Jan Vávra

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Censored Data Analysis (Exercise class)

SIS page : NMST531

Schedule : Monday 12:20 - 13:50 in classroom K11

Language : materials in English, instructed in Czech (unless anybody requires English)

Instructor e-mail : vavraj@karlin.mff.cuni.cz (for sending solutions to assignments)

Lecture web page : www.karlin.mff.cuni.cz/~kulich/vyuka/cens/index.html

Note : exercises will start by the end of October (untill then, lectures will replace exercise classes)

Credit

Presence at exercises (2 absences tolerated)
Satisfactory solution to given assignments by the prescribed deadline.
(If your solution will not be satisfactory enough, you might be asked for revision.)
Hand in printed (or hand written) report/solution in the next exercise class or send via email to address vavraj@karlin.mff.cuni.cz.

Overview

Exercise 1 (4th November)

Topic: Parametric regression models for censored data
Dataset: pbc data from library(survival)
Assignment: Find suitable model for survival time and interpret it.
Deadline: 11th November

Exercise 2 (11th November)

Topic: Non-parametric estimation of cumulative hazard and survival function
Dataset: fans
Assignment: Calculate and plot [NA], [KM], [FH] estimates both manually and using survfit function from library(survival).
Deadline: 18th November

Exercise 3 (18th November)

Topic: Actuarial (lifetable) estimator of the survival
Dataset: mort.m and mort.f from mort.RData
Assignment: Compare classical [KM] estimator with Actuarial (Lifetable) estimator and with the output from ČSÚ: males and females.
Deadline: 25th November

Exercise 4 (25th November)

Topic: Confidence intervals and bands for survival function
Dataset: km_all.RData
Assignment: Compute and plot [KM] estimates including Hall-Werner bands. Perform short (or long if you wish) simulation study.
Deadline: 2nd December

Exercise 5 (2nd December)

Topic: Testing equality of censored distributions
Datasets: km_all.RData, data(veteran),
Assignment: Calculate and plot [KM], [NA] estimates and smoothed estimator of hazard function when differentiating different groups. Perform two-sample tests and decide (based on the plots) which test statistic would be the most appropriate.
Deadline: 16th December (you have two weeks)

Exercise 6 (9th December)

Topic: The choice of two-sample test statistic
Assignment: Finish the assignment from previous exercise.
Deadline: 16th December

Exercise 7 (16th December)

Topic: Building Cox models for censored data (constant covariates)
Dataset: pbc dataset from library(survival)
Assignment: Perform exploratory analysis focused on the influence of covariates on the survival probability. Build a reasonable Cox model (starting from simple univariate models). Compare your final Cox model to your final model from Exercise 1.
Deadline: 6th January

Exercise 8 (6th January)

Topic: Time-varying covariates in the Cox model
Dataset: jasa and heart dataset from library(survival)
Assignment: Build and interpret Cox model with covariate indicating the time of heart transplantation and other fixed covariates. Does transplantation help patients to survive longer? Plot estimated survival functions.
Deadline: the sooner you deliver it, the sooner you get course credit.