A little book of r for biomedical statistics

A Little Book of R For Biomedical Statistics
Release 0.1

Avril Coghlan

August 29, 2011

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How to install R 1.1 Introduction to R . . . . . 1.2 Installing R . . . . . . . . 1.3 Installing R packages . . . 1.4 Running R . . . . . . . . 1.5 A brief introduction to R . 1.6 Links and Further Reading 1.7 Acknowledgements . . . 1.8 Contact . . . . . . . . . . 1.9 License . . .. . . . . . .

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3 3 3 5 7 7 10 10 10 11 13 13 13 15 17 17 20 21 23 24 25 27 27 28 28 29 31 33

2 Using R for Biomedical Statistics 2.1 Biomedical statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.2 Calculating Relative Risks for a Cohort Study . . . . . . . . . . . . . . . . . . . . . . . . . . 2.3 Calculating Odds Ratios for a Cohort or Case-Control Study. . . . . . . . . . . . . . . . . . 2.4 Testing for an Association Between Disease and Exposure, in a Cohort or Case-Control Study 2.5 Calculating the (Mantel-Haenszel) Odds Ratio when there is a Stratifying Variable . . . . . . 2.6 Testing for an Association Between Exposure and Disease in a Matched Case-Control Study . 2.7 Dose-response analysis: . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . 2.8 Calculating the Sample Size Required for a Randomised Control Trial . . . . . . . . . . . . . 2.9 Calculating the Power of a Randomised Control Trial . . . . . . . . . . . . . . . . . . . . . . 2.10 Making a Forest Plot for a Meta-analysis of Several Different Randomised Control Trials: . . 2.11 Links and Further Reading . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . 2.12 Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.13 Contact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.14 License . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Acknowledgements 4 5 Contact License

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A Little Book of R For Biomedical Statistics, Release 0.1

By Avril Coghlan, University College Cork, Cork, Ireland. Email: a.coghlan@ucc.ie This is a simple introduction to biomedical statistics using the R statistics software.

There is a pdf version of this booklet available athttps://github.com/avrilcoghlan/LittleBookofRBiomedicalStats/raw/master/_build/la If you like this booklet, you may also like to check out my booklet on using R for time series analysis, http://alittle-book-of-r-for-time-series.readthedocs.org/ and my booklet on using R for multivariate analysis, http://littlebook-of-r-for-multivariate-analysis.readthedocs.org/. Contents:

CONTENTS

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A Little Book of R For Biomedical Statistics, Release 0.1

2CONTENTS

CHAPTER

ONE

HOW TO INSTALL R
1.1 Introduction to R
This little booklet has some information on how to use R for biomedical statistics. R (www.r-project.org) is a commonly used free Statistics software. R allows you to carry out statistical analyses in an interactive mode, as well as allowing simple programming.

1.2 Installing R
To use R, you first need to install the R...