Mixed Effects Models and Extensions in Ecology with R

564 Pages·2009·21.15 MB·English

by  Alain F. Zuur

Statistics for Biology and Health
SeriesEditors:
M.Gail
K.Krickeberg
J.M. Samet
A.Tsiatis
W.Wong
Statistics for Biology and Health
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SolutionsUsingRandBioconductor
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Lazar:TheStatisticalAnalysisofFunctionalMRIData
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andSoftware
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Wu/Ma/Casella:StatisticalGeneticsofQuantitativeTraits:Linkage,Maps,andQTL
Zhang/Singer:RecursivePartitioningintheHealthSciences
Zuur/Ieno/Smith:AnalysingEcologicalData
Zuur/Ieno/Walker/Saveliev/Smith:MixedEffectsModelsandExtensionsinEcology
withR
· · ·
Alain F. Zuur Elena N. Ieno Neil J. Walker
·
Anatoly A. Saveliev Graham M. Smith
Mixed Effects Models
and Extensions in Ecology
with R
123
AlainF.Zuur ElenaN.Ieno NeilJ.Walker
HighlandStatisticsLtd. HighlandStatisticsLtd. CentralScienceLaboratory
Newburgh Newburgh Gloucester
UnitedKingdom UnitedKingdom UnitedKingdom
[email protected] [email protected] [email protected]
AnatolyA.Saveliev GrahamM.Smith
KazanStateUniversity BathSpaUniversity
Kazan Bath
Russia UnitedKingdom
[email protected] [email protected]
SeriesEditors
M.Gail K.Krickeberg J.Samet
NationalCancerInstitute LeChatelet DepartmentofPreventive
Rockville,MD20892 F-63270Manglieu Medicine
USA France KeckSchoolofMedicine
UniversityofSouthern
California
1441EastlakeAve.Room
4436,MC9175
LosAngeles,CA90089
A.Tsiatis W.Wong
DepartmentofStatistics DepartmentofStatistics
NorthCarolinaStateUniversity StanfordUniversity
Raleigh,NC27695 Stanford,CA94305-4065
USA USA
ISSN1431-8776
ISBN978-0-387-87457-9 e-ISBN978-0-387-87458-6
DOI10.1007/978-0-387-87458-6
LibraryofCongressControlNumber:2008942429
(cid:2)c SpringerScience+BusinessMedia,LLC2009
Allrightsreserved.Thisworkmaynotbetranslatedorcopiedinwholeorinpartwithoutthewritten
permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York,
NY10013, USA), except forbrief excerpts inconnection with reviews orscholarly analysis. Usein
connection with any form of information storage and retrieval, electronic adaptation, computer
software,orbysimilarordissimilarmethodologynowknownorhereafterdevelopedisforbidden.
The use in this publication of trade names, trademarks, service marks, and similar terms, even if
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theyaresubjecttoproprietaryrights.
Printedonacid-freepaper
springer.com
Thanks tomyparentsfor sharingtheburden
of myuniversityfees – AlainF.Zuur
To myfriends,colleagues,andformerstudents
who areactivelycommittedtotheprotectionand
careof theenvironment– ElenaN. Ieno
Thanks tomywifeTatianaforher patience
andmoralsupport– AnatolyA.Saveliev
Iwould liketo thankallfamilyand friendsfor
help andsupportthroughtimesgood andbad
duringthewritingof thisbook– Neil J.Walker
To myparentswho, evennow,continuetosupport
mein everythingIdo– GrahamM. Smith

