Forest Analytics with R: An Introduction

355 Pages·2011·2.95 MB·English

by  Andrew P. Robinson

Use R!
Series Editors
Robert Gentleman Kurt Hornik Giovanni Parmigiani
For a complete list of titles published in this series, go to www.springer.com/series/6991
Use R!
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Bivand/Pebesma/Go´mez-Rubio: Applied Spatial Data Analysis with R
Claude:Morphometrics with R
Cook/Swayne: Interactive andDynamic Graphics for Data Analysis: With R
and GGobi
Hahne/Huber/Gentleman/Falcon:Bioconductor Case Studies
Nason: Wavelet Methods in Statistics with R
Paradis: Analysis of Phylogenetics and Evolution with R
Peng/Dominici: Statistical Methods for Environmental Epidemiology with R:
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Pfaff: Analysis ofIntegrated and Cointegrated Time Series with R, 2nd edition
Sarkar: Lattice: MultivariateData Visualization with R
Spector:Data Manipulation with R
Andrew P. Robinson • Jeff D. Hamann
Forest Analytics with R
An Introduction
1 C
Andrew P. Robinson Jeff D. Hamann
Dept. Mathematics and Statistics Forest Informatics, Inc.
University of Melbourne PO Box 1421
Parkville 3010 VIC 97339-1421 Corvallis Oregon
Australia USA
[email protected] [email protected]
Series Editors:
Robert Gentleman Kurt Hornik
Program in Computational Biology Department of Statistik and Mathematik
Division of Public Health Sciences Wirtschaftsuniversität Wien Augasse 2-6
Fred Hutchinson Cancer Research Center A-1090 Wien
1100 Fairview Avenue, N. M2-B876 Austria
Seattle,Washington 98109
USA
Giovanni Parmigiani
The Sidney Kimmel Comprehensive
Cancer Center at Johns Hopkins University
550 North Broadway
Baltimore, MD 21205-2011
USA

ISBN 978-1-4419-7761-8 e-ISBN 978-1-4419-7762-5
DOI 10.1007/978-1-4419-7762-5
Springer New York Dordrecht Heidelberg London
© Springer Science+Business Media, LLC 2011
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to proprietary rights.
Printed on acid-free paper
Springer is part of Springer Science+Business Media (www.springer.com)
This book is dedicated to Grace, Felix, and M’Liss,
(and Henry and Yohan)
with grateful thanks for inspiration and patience.

Preface
R is an open-source and free software environment for statistical computing
and graphics. R compiles and runs on a wide variety of UNIX platforms
(e.g., GNU/Linux and FreeBSD), Windows, and Mac OSX. Since the late
1990s,Rhasbeendevelopedbyhundredsofcontributorsandnewcapabilities
are added each month. The software is gaining popularity because: 1) it is
platform independent, 2) it is free, and 3) the source code is freely available
and can be inspected to determine exactly what R is doing.
Our objectives for this book are to 1) demonstrate the use of R as a solid
platform upon which forestry analysts can develop repeatable and clearly
documentedmethods;2)provideguidanceinthebroadareaofdatahandling
and analysis for forest and natural resources analytics; and 3) to use R to
solve problems we face each day as forest data analysts.
This book is intended for two broad audiences: students, researchers, and
softwarepeoplewhocommonlyhandleforestrydata;andforestrypractition-
erswhoneedtodevelopactionablesolutionstocommonoperational,tactical,
and strategic problems. We often mention better and more complete treat-
ments of specific subject material for further reference (e.g., forest sampling,
spatial statistics, or operations research).
Wehopethatthisbookwillserveasafieldmanualforpracticingforestan-
alysts,managers,andresearchers.Wehopethatitwillbedog-eared,defaced,
coffee/tea-stained, and sticky-noted to near destruction. We hope the reader
will engage in the exercises, scrutinize its contents, forgive our weaknesses,
possibly and carefully absorb suggestions, and constructively criticize.
Acknowledgments
This book would not have been possible without the patient and generous
assistance of many people. We first thank all the authors of the literature
we cite, who were willing to publish their data as part of their research.
vii
viii Preface
Thesedataareoftenouronlylinkbetweenrepeatableresearchandanecdotal
opinion.
WethankValerieLeMayandTimothyGregoirefortheirkindcontribution
of tree measurement data and for their encouragement and leadership in
the field. We thank Boris Zeide for his generous contribution of the von
Guttenberg data. We thank Don Wallace and Bruce Alber for supplying
an interesting dataset to demonstrate the data management, plotting, and
file functions in Chapter 2. We thank the Oregon State University College
of Forestry Research Forests web site for posting a publicly available forest
inventory for Chapters 2 and 4. Without those data, many of the examples
and topics in this book would have to have been performed using simulated
data and frankly would have been much less interesting. We thank Martin
Ritchieforprovidingdata,funding,andsnippetsofcodeoncelostandfound
againduringthedevelopmentoftherconiferspackage,usedinChapter8.We
thankDavidHannfor,yearsago,providinganoriginalcopyofthemanuscript
that we used to generate the shared library example (chambers-1980.so) in
Chapter 8 (Chambers, 1980).
We have received considerable constructive criticism via the review pro-
cess, only some of which we can source. We especially thank John Kershaw
for generous and detailed comments on Chapter 3, Jeff Gove for his support
and useful commentary on Chapter 5, and David Ratkowsky and Graham
Hepworth for their thoughtful and thought-provoking comments on Chap-
ters 6 and 7, respectively. Numerous other useful comments were made by
anonymous reviewers. The collection of review comments improved the book
immeasurably.
WethankRCore,theRcommunity,andallthepackageauthorsandmain-
tainerswehavecometorelyupon.Specifically,wethankthefollowingpeople,
in no particular order: David B. Dahl (xtable); Lopaka Lee (R-GLPK); An-
drew Makhorin (GLPK); Roger Bivand (maptools); Deepayan Sarkar (lat-
tice); Hadley Wickham (ggplot2); Brian Ripley (MASS, class, boot); Jose
PinheiroandDouglasBates(nlme);FrankHarrell(Hmisc);AlvaroNovoand
JoeSchafer(norm);GregWarnes(gmodelsetal.);ReinhardFurrer,Douglas
Nychka, and Stephen Sain (fields); Thomas Lumley (survey); and Nicholas
J. Lewin-Koh and Roger Bivand (maptools).
We thank John Kimmel, our managing editor at Springer, for showing in-
crediblepatienceandHalHenglein,ourcopyeditor,forkeepingusconsistent.
ARwishestothankMarkBurgmanforprovidingspacetofinishthisbook
within a packed ACERA calendar, and for his substantial support and guid-
ance. AR also wishes to thank Geoff Wood, Brian Turner, Alan Ek, and
Albert Stage for their kindness and intellectual support along the way.
JH wishes to thank Martin Ritchie, David Marshall, Kevin Boston, and
John Sessions for their support along the way.
Finally, we wish to thank our wives, children, and friends for cheerful
perseverance and support in the face of a task that seemed at times like a
little slice of Sisyphus.
Preface ix
Melbourne and Corvallis Andrew Robinson
August 16, 2010 Jeff D. Hamann