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Statistical Methods for Hospital Monitoring with R PDF

428 Pages·2013·3.18 MB·English
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Statistical Methods for Hospital Monitoring with R STATISTICSINPRACTICE SeriesAdvisors HumanandBiologicalSciences StephenSenn CRP-Sante´,Luxembourg EarthandEnvironmentalSciences MarianScott UniversityofGlasgow,UK Industry,CommerceandFinance WolfgangJank UniversityofMaryland,USA FoundingEditor VicBarnett NottinghamTrentUniversity,UK StatisticsinPracticeisanimportantinternationalseriesoftextswhichprovidedetailedcover- ageofstatisticalconcepts,methodsandworkedcasestudiesinspecificfieldsofinvestigation andstudy. Withsoundmotivationandmanyworkedpracticalexamples,thebooksshowindown-to- earthtermshowtoselectanduseanappropriaterangeofstatisticaltechniquesinaparticular practicalfieldwithineachtitle’sspecialtopicarea. Thebooksprovidestatisticalsupportforprofessionalsandresearchworkersacrossarange ofemploymentfieldsandresearchenvironments.Subjectareascoveredincludemedicineand pharmaceutics;industry,financeandcommerce;publicservices;theearthandenvironmental sciences,andsoon. Thebooksalsoprovidesupporttostudentsstudyingstatisticalcoursesappliedtotheabove areas. The demand for graduates to be equipped for the work environment has led to such coursesbecomingincreasinglyprevalentatuniversitiesandcolleges. Itisouraimtopresentjudiciouslychosenandwell-writtenworkbookstomeeteveryday practicalneeds.Feedbackofviewsfromreaderswillbemostvaluabletomonitorthesuccess ofthisaim. Acompletelistoftitlesinthisseriesappearsattheendofthevolume. Statistical Methods for Hospital Monitoring with R Anthony Morton PrincessAlexandraHospital Brisbane,Australia Kerrie Mengersen ScienceandEngineeringFaculty QueenslandUniversityofTechnology Brisbane,Australia Michael Whitby GreenslopesClinicalSchool UniversityofQueensland Brisbane,Australia Geoffrey Playford PrincessAlexandraHospital Brisbane,Australia Thiseditionfirstpublished2013 (cid:2)C 2013JohnWiley&Sons,Ltd Registeredoffice JohnWiley&SonsLtd,TheAtrium,SouthernGate,Chichester,WestSussex,PO198SQ,UnitedKingdom Fordetailsofourglobaleditorialoffices,forcustomerservicesandforinformationabouthowtoapplyfor permissiontoreusethecopyrightmaterialinthisbookpleaseseeourwebsiteatwww.wiley.com. Therightoftheauthortobeidentifiedastheauthorofthisworkhasbeenassertedinaccordancewiththe Copyright,DesignsandPatentsAct1988. Allrightsreserved.Nopartofthispublicationmaybereproduced,storedinaretrievalsystem,ortransmitted,in anyformorbyanymeans,electronic,mechanical,photocopying,recordingorotherwise,exceptaspermittedby theUKCopyright,DesignsandPatentsAct1988,withoutthepriorpermissionofthepublisher. Wileyalsopublishesitsbooksinavarietyofelectronicformats.Somecontentthatappearsinprintmaynotbe availableinelectronicbooks. Designationsusedbycompaniestodistinguishtheirproductsareoftenclaimedastrademarks.Allbrandnamesand productnamesusedinthisbookaretradenames,servicemarks,trademarksorregisteredtrademarksoftheir respectiveowners.Thepublisherisnotassociatedwithanyproductorvendormentionedinthisbook. LimitofLiability/DisclaimerofWarranty:Whilethepublisherandauthorhaveusedtheirbesteffortsinpreparing thisbook,theymakenorepresentationsorwarrantieswithrespecttotheaccuracyorcompletenessofthecontents ofthisbookandspecificallydisclaimanyimpliedwarrantiesofmerchantabilityorfitnessforaparticularpurpose. Itissoldontheunderstandingthatthepublisherisnotengagedinrenderingprofessionalservicesandneitherthe publishernortheauthorshallbeliablefordamagesarisingherefrom.Ifprofessionaladviceorotherexpert assistanceisrequired,theservicesofacompetentprofessionalshouldbesought. LibraryofCongressCataloging-in-PublicationData Morton,AnthonyPark,1933–author. StatisticalmethodsforhospitalmonitoringwithR/AnthonyMorton,KerrieMengersen,GeoffreyPlayford, MichaelWhitby. p.;cm. Includesbibliographicalreferencesandindex. ISBN978-1-118-59630-2(cloth) I.Mengersen,KerrieL.,author. II.Playford,Geoffrey,author. III.Whitby,Michael,1950–author. IV.Title. [DNLM:1.HospitalAdministration. 