plotDualResponses: Plot of the DLE and efficacy curve side by side given a DLE...

In crmPack: Object-Oriented Implementation of CRM Designs

Plot of the DLE and efficacy curve side by side given a DLE pseudo model, a DLE sample, an efficacy pseudo model and a given efficacy sample

Description

Plot of the DLE and efficacy curve side by side given a DLE pseudo model, a DLE sample, an efficacy pseudo model and a given efficacy sample

Plot of the dose-DLE and dose-efficacy curve side by side given a DLE pseudo model and a given pseudo efficacy model without DLE and efficacy samples

Usage

plotDualResponses(DLEmodel, DLEsamples, Effmodel, Effsamples, data, ...)

## S4 method for signature 'ModelTox,Samples,ModelEff,Samples'
plotDualResponses(
  DLEmodel,
  DLEsamples,
  Effmodel,
  Effsamples,
  data,
  extrapolate = TRUE,
  showLegend = FALSE,
  ...
)

## S4 method for signature 'ModelTox,missing,ModelEff,missing'
plotDualResponses(DLEmodel, DLEsamples, Effmodel, Effsamples, data, ...)

Arguments

DLEmodel	the pseudo DLE model of ModelTox class object
DLEsamples	the DLE samples of Samples class object
Effmodel	the pseudo efficacy model of ModelEff class object
Effsamples	the Efficacy samples of Samples class object
data	the data input of DataDual class object
...	additional arguments for the parent method plot,Samples,Model-method
extrapolate	should the biomarker fit be extrapolated to the whole dose grid? (default)
showLegend	should the legend be shown? (not default)

Value

This returns the ggplot object with the dose-toxicity and dose-efficacy model fits

Functions

• plotDualResponses( DLEmodel = ModelTox, DLEsamples = Samples, Effmodel = ModelEff, Effsamples = Samples ): function todo

• plotDualResponses( DLEmodel = ModelTox, DLEsamples = missing, Effmodel = ModelEff, Effsamples = missing ): Plot the DLE and efficacy curve side by side given a DLE model and an efficacy model without any samples

Examples

## we need a data object with doses >= 1:
data <-DataDual(x=c(25,50,25,50,75,300,250,150),
                y=c(0,0,0,0,0,1,1,0),
                w=c(0.31,0.42,0.59,0.45,0.6,0.7,0.6,0.52),
                doseGrid=seq(25,300,25),
                placebo=FALSE)
##plot the dose-DLE and dose-efficacy curves in two plots with DLE and efficacy samples
##define the DLE model which must be of 'ModelTox' class 
##(e.g 'LogisticIndepBeta' class model)
DLEmodel<-LogisticIndepBeta(binDLE=c(1.05,1.8),DLEweights=c(3,3),DLEdose=c(25,300),data=data)
## define the efficacy model which must be of 'ModelEff' class
## (e.g 'Effloglog' class)
Effmodel<-Effloglog(Eff=c(1.223,2.513),Effdose=c(25,300),nu=c(a=1,b=0.025),data=data,c=0)
##define the DLE sample of 'Samples' class
##set up the same data set in class 'Data' for MCMC sampling for DLE
data1 <- Data(x=data@x,y=data@y,doseGrid=data@doseGrid)
##Specify the options for MCMC
options <- McmcOptions(burnin=100,step=2,samples=1000)


DLEsamples <- mcmc(data=data1,model=DLEmodel,options=options)
##define the efficacy sample of 'Samples' class
Effsamples <- mcmc(data=data,model=Effmodel,options=options)
##plot the dose-DLE and dose-efficacy curves with two plot side by side.
##For each curve the 95% credibility interval of the two samples are alos given
plotDualResponses(DLEmodel=DLEmodel,DLEsamples=DLEsamples,
         Effmodel=Effmodel,Effsamples=Effsamples,
         data=data)
## we need a data object with doses >= 1:
data <-DataDual(x=c(25,50,25,50,75,300,250,150),
                y=c(0,0,0,0,0,1,1,0),
                w=c(0.31,0.42,0.59,0.45,0.6,0.7,0.6,0.52),
                doseGrid=seq(25,300,25),
                placebo=FALSE)
##plot the dose-DLE and dose-efficacy curves in two plots without DLE and efficacy samples
##define the DLE model which must be of 'ModelTox' class 
##(e.g 'LogisticIndepBeta' class model)
DLEmodel<-LogisticIndepBeta(binDLE=c(1.05,1.8),DLEweights=c(3,3),DLEdose=c(25,300),data=data)
## define the efficacy model which must be of 'ModelEff' class
## (e.g 'Effloglog' class)
Effmodel<-Effloglog(Eff=c(1.223,2.513),Effdose=c(25,300),nu=c(a=1,b=0.025),data=data,c=0)
##plot the dose-DLE and dose-efficacy curves with two plot side by side.
plotDualResponses(DLEmodel=DLEmodel,
                  Effmodel=Effmodel,
                  data=data)

crmPack documentation built on Sept. 3, 2022, 1:05 a.m.