Preface
No sooner, it seems, had our first book Analysing Ecological Data gone to print,
thanweembarkedonthewritingofthenearly600pagetextyouarenowholding.
Thisprovedto be a labourof loveof sorts– we feltthatthere werecertain issues
sufficientlycommonintheanalysisofecologicaldatathatmeritedmoredetailedde-
scriptionandanalysis.Thusthepresentbookcanbeseenasa‘sequel’toAnalysing
EcologicalDatabutwithmuchgreateremphasisontheseveryissuessocommonly
encounteredinthecollectionof,andanalysisof,ecologicaldata.Inparticular,we
look at differentways of analysing nested data, heterogeneity of variance, spatial
andtemporalcorrelation,andzero-inflateddata.
The original plan was to write a text of about 350 pages, but to do justice to
the sheer range of problems and ideas we have well exceeded that original target
(as you can see!). Such is the scope of applied statistics in ecology. In particular,
partlyonthebackofreviewer’scomments,wehaveincludedachapteronBayesian
Monte-CarloMarkov-Chainapplicationsingeneralizedlinearmodelling.Wehope
thisservesasaninformativeintroduction(butnomorethananintroduction!)tothis
interestingandincreasinglyrelevantareaofstatistics.
We received lots of positive feedback on the approach and style we used in
AnalysingEcologicalData,especiallythecombinationofcasestudiesandatheory
section.We havethereforefollowedthe same approachwith this book.Thistime,
however,we have providedthe R code used for the analysis. Most of this R code
isincludedinthetext,butwherethecodewasparticularlylong,itisonlyavailable
fromthebook’swebsiteatwww.highstat.com.Inthecasestudies,wealsoincluded
adviceonwhattowriteinapaper.
Newburgh,UnitedKingdom AlainF.Zuur
Newburgh,UnitedKingdom ElenaN.Ieno
Gloucester,UnitedKingdom NeilJ.Walker
Kazan,Russia AnatolyA.Saveliev
Bath,UnitedKingdom GrahamM.Smith
December2008
vii

Acknowledgements
Thematerialinthisbookhasbeentaughtinvariouscoursesin2007and2008,and
we are greatly in debt to all participants who helped improving the material. We
would also like to thank a number of people who read and commented on parts
of earlier drafts, namely Chris Elphick, Alex Douglas, and Graham Pierce. The
manuscriptwasreviewedbyLovedayConquest(UniversityofWashington),Sarah
Goslee(USDA),ThomasKneib(LMUMunich),BretLarget(UniversityofWiscon-
sin),RuthSalway(UniversityofBath),JingHuaZhao(UniversityofCambridge),
andseveralanonymousreferees.Wethankthemallfortheirpositive,encouraging,
andusefulreviews.Theircommentsandcriticismsgreatlyimprovedthebook.
Themostdifficultpartofwritingabookisfindingpublicdomaindatawhichcan
be used in theory chapters. We are particularly thankful to the following persons
fordonatingdatasets.SoniaMendesandGrahamPierceforthewhaledata,Gerard
Janssen for the benthic data, Pam Sikkink for the grassland data, Graham Pierce
and Jennifer Smith for the squid data, Alexandre Roulin for the barn owl data,
MichaelReedandChrisElphickfortheHawaiianbirddata,TatianaRogovaforthe
Volzhsko-Kamskyforestrydata,RobertCruikshanks,MaryKelly-QuinnandJohn
O’Halloran for the Irish (sodium dominance index) river data, Chris Elphick for
thesparrowandCaliforniabirddata,MichaelPenstonforthesealicedata,Joaqu´ın
VicenteandChristianGorta´zarforthewildboaranddeerdata,KenMackenziefor
thecoddata,andAnto´nioMiraforthesnakedata.Theproperreferencesaregivenin
thetext.Wealsowouldliketothankallpeopleinvolvedinthecasestudychapters;
theyarecreditedwhererelevant.
Michelle Cronin provided the seal photo on the back cover, Joaquin Vicente
the deer photo, and Malena Sabatino gave us the bee photo. The photograph of
thekoalaswasprovidedbyAustralianKoalaFoundation(www.savethekoala.com).
Thephotoonthefrontcoverisfrom(cid:2)c WayneLynch/Arcticphoto.com.
Finally, we would like to thank John Kimmel for giving us the opportunity to
writethisbookandforpatientlyacceptingthe6-monthdelay.Uptothenextbook.
ix