Censored Data Analysis - Exercise class

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• SIS page: NMST531
• Schedule: officially on Monday 15:40 - 17:10 in classroom K4
• Language: materials in English, instructed in Czech (unless anybody requires English)
• Instructur e-mail: vavraj@karlin.mff.cuni.cz
• Lecture web page: http://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)
• CORONAVIRUS
  • Untill anti-coronavirus restriction measures are cancelled, the exercises will be held in a distant form.
  • Actual form of the exercise class will be decided based on agreement with all participants.
  • Preferable form:
    • regular self-study of given materials,
    • completing given homework assignments in pre-specified deadlines,
    • discussions over the last exercise and homework via ZOOM session shortly after the deadline.
  • ZOOM session - each Monday at 15:40 - discussion over the solutions of homework assignments

Credit

• Satisfactory solution to given assignments by the prescribed deadline.
  (If your solution will not be satisfactory enough, you might be asked for revision.)

Overview

Exercise 1 (26th October - 9th November)

• Topic: Parametric regression models for censored data
• Dataset: pbc dataset from library(survival)
• Assignment: Find suitable model for survival time and interpret it.
• Deadline: Monday 9th November 9:00

Exercise 2 (9-16th 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: Monday 16th November 9:00

Exercise 3 (16-23rd November)

• Topic: Actuarial (lifetable) estimator of the survival
• Dataset: nurshome, mort.m and mort.f from mort.RData
• Assignment: Compare non-grouped and grouped approaches for estimation survival and hazard function for two subpopulations in nurshome dataset. Compare survival estimators with the output from ČSÚ: males and females.
• Deadline: Monday 23rd November 9:00

Exercise 4 (23-30th 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: Monday 30th November 9:00

Exercise 5 (30thNovember - 7th December)

• Topic: Testing equality of censored distributions
• Datasets: km_all.RData
• 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: Monday 7th December 9:00

Exercise 6 (7-14th December)

• Topic: The choice of two-sample test statistic
• Datasets: data(veteran), nurshome
• Assignment: Fill table of appropriateness of different weights in two-sample survival tests in different situations. Perform several real data analyses and simulation study.
• Deadline: Monday 14th December 9:00

Exercise 7 (14th December - 4th January)

• 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: Monday 4th January 9:00

Exercise 8 (4-11th January)

• Topic: Time-varying covariates in the Cox model
• Dataset: jasa and heart dataset from library(survival)
• Assignment: Try to reproduce heart dataset from jasa. 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: Monday 18th January 9:00