20/02/2020

Staff – Coordinators

Dr Enes Makalic
Biostatistics POPH90013
High Dimensional Analytics (Unit Head)
Enes Makalic Room 309, Level 3, 207 Bouverie Street
Centre for Epidemiology and Biostatistics
Melbourne School of Population and Global Health

Phone: +61 (3) 8344 0860

emakalic@unimelb.edu.au

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Suggested Reading Statistics Software

• To purchase a Stata license:

Essential Medical Statistics – https://surveydesign.com.au/buystudent.html

Kirkwood BR, Sterne JAC. • If you are only doing Biostatistics and will NOT be enrolling into other statistics subjects
– Stata/IC 16, 6 Month license (~$82)
2nd Edition, 2003
• Biostatistics subjects in the future
Wiley-Blackwell – Stata/IC 16, Perpetual license (~$382)

• Stat/Transfer; Stata SE not required

• Stata Book: “Getting Started with Stata for Windows”

• Free, online version: http://www.stata.com/bookstore/getting-started-windows/

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Calculators Sessions (1 – 6)

Teaching
• The only University approved calculator is Week
Lecture Chapter Practicals Date

– Casio FX82 (any suffix) 1 Introduction, datasets & types of variables 2 None March 4th

2 Displaying, presenting & graphing data 3 Tutorial March 11th

• Other models of calculators will NOT be permitted! 3

Measures of central tendency and spread,
sampling variation & standard error
4
Tutorial
Stata Practical*
March 18th
Thu/Fri 19th/20th

4 The normal distribution 5&6 Tutorial March 25th

[Note – cannot use calculators on mobile phones in exam] Confidence interval for a mean, April 1st
5 7 Tutorial
comparison of two means Thu/Fri 2nd/3rd
Tutorial
6 Interpreting results of statistical analyses 8 April 8th
Stata Practical*

Teaching Break (Friday, 10th April - Sunday, 19th April)

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Sessions (7 – 12) Assessment

Teaching
Lecture Chapter Practicals Date
Week Date & Time Due Content
7 Proportions & confidence intervals 15 & 16 Tutorial April 22nd Assignment 1 Monday 20th April, 1pm All material covered in the
30% of the total mark lectures, tutorials and Stata
8 Measures of association 16 & 37 Tutorial April 29th sessions in weeks 1 to 6.
Controlling for confounding: stratification & Tutorial May 6th
9 18, 19 & 20 Monday 18th May, 1pm All material covered in the
regression Stata Practical* Thu/Fri 7th/8th Assignment 2
40% of the total mark lectures, tutorials and Stata
10 Design, sample size & statistical power 35 Tutorial May 13th
sessions in weeks 7 to 10.
Tutorial May 20th
11 Simple linear regression 10
Stata Practical* Thu/Fri 21st/22nd
Examination June All material covered in
12 Revision Tutorial May 27th (2.0 hours, 15 minutes reading time) 30% of the total mark weeks 1 to 11.
Open book, basic calculator required.

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Extension requests Special consideration requests

• Students may apply for an extension if… • Students whose studies are genuinely and significantly
– unforeseen circumstances arise that impair a student’s impacted by:
ability to submit an assessment
– Exceptional or extenuating circumstances outside of
their control
• Extension
– Should be submitted before the assignment due date – Events or circumstances of national or state
– Maximum extension is 10 working days significance

• Policy and how to apply: Canvas, Assessment section • Detailed information: Canvas, Assessment section

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Late submission Submitting assignments in Canvas

• A reduction of 5% for each day the work is late within the first • Submitting the correct assignment is your responsibility
week

• Eight to fourteen days after the due date, 50% will be • Submission of wrong file:
deducted
• Late assignment penalties apply
• After 14 days no mark will be awarded • Or treated as non-submission (0%) if the error is not found
prior to return of the assignments
• If you have applied for an extension or special consideration
these penalties do not apply

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Academic Honesty & Plagiarism Biostatistics

• Information on definitions, advice & penalties • Statistical methods may seem very difficult
– But only from the first look
https://academichonesty.unimelb.edu.au/

• In practice, they are…logical, intuitive and fun!

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Introduction, datasets and types of variables

• To introduce using samples to

Lecture 1 make inferences about populations

Introduction, datasets and types of variables • Datasets, variables and

observations
• Types of variables
– Data types
– Outcomes and exposures

[See Kirkwood & Sterne: Chapter 2 – Defining the data]

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Inferential statistics Statistical Inference – Example 1 (Height)

• Population All students enrolled in POPH90013

10 students enrolled in
– Complete set of similar ‘items’ POPH90013 attending
Lecture 1

• Sample POPULATION SAMPLE

– Subset (subgroup) drawn from the population

• Statistics
Avg. Height = 173cm
– Uses the sample to make inferences about the population
INFERENCE

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Statistical Inference – Example 2 (Mobile phones) Data sets, observations and variables

UK Women aged 50 and over

791,710 women aged 50 • We study samples by gathering data
and over in the UK who
participated in the Million – Collectively called a data set
Women Study

POPULATION SAMPLE • Data set is a table

– Records about individual members of the sample (rows)
• A variable is any observation that is measured (columns)
During 7 years
follow-up, 51,680
(6.5%) incidence of
INFERENCE invasive cancers

Source: Benson V.S. et al. Int. Jrnl. of Epi. 2013;42:792-802

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Example data set Pregnant women & malaria dataset

• To study the effects of vivax malaria infection during pregnancy ID Maternal age Birthweight Vivax malaria
(years) of baby ever during
(gms) pregnancy

1 17 2900 No
2 16 2600 No
3 19 2950 Yes
4 18 3200 No
5 19 2500 No
6 35 2900 No
Source: Nosten F et al. Lancet 1999; 354:546-549

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Types of variables Numerical variables

• Numerical • Continuous
– Continuous – Can take any value
– Discrete – Measured on a continuous scale
– Examples: Height, body weight, blood pressure,
• Categorical haemoglobin level
– Nominal
– Ordinal

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Numerical variables Categorical variables

• Discrete • Nominal
– Can only take certain values – No ‘natural’ ordering
– Binary variable – two values only
– Usually whole numbers
– Examples: male or female; alive or dead;
– Examples: Parity, number of visits to hospital, number experimental groups; blood group O, A, B, or AB;
of people in a household place of birth

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Categorical variables Derived variables

• Ordinal • To simplify display or analysis

– Have a ‘natural ordering’ (ranking) – Often need to classify or transform variables

– Examples: social class, grade of breast cancer

• Examples:
• How do you rate the MSPGH statistics course?
– Calculate or categorise body mass index, age groups
– poor / fair / good / very good / excellent
– Categorise by threshold values
• Low birthweight (<2.5 kg)
• Hypertension (Yes / No; diastolic blood pressure > 90mmHg)

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Outcome and exposure variables Why is it important to know the variable type?

• Outcomes are the variables we want to know more about • Absolutely critical to choosing the appropriate form of
statistical analysis
• Exposures are the variables we think might explain the
variation in outcomes • Type of the outcome variable
– Dictates the chosen statistical model
• Statistics quantifies the association between outcomes
and exposures

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Summary

• Population, sample

• Variables
– Numerical
• Continuous, discrete
– Categorical
• Nominal, ordinal
– Derived

• Outcome vs. Exposure

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