Graphical Models with R

Graphical models in their modern form have been around since the late 1970s and appear today in many areas of the sciences.  Along with the ongoing developments of graphical models, a number of different graphical modeling software programs have been

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Kurt Hornik

For further volumes: www.springer.com/series/6991

Giovanni G. Parmigiani

Søren Højsgaard r David Edwards Steffen Lauritzen

r

Graphical Models with R

Søren Højsgaard Department of Mathematical Sciences Aalborg University Aalborg Denmark

Steffen Lauritzen Department of Statistics University of Oxford Oxford UK

David Edwards Centre for Quantitative Genetics and Genomics Department of Molecular Biology and Genetics Aarhus University Aarhus Denmark Series Editors: Robert Gentleman Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA USA

Kurt Hornik Department of Statistik and Mathematik Wirtschaftsuniversität Wien Wien Austria

Giovanni G. Parmigiani The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University Baltimore, MD USA

ISBN 978-1-4614-2298-3 e-ISBN 978-1-4614-2299-0 DOI 10.1007/978-1-4614-2299-0 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2012931941 © Springer Science+Business Media, LLC 2012 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)

Preface

Graphical models in their modern form have been around since the late 1970s and appear today in many areas of the sciences. Along with the ongoing developments of graphical models, a number of different graphical modelling software programs have been written over the years. In recent years many of these software developments have taken place within the R community, either in the form of providing an R interface to existing software or in the form of new R packages. At the time of writing, the taskview for graphical models in R at http://cran.r-project.org/web/views/gR.html

lists some thirty packages related to graphical models. It is expected that this number will grow considerably, and the packages will be extended and modified. This book attempts to give the reader a gentle introduction to graphical modelling using R and the main features of some of these packages, hopefully sharpening the appetite for using and developing these packages further. In addition, we shall give a few examples of how more advanced aspects of graphical modelling can be represented and handled within R. We emphasize that this book is not a manual to the collection of packages mentione