2.StatisticsasTopic. WX150.1] RA971 362.11068–dc23 2013008301 AcataloguerecordforthisbookisavailablefromtheBritishLibrary. ISBN:978-1-118-59630-2 Setin10/12ptTimesbyAptaraInc.,NewDelhi,India. 1 2013 Contents RLibraries x RFunctions xi Preface xvi Introduction 1 0.1 Overviewandrationaleforthisbook 1 0.1.1 Motivationforthebook 1 0.1.2 WhyR? 2 0.1.3 OtherreadingforR 2 0.2 Whatmethodsarecoveredinthebook? 3 0.3 Structureofthebook 4 0.4 UsingR 5 0.4.1 Enteringdata 6 0.4.2 Dates 8 0.4.3 Exportingdata 10 0.5 Furthernotes 11 0.6 Abriefintroductiontorprogschartsandfigures 11 0.6.1 Whatifthereisnodatecolumn? 18 0.7 Appendixmenus 20 0.7.1 IMenu() 20 0.7.2 CCMenu() 21 1 Introductiontoanalysisofbinaryandproportiondata 24 1.1 Singleproportion,samplesandpopulation 24 1.1.1 Calculatingtheconfidenceinterval 26 1.1.2 Comparisonwithanexpectedrate 27 1.2 Likelihoodratio(Bayesfactor)&supportedrange 29 1.3 Confidenceintervalsforaseriesofproportions 30 1.4 Differencebetweentwoproportions 33 1.4.1 Confidenceintervals 33 1.4.2 Hypothesistest 35 1.4.3 Thetwoproportionsfunction 37 vi CONTENTS 1.5 IntroducingaBayesianapproach 39 1.6 Whenthedataarenotjustoneortwoindependentsamples 39 1.6.1 Morethantwoindependentproportions 40 1.6.2 Example1,yearlydata 40 1.6.3 Example2,hospitaldata 43 1.6.4 Proptestandsmallsamples 47 1.7 Summarisingstratifiedproportiondata 48 1.8 Stratifiedproportiondata,differencesbetweenrates 50 1.8.1 Yearlydata 52 1.8.2 Hospitaldata 54 1.9 Mantel-Haenszel,homogeneityandtrendtests 54 1.9.1 Yearlydata 56 1.9.2 Datastratifiedbyhospital 59 1.10 Stratifiedratesandoverdispersion 63 2 Theanalysisofaggregatedbinarydata 67 2.1 Risk-adjustment 68 2.1.1 Usingstratification 68 2.1.2 Usinglogisticregression 70 2.2 Discriminationandcalibration 71 2.3 Using2005–06data 76 2.3.1 Displayingandanalysingdatafrommultipleinstitutions 77 2.3.2 Tabulations 78 2.3.3 Funnelplotandplotofmultipleconfidenceintervals 83 2.4 WhentheEsarenotfixed 99 2.5 ComplexSurgicalSiteInfections 102 2.5.1 Funnelplotanalysis 102 2.5.2 Shrinkageanalysis 104 2.6 ComplexSSIrisk-adjustmentdiscrimination 106 2.7 Appendix1–Furthertabulationmethods 106 2.8 Appendix2–SMRCIsandtests,furtherscripts.Hospitalexpectedvalues fromotherhospitalsingroup 109 3 Sequentialbinarydata 116 3.1 CUSUMandrelatedchartsforbinarydata 117 3.2 CumulativeObserved-Expected(O-E)chartandcombinedCUSUM andO-Echart 120 3.3 CumulativefunnelplotandcombinedCUSUMandfunnelplot 120 3.4 Example 121 3.5 Includingriskadjustment 124 3.6 CUSUMchart 125 3.7 Cumulativeobservedminusexpected(O-E)chart 125 3.8 Funnelplot 127 3.9 Discriminationandcalibrationofriskadjustment 128 3.10 ShewhartPchartandEWMAchart 132 3.11 NoteontheRun-sumchart 135 3.12 TheEWMAchart 135 3.13 Plottingtheexpectedvalues 138 CONTENTS vii 3.14 Usingasplineorgeneralisedadditivemodel(GAM)chart 139 3.15 Whentherearefewtimeperiods 141 3.16 Chartsforquarterlydataanddatawithoutafirstdatecolumn 143 3.17 Chartsforcompositemeasures 146 3.18 Additionaltabulations 146 3.19 Theissueofunder-reporting 151 3.20 NewCUSUMandEWMAcharts,low-ratedata 151 3.20.1 Therisk-adjustedBernoulliCUSUM 153 3.20.2 TheEWMA 156 3.20.3 Quarterlyrates 157 3.21 Intervalsbetweenuncommonbinaryadverseevents 159 3.22 Appendix,proposedEWMAforlowratedata 164 4 Introductiontoanalysisofcountandratedata 168 4.1 Introduction 168 4.2 Rateandcountdata 169 4.3 Singlecountorrate 169 4.3.1 Confidenceinterval 170 4.3.2 Significancetest 171 4.4 Confidencelimitsforcolumnsofcountsandrates 173 4.5 Twoindependentrates 175 4.5.1 