2contrastlmcontrastlmGeneralContrastsofRegressionCoef2cientsDescriptionThisfunctioncomputesoneormorecontrastsoftheestimatedregressioncoef2cientsina2tfromoneofthefunctionsinDesignalongwithstandarderror ID: 885303
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1 Package`contrast'March19,2020TitleAColle
Package`contrast'March19,2020TitleACollectionofContrastMethodsVersion0.22DescriptionOnedegreeoffreedomcontrastsfor lm , glm , gls ,and geese objects.LicenseGPL-2URLhttps://github.com/topepo/contrastEncodingUTF-8LazyDatatrueDependsR�(=2.10)Importsnlme,sandwich,rmsSuggestsknitr,kableExtra,dplyr,ggplot2,tidyr,rmarkdown,testthat,covr,geepackRoxygenNote7.0.2.9000VignetteBuilderknitrNeedsCompilationnoAuthorAlanO Callaghan[aut,cre],MaxKuhn[aut],SteveWeston[aut],JedWing[aut],JamesForester[aut],ThornThaler[aut]MaintainerAlanO Callaghan lan;&#x.oca;&#xllag;&#xhan@;&#xoutl;&#xook.;om0;RepositoryCRANDate/Publication2020-03-1914:10:02UTCRtopicsdocumented:contrast.lm.........................................2print.contrast........................................4two_factor_crossed.....................................5two_factor_incompl.....................................5Index71 2contrast.lm contrast.lmGeneralContrastsofRegressionCoefcients DescriptionThisfunctioncomputesoneo
2 rmorecontrastsoftheestimatedregressionco
rmorecontrastsoftheestimatedregressioncoefcientsinatfromoneofthefunctionsinDesign,alongwithstandarderrors,condencelimits,torZstatistics,P-values.Usage##S3methodforclass'lm'contrast(fit,...)##S3methodforclass'gls'contrast(fit,...)##S3methodforclass'lme'contrast(fit,...)##S3methodforclass'geese'contrast(fit,...)contrast_calc(fit,a,b,cnames=NULL,type=c("individual","average"),weights="equal",conf.int=0.95,fcType="simple",fcFunc=I,covType=NULL,...,env=parent.frame(2))ArgumentsfitAtofclasslm,glm,etc....Forcontrast(),thesepassargumentstocontrast_calc().Forcontrast_calc(),theyarenotused.a,bListscontainingconditionsforallpredictorsinthemodelthatwillbecontrastedtoformthehypothesisH0:a=b.Thegendatafunctionwillgeneratetheneces-sarycombinationsanddefaultvaluesforunspeciedpredictors.Seeexamplesbelow. contrast.lm3cnamesAvectorofcharacterstringsnamingthecontrastswhentype="individual".Usuallycnamesisnotnecessaryasthefunctiontriestonamethecontrastsbyexaminingwhichpredictorsarevaryingconsistentlyinthetwolists.cnamesw
3 illbeneededwhenyoucontrast"non-comparabl
illbeneededwhenyoucontrast"non-comparable"settings,e.g.,youcomparelist(treat="drug",age=c(20,30))withlist(treat="placebo",age=c(40,50).typeAcharacterstring.Settype="average"toaveragetheindividualcontrasts(e.g.,toobtaina"TypeII"or"TypeIII"contrast).weightsAnumericvector,usedwhentype="average",toobtainweightedcontrasts.conf.intThecondencelevelforcondenceintervalsforthecontrasts.fcTypeAcharacterstring:"simple","log"or"signed".fcFuncAfunctiontotransformthenumeratoranddenominatoroffoldchanges.covTypeAstringmatchingthemethodforestimatingthecovariancematrix.Thedefaultvalueproducesthetypicalestimate.Seesandwich::vcovHC()foroptions.envAnenvironmentinwhichevaluatet.DetailsThesefunctionsmirrorrms::contrast.rms()buthavefeweroptions.Therearesomebetween-packageinconsistenciesregardingdegreesoffreedominsomemodels.Seethepackagevignetteformoredetails.Foldchangesarecalculatedforeachhypothesis.WhenfcType="simple",theratiooftheagrouppredictionsoverthebgrouppredictionsareused.WhenfcType="signed",theratioisusedifitisgreaterthan1
4 ;otherwisethenegativeinverse(e.g.,-1/rat
