Springer - A Practical Guide to Ecological Modelling - Using R as a Simulation Platform - Nov 2008.pdf

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A Practical Guide to Ecological Modelling
A Practical Guide
to Ecological Modelling
Using R as a Simulation Platform
Karline Soetaert and Peter M.J. Herman
Netherlands Institute of Ecology, Yerseke, The Netherlands
13
Dr. Karline Soetaert
Netherlands Institute of Ecology
Centre for Estuarine & Marine Ecology
(NIOO-CEME)
4400 AC Yerseke
PO Box 140
The Netherlands
k.soetaert@nioo.knaw.nl
Dr. Peter M.J. Herman
Netherlands Institute of Ecology
Centre for Estuarine & Marine Ecology
(NIOO-CEME)
PO Box 140
4400 AC Yerseke
The Netherlands
p.herman@nioo.knaw.nl
Additional material, the R-examples and the R-code of all figures, is available as an R-package (ecolMod),
which can be found on the official R-website (http://cran.r-project.org/).
The R-example files are also available on the website of this book at www.springer.com
ISBN: 978-1-4020-8623-6
e-ISBN: 978-1-4020-8624-3
Library of Congress Control Number: 2008933286
Springer Science+Business Media B.V. 2009
No part of this work may be reproduced, stored in a retrieval system, or transmitted
in any form or by any means, electronic, mechanical, photocopying, microfilming, recording
or otherwise, without written permission from the Publisher, with the exception
of any material supplied specifically for the purpose of being entered
and executed on a computer system, for exclusive use by the purchaser of the work.
Cover illustration : View at the Oosterschelde from the Netherlands Institute of Ecology, Yerseke,
The Netherlands. Photograph taken by Thomas Haverkamp.
Printed on acid-free paper
987654321
springer.com
c
Preface
Why Another Ecological Modelling Book?
For several years we have taught courses on ecological modelling at the level of
graduates or starting PhD students. The audience typically consists of students
from biology, geology, bio-engineering, and, less frequently, from sciences such as
physics and chemistry. For most of these students our course was a first acquaintance
with the field of ecological mathematical modelling. Although often difficult, it was
an intellectual adventure both for them and for us. The course was set up as an
initiation to the subject, starting from the most basic of principles but nevertheless
leading to quite advanced applications.
This book is based on lecture notes that were written in 2001 and that accompany
this modelling course. We prepared the original notes because we felt there was
shortage of a book covering all the material that we wanted to address in our lectures.
The notes also served as a readable text that the students can consult while preparing
for the exam. This allowed us to teach the theory in rather short lessons, leaving
more time to cover the practical exercises, during which we directly interacted with
the students individually.
This book is written for young researchers who want to get more out of their
data than just description. Even when they see the possibilities of modelling to help
them gaining insight in the processes they study, two factors might frighten them
away from this path. One is mathematical formalism, theorems and detailed proofs,
the bread and butter of the applied mathematician. The other is complicated, se-
mantic and near-philosophical ecological theory. We have steered away from these
two extremes. We have tried to write a book that is readable for an audience with a
basic formation in ecology and a basic knowledge of mathematics. Although enough
material is presented that may also interest the more experienced ecologic modeller,
it is not a book only readable for either full-blown mathematicians or ecological
theoreticians.
Throughout the book we have tried to be practical, emphasizing the diversity
that exists in mathematical models and techniques. We discuss only the essential
aspects of mathematical methods, without pretension to mathematical rigour: often
one does not need to understand the fine details of a technique to correctly apply
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