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Using R for the self-controlled case series method

All script files were written by Heather Whitaker for R version 2.5.0 (free software available from http://www.r-project.org/). Please let us know if you have any suggestions for improving them.

There are two ways in which we can fit the case series model after the data have been reformatted:

  1. Download the gnm package and use gnm to fit a conditional poisson regression model with eliminate = indiv (where indiv is a factor for each individual in the data set)
  2. Use the survival package (included in R 2.5.0, so no need to download) and use clogit to fit a logistic regression model with strata = event (where event is a factor for each event in the data set, rather than a factor for each individual). Here, we fit a conditional logistic regression model rather than a conditional poisson regression model: because recurrent events are assumed to be independent the conditional logistic likelihood is equivalent if each event is treated like a separate individual.

We are currently exploring which is the most efficient. We hope to put R scripts for all the examples in the tutorial paper here soon. For the time being, here are a few examples using clogit: 

MMR and meningitis in Oxford example

To run the MMR and meningitis in Oxford example detailed in the tutorial paper save these two files:

'ox.txt', the data in a tab-delimited text file.

'oxford.r', the commands in an r script file.

Open oxford.r and select 'run all' under the edit menu.

ITP and MMR example

'itp.r' fits the multiple risk periods example on p.1782-1783 of the tutorial paper.

'itp.txt', data

'itp.r', r script file

Intussusception and oral polio vaccine example

'intuss.r' fits analysis 5, repeat exposures example detailed on p.1787-1789 of the tutorial paper.

'intuss.txt', data

'intuss.r', r script file

Apologies for the lack of explanation in the script files, we will update these soon, please ask if you need any help!

R package for the case series analysis for censored, perturbed or curtailed post event exposures

An R package, adSCCS, has been written by Ronny Kuhnert (Robert Koch Institute, Berlin) to fit the extended self-controlled case series method for the situation when no exposure can occur after an event. This is the method outlined in the paper: Farrington, Whitaker and Hocine (2008). Case series analysis for censored, perturbed, or curtailed post-event exposures. Biostatistics, 10(1): 3-16.

adSCCS package version 1.5

adSCCS manual


The self-controlled case series method / Heather Whitaker / updated May 2007