter. Narrower CIs indicate greater accuracy.
P-values measure the amount of evidence in the sample data against
the null hypothesis. The closer the p-value to zero, the greater the
evidence.

Most of the commonly used CI and p-value formulae are based on the
assumption that the estimator (or a transformation of it) has a Normal
sampling distribution. For moderate and large sample sizes, this is
approximately true.
General formulae
The general form of these approximate formulae for a single parameter is

95% CI estimate (Z
95
or t
95
) x SE with Z
95
=1.96

SE
value ed hypothesis - estimate
statistic Test =
With p-value from Z (or t) distribution

Most (but not all) approximate formulae come from asymptotic likelihood theory
which provides
- an estimator (maximum likelihood estimator MLE)
- an approximate standard error (and hence a 95% CI)
- and three approximate p-value formulae (Wald, Score, Likelihood ratio)

The p-value method described above is the Wald p-value.

When we are testing hypotheses involving more than one parameter, the test
statistic often has an asymptotic chi-squared distribution.
When we are comparing variances, the test statistic often has an F distribution.
L1.13
Statistical inference formulae for a single mean ()
s and y = =
n

SE

= and 95% CI is SE t
95


Testing
0 0
: H =

SE
-
t statistic Test
0

= and (two-tailed) p-value from t
distribution with n-1 df.

These formulae give exact CIs and p-values if the
population distribution for Y is Normal, otherwise they
are approximate.
For large n, t may be replaced by Z (standard Normal).
Statistical inference formulae for single proportion (p)
n
) p - (1 p
SE = and 95% CI is SE 1.96 p

Testing
0 0
p p : H =

SE
p - p
Z statistic Test
0
= and p-value from Z
distribution

These are approximate, the exact CI and p-value are
based on Binomial calculations.
L1.14
Statistical inference formulae for single rate ()
T

SE

= and 95% CI is SE 1.96

where T =total person-time

Testing
0 0
: H =
SE
-

Z statistic Test
0

= and p-value from Z
distribution

These are approximate, the exact CI and p-value are
based on Poisson calculations.
Statistical inference formulae in other situations
Formulae for estimation and testing of effect measures in
simple situations such as the comparison of two groups are
readily available (and can also be done on hand-calculator).

Comparing two means via difference (see Section 2.1)
Comparing two proportions via odds ratio (see section 3.1)
Comparing two rates via rate ratio (see section 4.1)
Comparing two survival curves (see section 4.3)

In more complex situations the formulae are more complicated
and we must rely on computer programs to obtain the estimate,
its SE, its 95% CI and the test statistic value.
L1.15
Probability distributions and
statistical tables
The hand-calculation methods throughout the unit sometimes involve
looking up statistical tables for specific probability distributions, usually
to obtain the p-value associated with a particular value of the test
statistic, but sometimes to get the SE multiplier for a 95% confidence
interval.
The probability distributions used in this unit are
Standard Normal distribution (Z)
t- distribution (t)
Chi-squared distribution (_
2
)
F- distribution (F)
Tables for these distributions and how to use these tables are provided
in Course Reader.
Datasets used throughout semester
Data set Files
Diabetes data diabet.dat and diabet.sas
Busselton 1981 survey data bsn81.dat and bsn81.sas
US city air pollution data so2cit.dat
BCG case-control data bcg.sas
Endometrial cancer case-control data endomet.dat and endomet.sas
Grouped smoking death cohort data smokdth.sas
Lymphoma survival data lymphoma.sas
filename.sas is a SAS program file (which sometimes includes data)
filename.dat is a data file
L1.16
Diabetes data
The diabetes dataset relates to baseline and mortality follow-up data
for a cohort of 498 persons with diabetes.
AGE age in years
SEX 0 =female
1 =male
DURATION duration of diabetes in years
TREAT 1 =insulin injections
2 =tablets
3 =special diet
PDW percent of desirable weight
SBP systolic blood pressure in mmHg
HAEM glycosylated haemoglobin in
mmol/L
DIED5 0 =have not died within 5 years
1 =died within 5 years

First 4 rows of diabet.dat
41 1 12 2 99.7 132 10.6 0
47 0 3 2 134.3 170 12.2 0
62 1 5 2 143.6 170 10.6 0
69 0 3 1 135.6 170 10.8 0
Numbers separated by spaces
SAS program to produce summary of data
data di abet es;
i nf i l e C: \ Bi ost at 2\ di abet . dat ' ;
i nput age sex dur at i on t r eat pdw sbp haemdi ed5;
run;
proc means dat a=di abet es maxdec=3;
run;
The MEANS Procedure
Variable N Mean Std Dev Minimum Maximum

age 498 63.873 9.550 40.000 80.000

sex 498 0.554 0.498 0.000 1.000
duration 498 8.092 6.426 1.000 39.000
treat 498 1.859 0.672 1.000 3.000
pdw 498 123.594 14.336 76.600 149.900
sbp 498 152.442 21.560 98.000 198.000
haem 498 10.652 2.022 6.300 18.800
died5 498 0.215 0.411 0.000 1.000

