Biostatistics III in R

In biostat3: Utility Functions, Datasets and Extended Examples for Survival Analysis

Exercise 1: Life tables and Kaplan-Meier estimates of survival

library('knitr')
read_chunk('../q1.R')
opts_chunk$set(cache=FALSE, fig.width=7, fig.height=6)
options(width=90)

(a) Hand calculation: Life table and Kaplan-Meier estimates of survival

The results are contained in an Excel file and are also shown in the R output below.

(b) Using R to validate the hand calculations done in part 1 (a)

First, load the biostat3 library for the dataset , survminer for plots and knitr for nice html output:

Following are the life table estimates. Note that in the lectures, when we estimated all-cause survival, there were 8 deaths in the first interval. One of these died of a cause other than cancer so in the cause-specific survival analysis we see that there are 7 ‘deaths’ and 1 censoring (Stata uses the term ‘lost’ for lost to follow-up) in the first interval.

Following is a table of Kaplan-Meier estimates. Although it’s not clear from the table, the person censored (lost) at time 2 was at risk when the other person dies at time 2. On the following is a graph of the survival function.

biostat3 documentation built on Oct. 29, 2024, 5:07 p.m.