Jan Vávra

NMST531 - Censored Data Analysis (Exercise class)

SIS page : NMST531

Schedule : on Monday 12:20 - 13:50 in classroom K4

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 (from previous year): www.karlin.mff.cuni.cz/~kulich/vyuka/cens/index.html

Note : exercises will start by the end of October

CORONAVIRUS : We have to be ready for any potential government restrictions.

Presence form:
- weekly exercise class on schedule,
- completing given homework assignments in pre-specified deadlines (usually a day before the next exercise),
- exercise class will be opened with discussion over previous homework,
- we will go through the materials for exercise class together,
- there will be time for you to ask questions, work on given assigments, ...
- no attendance requirement for course credit.
Distant form:
- regular self-study of given materials,
- completing given homework assignments in pre-specified deadlines,
- feedback and discussions over the last exercise and homework via ZOOM session shortly after the deadline,
- also in ZOOM: assignment of a new homework for the next week with a short commentary,
- not in ZOOM: full lecture and detailed exploration of given materials (everybody has his/her own pace while working with R).

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.
Recommended form: Rmarkdown output (PDF or HTML)

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 21st November 9:00

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 28th November 9:00

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 5th December 9:00

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: Tuesday 13th December 9:00 (also for Ex 6!)

HELD TOGETHER WITH Ex5 on 5th December at 12:20!
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: Tuesday 13th December 9:00 (also for Ex 5!)

Held on Tuesday 13th December at 14:00!!! On Monday 12th December there will be a lecture on Cox model by doc. Hlubinka.
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 2nd January 9:00

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 16th January 9:00