;otherwisethenegativeinverse(e.g.,-1/ratio)isreturned.Valuealistofclasscontrast.DesigncontainingtheelementsContrast,SE,Z,var,df.residualLower,Upper,Pvalue,X,cnames,andfoldChange,whichdenotethecontrastestimates,stan-darderrors,Zort-statistics,variancematrix,residualdegreesoffreedom(thisisNULLifthemodelwasnotols),loweranduppercondencelimits,2-sidedP-value,designmatrix,andcontrastnames(orNULL).SeeAlsorms::contrast.rms(),sandwich::vcovHC()Exampleslibrary(nlme)Orthodont2OrthodontOrthodont2$newAgeOrthodont$age-11fm1Orth.lme2lme(distance~Sex*newAge,data=Orthodont2,random=~newAge|Subject)summary(fm1Orth.lme2) 4print.contrastcontrast(fm1Orth.lme2,a=list(Sex=levels(Orthodont2$Sex),newAge=8-11),b=list(Sex=levels(Orthodont2$Sex),newAge=10-11))#------------------------------------------------------------------------------anova_modellm(expression~diet*group,data=two_factor_crossed)anova(anova_model)library(ggplot2)theme_set(theme_bw()+theme(legend.position="top"))ggplot(two_factor_crossed)+aes(x=diet,y=expression,col=group,shape
5 =group)+geom_point()+geom_smooth(aes(gro
=group)+geom_point()+geom_smooth(aes(group=group),method=lm,se=FALSE)int_modellm(expression~diet*group,data=two_factor_crossed)main_effectslm(expression~diet+group,data=two_factor_crossed)#Interactioneffectisprobablyreal:anova(main_effects,int_model)#Testtreatmentinlowfatdiet:veh_grouplist(diet="lowfat",group="vehicle")trt_grouplist(diet="lowfat",group="treatment")contrast(int_model,veh_group,trt_group)#------------------------------------------------------------------------------car_modlm(mpg~am+wt,data=mtcars)print(summary(car_mod),digits=5)mean_wtmean(mtcars$wt)manual_translist(am=0,wt=mean_wt)auto_translist(am=1,wt=mean_wt)print(contrast(car_mod,manual_trans,auto_trans),digits=5) print.contrastPrintaContrastObject DescriptionPrintaContrastObjectUsage##S3methodforclass'contrast'print(x,X=FALSE,fun=function(u)u,...) two_factor_crossed5ArgumentsxResultofcontrast().XAlogical:setTRUEtoprintdesignmatrixusedincomputingthecontrasts(ortheaveragecontrast).funAfunctiontotransformthecontrast,SE,andloweranduppercondencelimi
6 tsbeforeprinting.Forexample,specifyfun=e
tsbeforeprinting.Forexample,specifyfun=exptoanti-logthemforlogisticmodels....Notused. two_factor_crossedCompleteTwo-FactorExperiment DescriptionCompleteTwo-FactorExperimentDetailsAgeneexpressionexperimentwasruntoassesstheeffectofacompoundundertwodifferentdiets:highfatandlowfat.Themaincomparisonsofinterestarethedifferencebetweenthetreatedanduntreatedgroupswithinadiet.Theinteractioneffectwasasecondaryhypothesis.Forillustration,weonlyincludetheexpressionvalueofoneofthegenes.Thestudydesignwasafulltwo-wayfactorialwithn=24samples.Valuetwo_factor_crossedAdataframeExamplestwo_factor_crossed two_factor_incomplIncompleteTwo-FactorExperimentwithRepeatedMeasurments DescriptionIncompleteTwo-FactorExperimentwithRepeatedMeasurments 6two_factor_incomplDetailsInageneexpressionexperiment,stemcellsweredifferentiatedusingasetoffactors(suchasmediatypes,cellspreadsetc.).Thesefactorswerecollapsedintoasinglecellenvironmentcongurationsvariable.Thecelllineswereassaysoverthreedays.Twoofthecongurationswereonlyrunontherstdayandtheother
7 twowereassaysatbaseline.Togetthematerial
twowereassaysatbaseline.Togetthematerials,threedonorsprovidedmaterials.Thesedonorsprovided(almost)equalrepli-cationacrossthetwoexperimentalfactors(dayandconguration).Oneofthegoalsofthisexperimentwastoassesspre-specieddifferencesinthecongurationateachtimepoint.Forexample,thedifferencesbetweencongurationsAandBatdayoneisofinterest.Also,thedifferencesbetweencongurationsCandDateachtimepointswereimportant.Sincetherearemissingcellsinthedesign,itisnotacompletetwo-wayfactorial.Onewaytoanalyzethisexperimentistofurthercollapsethetimeandcongurationdataintoasinglevariableandthenspecifyeachcomparisonusingthisfactor.Valuetwo_factor_incomplAdataframeExamplestwo_factor_incompl IndexTopicdatasetstwo_factor_crossed,5two_factor_incompl,5Topicmodelscontrast.lm,2Topicregressioncontrast.lm,2contrast.geese(contrast.lm),2contrast.gls(contrast.lm),2contrast.lm,2contrast.lme(contrast.lm),2contrast_calc(contrast.lm),2print.contrast,4rms::contrast.rms(),3sandwich::vcovHC(),3two_factor_crossed,5two_factor_incompl