Unit convenor and teaching staff |
Unit convenor and teaching staff
Unit Convenor
Kenneth Beath
Contact via ken.beath@mq.edu.au
E4A 507
Friday 2-4
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Credit points |
Credit points
4
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Prerequisites |
Prerequisites
Admission to MRes
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Corequisites |
Corequisites
STAT710
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Co-badged status |
Co-badged status
Unit SVA in the Biostatistics Collabaration Australia (BCA) programme.
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Unit description |
Unit description
This unit explores biostatistical applications of survival analysis. These begin with the Kaplan-Meier curve definition and its extension to the comparison of survival of several groups of subjects. The Cox proportional hazards model is introduced as a method for handling continuous covariates and parametric accelerated failure-time models are also covered. Time-dependent covariates and multiple outcomes are also considered.
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Information about important academic dates including deadlines for withdrawing from units are available at https://www.mq.edu.au/study/calendar-of-dates
On successful completion of this unit, you will be able to:
Name | Weighting | Due |
---|---|---|
Exercises | 10% | 24 March, 28 April |
Assignment 1 | 26% | 7 April |
Assignment 2 | 36% | 12 May |
Assignment 3 | 28% | 10 June |
Due: 24 March, 28 April
Weighting: 10%
2 short answer exercises each worth 5%. These will be made available at least 2 weeks before the due date. They will require brief answers and no data analysis.
Due: 7 April
Weighting: 26%
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Due: 12 May
Weighting: 36%
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Due: 10 June
Weighting: 28%
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The unit is offered in distance mode. Our means of communication will be via printed notes which will be mailed out, e-mail, and elearning (http://elearning.sydney.edu.au/), the University of Sydney's e-learning site. Our primary communication method is via elearning and we expect you to log in at least weekly to check for announcements and release of assignments and so on. To access elearning a uniKey is required. If you have not been sent one then contact Ken Beath.
The unit relies heavily on the prescribed text Hosmer, Lemeshow and May (see below). The study notes provide a guide to readings in this text, as well as sometimes to other readings, which will be provided. They also provide additional explanation where this is needed. In the study notes for each module, tutorial exercises are given, mostly referring to exercises in Hosmer, Lemeshow and May.
Study notes will be mailed to you, at the beginning of semester and will also be posted on the iLearn site. If you do not receive these within a few days then please contact Lesley Mooney.
We will be using elearning for online, posting of course notes, assignments, solutions and data sets, and submission of exercises, assignments and the take-home test.
The prescribed text is Hosmer DW, Lemeshow S and May S (2008). Applied Survival Analysis}, John Wiley and Sons, Second Edition. There are numerous texts on survival analysis which you may wish to consult, but the following may be particularly helpful because of its use of Stata:
Cleves MA, Gould WW, Gutierrez RG and Marchenko Y (2010). An Introduction to Survival Analysis using Stata, Third Edition, Stata Press.
Other useful texts are:
Klein JP and Moeschberger ML (2003). Survival analysis : techniques for censored and truncated data}, Springer. Kleinbaum DG (1995). Survival analysis : a self-learning text}, Springer-Verlag.
We will be using Stata (version 11 or later). The current version of Stata is 13. While Stata has a GUI we will be using the command language. It is still useful to experiment with the GUI, as the corresponding commands are available in the Review pane. The software is available in the computer laboratories on Macquarie University campus. If you need your own copy of Stata, you will need to purchase it directly from the suppliers. You can place your order via the Survey Design website at http://www.survey-design.com.au. For those that haven't used Stata previously there is much introductory material on the web. A useful starting point is http://www.stata.com/links/resources1.html, and particularly good is http://www.ats.ucla.edu/stat/stata
Advanced GradPlan Intercooled Stata 13 with perpetual licence (consisting of CD for Windows, Mac or Linux, including PDF of manuals) = AU\$212 (+ postage)
Basic GradPlan Intercooled Stata 13 - as above but with a one-year licence = AU\$118 (+ postage)
Basic GradPlan Intercooled Stata 13 - as above but with a six month licence = AU\$88 (+ postage)
There is also a Small Stata option; however, this is limited to around 1,000 observations which will not be sufficient.
Go to the Survey Design website listed above and go to the Grad Plan page (LH column `GradPlan' link). Above the prices is a link to an order form. Followthe instructions and you should order a GradPlan Intercooled package. On the order form you should note that you are enrolled in a BCA course (BCA students) or STAT827 (MU students), your student ID number, the university in which you are enrolled, and the operating system of the computer that you will be using. For GradPlan orders delivery is normally within a few days of payment being cleared.
Removed Take-home Test and one exercise. Expanded use of new categorical variables.
The unit timetable is based on the University of Sydney timetable, which starts a week later than Macquarie University, and has only a one week mid-semester break, at a different time.
Module | Weeks | Content |
1 |
1,2 (3March) |
The nature of survival data, including censoring; the survival (or survivorship) function: definition and estimation via the Kaplan-Meier curve; the stset command in Stata;Kaplan-Meier estimate of the survival (or survivorship) function: confidence intervals and hypothesis testing. |
2 |
3,4 (17 March) |
The density, survival, hazard and cumulative hazard functions; the Nelson-Aalen estimate of the cumulative hazard function; Definition of the proportional hazards model; construction of the partial likelihood for the Cox model; the treatment of tied failure times; hypothesis testing on the coefficients, using Wald and partial likelihood ratio tests. |
3 |
5,6 (31 March) |
For the Cox PH model: hypothesis testing on the coefficients, contd; estimation of the baseline functions S0(t) and H0(t), and their adjustment for covariate values; the effect of a change in scale and origin of units of measurement of covariates. |
4 |
7,8 (14 April) |
Model diagnostics for the Cox PH model; the stratified Cox model |
5 |
9,10 (5 May) |
Time-dependent covariates in the Cox model; parametric survival time models, in particular the accelerated failure time model, with an exponential and Weibull distrubution; discrete-time logistic model |
6 |
11,12 (19 May) |
Correlated survival data; clustered survival data; recurrent events models;competing-risks models |
7 |
13 (2 June) |
Sample size determination for comparing two response rates and two survival distributions; good practice for the display of survival analysis results in scientific publications |
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Academic Honesty Policy http://mq.edu.au/policy/docs/academic_honesty/policy.html
Assessment Policy http://mq.edu.au/policy/docs/assessment/policy.html
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Disruption to Studies Policy http://www.mq.edu.au/policy/docs/disruption_studies/policy.html The Disruption to Studies Policy is effective from March 3 2014 and replaces the Special Consideration Policy.
In addition, a number of other policies can be found in the Learning and Teaching Category of Policy Central.
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