Meta-Analysis with R PDF
Preview Meta-Analysis with R
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
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