Meta-Analysis with R

256 Pages·2015·3.89 MB·English

by  Guido Schwarzer

UseR!
Guido Schwarzer
James R. Carpenter
Gerta Rücker
Meta-
Analysis
with R
Use R!
Serieseditors
RobertGentleman
KurtHornik
GiovanniParmigiani
Moreinformationaboutthisseriesathttp://www.springer.com/series/6991
Guido Schwarzer • James R. Carpenter (cid:129)
Gerta RuRcker
Meta-Analysis with R
123
GuidoSchwarzer JamesR.Carpenter
InstituteforMedicalBiometry MRCClinicalTrialsUnit,London
andStatistics andLondonSchoolofHygiene
MedicalCenter–UniversityofFreiburg andTropicalMedicine
Freiburg,Germany London,UnitedKingdom
GertaRuRcker
InstituteforMedicalBiometryandStatistics
MedicalCenter–UniversityofFreiburg
Freiburg,Germany
ISSN2197-5736 ISSN2197-5744 (electronic)
UseR!
ISBN978-3-319-21415-3 ISBN978-3-319-21416-0 (eBook)
DOI10.1007/978-3-319-21416-0
LibraryofCongressControlNumber:2015949262
SpringerChamHeidelbergNewYorkDordrechtLondon
©SpringerInternationalPublishingSwitzerland2015
Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof
thematerialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,
broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation
storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology
nowknownorhereafterdeveloped.
Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication
doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant
protectivelawsandregulationsandthereforefreeforgeneraluse.
Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbook
arebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsor
theeditorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinorforany
errorsoromissionsthatmayhavebeenmade.
Printedonacid-freepaper
Springer International Publishing AG Switzerland is part of Springer Science+Business Media
(www.springer.com)
Preface
Meta-analysisplaysa keyrolein evidencesynthesisin manyresearchdisciplines,
not least the social sciences, medicine and economics. The aim of this book is to
equip those involved in such work (who are often not trained statisticians) to use
R for meta-analysis, and thus promote both the use of R and the latest statistical
methodsinthisarea.
TheattractionsofRinthiscontext(besidesitsfreeavailabilityfromhttp://www.
r-project.org/)areitsfastyetpowerfulandflexiblegraphicsanditswell-established
algorithmicbase.
ThebookassumesnopriorknowledgeofR,andtakesreadersthrougheverystep
of the way from installing R, loading data from other packages, performing and
interpretingtheanalyses.PartsIandIIcovertheessentials,whilePartIIIconsiders
moreadvancedtopics,whichremainthesubjectofactiveresearch.
Throughout,theideasareillustratedwithexamples,andallthecodesnecessary
torepeatthese examples(includingcreatingalltheplotsinthebook)areeitherin
thetextitselfortheweb-appendixhttp://meta-analysis-with-r.org/.Inselectingthe
codetoincludeinthemaintext,wehaveassumedreadersarerelativelynewtoR.
Moreexperienceduserscaneasilyskipoverfamiliarmaterial.
Freiburg,Germany GuidoSchwarzer
London,UK JamesR.Carpenter
Freiburg,Germany GertaRücker
December,2014
v

Acknowledgements
ThisbookwasfundedpartlybytheGermanResearchFoundation(DFG),Research
Unit 534, FOR Schw 821/2-2. Subsequently, Gerta Rücker was funded by the
GermanResearchFoundation(RU1747/1-1).JamesCarpenterisgratefulforfund-
ingfromtheUKMedicalResearchCouncil’sLondonHubforTrialsMethodology.
We aregratefulto themembersoftheRCore Teamwhoprovideandmaintain
thestatisticalpackageR.Wewouldalsoliketoacknowledgeourdebttotheauthors
of R packages for meta-analysis, which we use in this book. Particular thanks
go to Wolfgang Viechtbauer for the comprehensive R package metafor, Antonio
Gasparrini for the versatile R package mvmeta for multivariate meta-analysis,
and for advice on its use, and Philipp Doebler for the R package mada and his
contributiontothechapteronmeta-analysisofdiagnostictestaccuracystudies.
Special thanks are also due to Ulrike Krahn for her advice and encouragement
withthe chapteronnetworkmeta-analysis.We are alsogratefulto AnnaWiksten,
JanBeyersmann,KarinSchiefele,HarrietSommerandtwoanonymousrefereesfor
readingearlierversionsofthemanuscriptandmanyhelpfulanddetailedcomments.
Thesehavesubstantiallyimprovedthebook.Wearealsogratefultoourfamiliesfor
theirforbearanceoverthecourseoftheproject.
Despite thisencouragementandsupport,the textinevitablycontainserrorsand
shortcomings,forwhichwetakefullresponsibility.
Lastbutnotleast, wehavefoundcollaboratingonthisprojectbothinformative
andfun;ifreadersfeelthesameafterreadingthebook,wewillbeverysatisfied!
vii

Contents
PartI GettingStarted
1 AnIntroductiontoMeta-AnalysisinR ................................... 3
1.1 GettingStartedwithR ................................................. 4
1.1.1 QuittingR...................................................... 5
1.1.2 RasaCalculator............................................... 5
1.1.3 GettingHelp ................................................... 6
1.2 Loading,SavingandRestoringData.................................. 6
1.2.1 ImportingDatafromOtherPackages......................... 9
1.3 SelectVariablesfromanRDataset.................................... 10
1.4 RunningScripts......................................................... 12
1.5 InstallingandUsingLibrariesofAdditionalFunctions.............. 13
1.6 AFirstMeta-AnalysiswithR.......................................... 13
1.7 Summary................................................................ 16
References..................................................................... 16
PartII StandardMethods
2 FixedEffectandRandomEffectsMeta-Analysis ........................ 21
2.1 EffectMeasuresforContinuousOutcomes ........................... 22
2.1.1 MeanDifference............................................... 22
2.1.2 StandardisedMeanDifference................................ 25
2.2 FixedEffectModel..................................................... 28
2.3 RandomEffectsModel................................................. 34
2.3.1 EstimationofBetween-StudyVariance ...................... 36
2.3.2 Hartung–KnappAdjustment.................................. 37
2.3.3 PredictionIntervals............................................ 39
2.4 TestsandMeasuresofHeterogeneity ................................. 40
2.5 SubgroupAnalysis ..................................................... 41
ix