Must be in data
file order
Location of file
Note: mean of died5 =proportion of values equal to 1
L1.17
Busselton 1981 survey data
AGE age in years (range 40-69)
ALCGRAMS alcohol consumed per week in grams
ANGINA ever had angina 0 =no, 1 =yes
ASTHMA ever had asthma 0 =no, 1 =yes
BMI body mass index (weight/height
2
) in kg/m
2

BRONCH ever had bronchitis 0 =no, 1 =yes
CHOL blood cholesterol in mmol/L
CIGSDAY number of cigarettes smoked per day
CVDCENS died from cardiovascular disease 0 =no, 1 =yes
DBP diastolic blood pressure in mmHg
DIABETES have diabetes 0 =no, 1 =yes
DRINKING 1 =never, 2 =ex, 3=<20 grams/day
4 =20 60 grams/day, 5 =>60 grams/day
DTHCENS died during follow-up 0 =no, 1 =yes
DYSPNOEA get shortness of breath
0 =never, 1 =hurrying or walking up a hill
2 =1 and when walking with people of same age on level ground
3 =1, 2 and when walking at my own pace on level ground
EXERCISE number of days exercise per week

This dataset relates to baseline (in 1981) and mortality follow-up
data (to 1995) for the 1552 participants aged 40-69 years in the
1981 Busselton Health survey.
Busselton 1981 survey data (more)
FEV forced expiratory volume in 1 second in L
FVC forced vital capacity in L
HAYFEVER ever had hayfever 0 =no, 1 =yes
HEIGHT height in m
MARITAL 1 =single, 2 =divorce, widowed, separated, 3 =married or de facto
MYOCARD ever had myocardial infarction 0 =no, 1 =yes
OCCUP 1 =professional, 2 =farmer, 3 =manual
4 =home duties/unemployed/pensioner
RXHYPER on treatment for hypertension 0 =no, 1 =yes
SBP systolic blood pressure in mmHg
SEX 0 =male, 1 =female
SMOKING 1 =never, 2 =ex, 3 =<15 cigarettes/day, 4 =15+cigarettes/day
STENCHD coronary heart disease 0 =no, 1 =possible, 2 =definite
SURVTIME follow-up time from survey date in years
WEIGHT weight in kg
YEARSMOK years of smoking

L1.18
SAS summary of bsn81 data
The MEANS Procedure
Variable N Mean Std Dev Minimum Maximum

age 1552 55.816 8.486 40.020 69.980

alcgrams 1552 89.470 156.437 0.000 2450.000
angina 1552 0.037 0.188 0.000 1.000
asthma 1552 0.075 0.263 0.000 1.000
bmi 1552 26.100 3.963 16.800 45.300
bronch 1552 0.193 0.395 0.000 1.000
chol 1552 6.151 1.169 3.010 14.410
cigsday 1552 3.233 7.968 0.000 70.000
cvdcens 1552 0.050 0.219 0.000 1.000
dbp 1552 79.259 11.857 30.000 178.000
diabetes 1552 0.025 0.157 0.000 1.000
drinking 1552 2.624 1.081 1.000 5.000
dthcens 1552 0.114 0.318 0.000 1.000
dyspnoea 1552 0.387 0.752 0.000 3.000
exercise 1552 3.110 2.932 0.000 7.000
fev 1552 2.623 0.818 0.300 5.900
fvc 1552 3.490 0.961 1.000 7.200
hayfever 1552 0.189 0.392 0.000 1.000
height 1552 1.665 0.086 1.440 1.920
marital 1552 2.860 0.415 1.000 3.000
myocard 1552 0.017 0.128 0.000 1.000
occup 1552 3.229 1.134 1.000 4.000
rxhyper 1552 0.188 0.390 0.000 1.000
sbp 1552 131.182 19.392 84.000 223.000
sex 1552 0.557 0.497 0.000 1.000
smoking 1552 1.800 1.004 1.000 4.000
stenchd 1552 0.348 0.639 0.000 2.000
survtime 1552 13.368 2.459 0.340 14.120
weight 1552 72.558 13.258 37.800 126.000
yearsmok 1552 14.135 16.764 0.000 56.000

Busselton Health Study website

http://www.busseltonhealthstudy.com/
L1.19
BEFORE NEXT WEEK
Get a Course Reader(if still dont have one)
Get or borrow a hand-calculator
Attempt Topic 1 problems
Do Intro to SAS session
Get a USB flash drive?
Get a text book?
Review how to use statistical tables for Normal and t-
distributions.
Arrange SAS for your own PC and get course files.