Confidenceinterval 175 4.5.2 Hypothesistest 176 4.5.3 Bayesianapproach 177 4.6 Chi-squaredandtrendtestsforcountandratedata 177 4.7 Stratifiedcountandratedata 180 4.7.1 Obtainingasummaryrate 180 4.7.2 Stratifiedcountandratedata,twosetsofrates 181 4.7.3 Indirectstandardisation 182 4.7.4 Directstandardisation 184 4.8 Mantel-Haenszel,homogeneityandtrendtests 187 4.8.1 Fixedeffectsanalysis,stratificationbyyears 187 4.8.2 Randomeffectsanalysis,stratificationbyhospitals 190 4.9 Illustrationofdealingwithoverdispersedrates 193 4.10 Theimportanceofcountdatavariation 196 4.11 Complexsystems,networksandvariation 201 5 Tablesandchartsforaggregatedcountdata 203 5.1 Introduction,data,limitationsofaggregatedcountdataanalysis 203 5.2 ConfidenceintervalsforStaphylococcusaureusbacteraemiaSMRdata 206 5.3 FunnelplotsforStaphylococcusaureusbacteraemiaSMRdata 212 5.4 TabulationsandZ-scores 219 5.5 Moreonoverdispersion,falsediscovery,verysmallexpectedcounts 221 5.5.1 ProposalforBenjamini-Hochbergmodifiedfunnelplot 223 5.6 Bayesianshrinkageplot 227 5.6.1 UsingOpenBUGS 228 5.6.2 UsingempiricalBayesmethods 229 5.7 PerformingfurthertabulationsinR 231 viii CONTENTS 5.8 AdjustinghospitallevelsforMRSAbacteraemia 234 5.9 Bacteraemiariskadjustment 237 6 Sequentialcountandratedata 242 6.1 Groupingdata 243 6.2 Meansandvariances,predictability 243 6.3 Tabulations 244 6.4 Denominators 246 6.5 Shewhart,EWMAandGAMcontrolchartswithoutdenominators 247 6.5.1 Shewhart/EWMAcharts 257 6.6 Shewhart,EWMAandGAMcontrolchartswithdenominators 264 6.6.1 Overdisperseddata 273 6.7 Chartsforquarterlydataanddatawithoutafirstdatecolumn 280 6.8 Whentherearefewtimeperiods 282 6.9 Cross-tabulationinwideformat 286 6.10 UncommoncountdataAEs 291 6.11 Additionalscriptsfortabulationsandcharts 297 6.12 Intervalsbetweenuncommoncountdataevents 300 6.13 Noteoncalculationofnegativebinomialparametersforcontrolcharts whendenominatorsvary 303 6.13.1 Simpleweightedvariance 303 6.13.2 Linearapproximation(Bissell) 303 6.13.3 ComparisonofsimpleweightedvarianceandBissell’slinear approximation 304 7 MiscellaneousAEs 307 7.1 MROprevalence 308 7.2 Antibioticusage 315 7.3 Spuriousproportions,somebloodculturedata 316 7.4 RIDITcharts,ECGdata 321 7.5 Numericaldata–theatreutilisation 326 7.6 Lengthofstay(LOS)data 329 7.7 Changepoint 339 7.8 Assessingagreement 346 7.8.1 Numericaldataagreement 348 7.9 Makingdecisions(decisionanalysis) 350 7.10 Investigatingoutbreaks,furtheranalysisofstratifieddata 352 7.10.1 Reviewingstratifieddataanalysis 355 7.10.2 Outbreakinvestigationexample 361 8 Hospitalsafetyandadverseeventprevention 374 8.1 Introduction 374 8.2 Anoverviewofhospitalqualityimprovement,fivepillars 375 8.2.1 TheCustomer,thefirstpillar 375 8.2.2 ThePractitioner,thesecondpillar 375 8.2.3 TheSystem,thethirdandmainpillar 375 CONTENTS ix 8.3 Medicalerror 376 8.3.1 Backgroundofmedicalerror(Vincent,Taylor-Adams& Vincent) 376 8.4 Improvingthesystem 377 8.4.1 Evidence-basedsystems 377 8.4.2 Theroleofbundlesandchecklists 377 8.5 Error-proofingsystems 379 8.6 Disciplineandaccountability 379 8.7 Limitationsofimposingquality 380 8.8 Performanceandpredictablevariation 380 8.9 Thekeystoagoodsystem 381 8.10 Analysingandimplementingevidence-basedsystems 381 8.11 Theroleofpatient-carestaff 382 8.12 Theroleofcentralauthority 382 8.13 Changemanagement,thefourthpillar 383 8.14 Feedbackloops,thefifthpillar 383 8.15 ImplementationoftheQualityImprovementProcess 384 8.15.1 Implementation 384 8.15.2 Obtainingdata 386 8.15.3 SpecialissueswithQIstudies 386 8.16 Thehospitalasanetwork 389 References 391 Index 399 R Libraries arm gee PropCIs bmem geepack psy chron hglm qAnalyst Epi Kendall qcc epibasix lme4 rmeta epicalc MASS spc epiR meta splines epitools mgcv surveillance exactci MKmisc tseries

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