plot-DualSimulationsSummary-missing-method: Plot summaries of the dual-endpoint design simulations

In 0liver0815/onc-crmpack-test: Object-Oriented Implementation of CRM Designs

Description

This plot method can be applied to DualSimulationsSummary objects in order to summarize them graphically. Possible type of plots at the moment are those listed in plot,SimulationsSummary,missing-method plus:

meanBiomarkerFit

Plot showing the average fitted dose-biomarker curve across the trials, together with 95% credible intervals, and comparison with the assumed truth (as specified by the trueBiomarker argument to summary,DualSimulations-method)

You can specify any subset of these in the type argument.

Usage

## S4 method for signature 'DualSimulationsSummary,missing'
plot(
  x,
  y,
  type = c("nObs", "doseSelected", "propDLTs", "nAboveTarget", "meanFit",
    "meanBiomarkerFit"),
  ...
)

Arguments

x	the DualSimulationsSummary object we want to plot from
y	missing
type	the types of plots you want to obtain.
...	not used

Value

A single ggplot object if a single plot is asked for, otherwise a gridExtra{gTree} object.

Examples

# Define the dose-grid
emptydata <- DataDual(doseGrid = c(1, 3, 5, 10, 15, 20, 25, 40, 50, 80, 100))

# Initialize the CRM model 
model <- DualEndpointRW(mu = c(0, 1),
                        Sigma = matrix(c(1, 0, 0, 1), nrow=2),
                        sigma2betaW = 0.01,
                        sigma2W = c(a=0.1, b=0.1),
                        rho = c(a=1, b=1),
                        smooth="RW1")

# Choose the rule for selecting the next dose 
myNextBest <- NextBestDualEndpoint(target=c(0.9, 1),
                                   overdose=c(0.35, 1),
                                   maxOverdoseProb=0.25)

# Choose the rule for the cohort-size 
mySize1 <- CohortSizeRange(intervals=c(0, 30),
                           cohortSize=c(1, 3))
mySize2 <- CohortSizeDLT(DLTintervals=c(0, 1),
                         cohortSize=c(1, 3))
mySize <- maxSize(mySize1, mySize2)

# Choose the rule for stopping
myStopping4 <- StoppingTargetBiomarker(target=c(0.9, 1),
                                       prob=0.5)
# only 10 patients here for illustration!
myStopping <- myStopping4 | StoppingMinPatients(10)

# Choose the rule for dose increments
myIncrements <- IncrementsRelative(intervals=c(0, 20),
                                   increments=c(1, 0.33))

# Initialize the design
design <- DualDesign(model = model,
                     data = emptydata,
                     nextBest = myNextBest,
                     stopping = myStopping,
                     increments = myIncrements,
                     cohortSize = CohortSizeConst(3),
                     startingDose = 3)
  
# define scenarios for the TRUE toxicity and efficacy profiles
betaMod <- function (dose, e0, eMax, delta1, delta2, scal)
{
  maxDens <- (delta1^delta1) * (delta2^delta2)/((delta1 + delta2)^(delta1 + delta2))
  dose <- dose/scal
  e0 + eMax/maxDens * (dose^delta1) * (1 - dose)^delta2
}

trueBiomarker <- function(dose)
{
  betaMod(dose, e0=0.2, eMax=0.6, delta1=5, delta2=5 * 0.5 / 0.5, scal=100)
}

trueTox <- function(dose)
{
  pnorm((dose-60)/10)
}

# Draw the TRUE profiles
par(mfrow=c(1, 2))
curve(trueTox(x), from=0, to=80)
curve(trueBiomarker(x), from=0, to=80)

# Run the simulation on the desired design
# We only generate 1 trial outcome here for illustration, for the actual study
##For illustration purpose we will use 5 burn-ins to generate 20 samples
# this should be increased of course
mySims <- simulate(design,
                   trueTox=trueTox,
                   trueBiomarker=trueBiomarker,
                   sigma2W=0.01,
                   rho=0,
                   nsim=1,
                   parallel=FALSE,
                   seed=3,
                   startingDose=6,
                   mcmcOptions =
                     McmcOptions(burnin=5,
                                 step=1,
                                 samples=20))

# Plot the summary of the Simulations
plot(summary(mySims,
             trueTox = trueTox,
             trueBiomarker = trueBiomarker))



  

0liver0815/onc-crmpack-test documentation built on Feb. 19, 2022, 12:25 a.m.