size | R Documentation |
This function determines the size of the next cohort.
size(cohortSize, dose, data, ...) ## S4 method for signature 'CohortSizeRange,ANY,Data' size(cohortSize, dose, data, ...) ## S4 method for signature 'CohortSizeDLT,ANY,Data' size(cohortSize, dose, data, ...) ## S4 method for signature 'CohortSizeMax,ANY,Data' size(cohortSize, dose, data, ...) ## S4 method for signature 'CohortSizeMin,ANY,Data' size(cohortSize, dose, data, ...) ## S4 method for signature 'CohortSizeConst,ANY,Data' size(cohortSize, dose, data, ...) ## S4 method for signature 'CohortSizeParts,ANY,DataParts' size(cohortSize, dose, data, ...)
cohortSize |
The rule, an object of class
|
dose |
the next dose |
data |
The data input, an object of class |
... |
additional arguments |
the size as integer value
size(cohortSize = CohortSizeRange, dose = ANY, data = Data)
: Determine the cohort size based on the range into which the
next dose falls into
size(cohortSize = CohortSizeDLT, dose = ANY, data = Data)
: Determine the cohort size based on the number of DLTs so
far
size(cohortSize = CohortSizeMax, dose = ANY, data = Data)
: Size based on maximum of multiple cohort size rules
size(cohortSize = CohortSizeMin, dose = ANY, data = Data)
: Size based on minimum of multiple cohort size rules
size(cohortSize = CohortSizeConst, dose = ANY, data = Data)
: Constant cohort size
size(cohortSize = CohortSizeParts, dose = ANY, data = DataParts)
: Cohort size based on the parts
# Create the data data <- Data(x=c(0.1, 0.5, 1.5, 3, 6, 10, 10, 10), y=c(0, 0, 0, 0, 0, 0, 1, 0), cohort=c(0, 1, 2, 3, 4, 5, 5, 5), doseGrid= c(0.1, 0.5, 1.5, 3, 6, seq(from=10, to=80, by=2))) # Initialize the CRM model used to model the data model <- LogisticLogNormal(mean=c(-0.85, 1), cov= matrix(c(1, -0.5, -0.5, 1), nrow=2), refDose=56) # Set-up some MCMC parameters and generate samples from the posterior options <- McmcOptions(burnin=100, step=2, samples=2000) set.seed(94) samples <- mcmc(data, model, options) # Define the rule for dose increments and calculate the maximum dose allowed myIncrements <- IncrementsRelative(intervals=c(0, 20), increments=c(1, 0.33)) nextMaxDose <- maxDose(myIncrements, data=data) # Define the rule which will be used to select the next best dose # based on the class 'NextBestNCRM' myNextBest <- NextBestNCRM(target=c(0.2, 0.35), overdose=c(0.35, 1), maxOverdoseProb=0.25) # Calculate the next best dose doseRecommendation <- nextBest(myNextBest, doselimit=nextMaxDose, samples=samples, model=model, data=data) # Rule for the cohort size: # - having cohort of size 1 for doses <10 # - and having cohort of size 3 for doses >=10 mySize <- CohortSizeRange(intervals=c(0, 10), cohortSize=c(1, 3)) # Determine the cohort size for the next cohort size(mySize, dose=doseRecommendation$value, data = data) # Create the data data <- Data(x=c(0.1, 0.5, 1.5, 3, 6, 10, 10, 10), y=c(0, 0, 0, 0, 0, 0, 1, 0), cohort=c(0, 1, 2, 3, 4, 5, 5, 5), doseGrid= c(0.1, 0.5, 1.5, 3, 6, seq(from=10, to=80, by=2))) # Initialize the CRM model used to model the data model <- LogisticLogNormal(mean=c(-0.85, 1), cov= matrix(c(1, -0.5, -0.5, 1), nrow=2), refDose=56) # Set-up some MCMC parameters and generate samples from the posterior options <- McmcOptions(burnin=100, step=2, samples=2000) set.seed(94) samples <- mcmc(data, model, options) # Define the rule for dose increments and calculate the maximum dose allowed myIncrements <- IncrementsRelative(intervals=c(0, 20), increments=c(1, 0.33)) nextMaxDose <- maxDose(myIncrements, data=data) # Define the rule which will be used to select the next best dose # based on the class 'NextBestNCRM' myNextBest <- NextBestNCRM(target=c(0.2, 0.35), overdose=c(0.35, 1), maxOverdoseProb=0.25) # Calculate the next best dose doseRecommendation <- nextBest(myNextBest, doselimit=nextMaxDose, samples=samples, model=model, data=data) # Rule for the cohort size: # - having cohort of size 1 if no DLTs were yet observed # - and having cohort of size 3 if at least 1 DLT was already observed mySize <- CohortSizeDLT(DLTintervals = c(0, 1), cohortSize = c(1, 3)) # Determine the cohort size for the next cohort size(mySize, dose=doseRecommendation$value, data = data) # Create the data data <- Data(x=c(0.1, 0.5, 1.5, 3, 6, 10, 10, 10), y=c(0, 0, 0, 0, 0, 0, 1, 0), cohort=c(0, 1, 2, 3, 4, 5, 5, 5), doseGrid= c(0.1, 0.5, 1.5, 3, 6, seq(from=10, to=80, by=2))) # Initialize the CRM model used to model the data model <- LogisticLogNormal(mean=c(-0.85, 1), cov= matrix(c(1, -0.5, -0.5, 1), nrow=2), refDose=56) # Set-up some MCMC parameters and generate samples from the posterior options <- McmcOptions(burnin=100, step=2, samples=2000) set.seed(94) samples <- mcmc(data, model, options) # Define the rule for dose increments and calculate the maximum dose allowed myIncrements <- IncrementsRelative(intervals=c(0, 20), increments=c(1, 0.33)) nextMaxDose <- maxDose(myIncrements, data=data) # Define the rule which will be used to select the next best dose # based on the class 'NextBestNCRM' myNextBest <- NextBestNCRM(target=c(0.2, 0.35), overdose=c(0.35, 1), maxOverdoseProb=0.25) # Calculate the next best dose doseRecommendation <- nextBest(myNextBest, doselimit=nextMaxDose, samples=samples, model=model, data=data) # Rule for having cohort of size 1 for doses <30 # and having cohort of size 3 for doses >=30 mySize1 <- CohortSizeRange(intervals = c(0, 10), cohortSize = c(1, 3)) # Rule for having cohort of size 1 until no DLT were observed # and having cohort of size 3 as soon as 1 DLT is observed mySize2 <- CohortSizeDLT(DLTintervals=c(0, 1), cohortSize=c(1, 3)) # Combining the two rules for cohort size by taking the maximum of the sample sizes # of the single rules mySize <- maxSize(mySize1, mySize2) # Determine the cohort size for the next cohort size(mySize, dose=doseRecommendation$value, data = data) # Create the data data <- Data(x=c(0.1, 0.5, 1.5, 3, 6, 10, 10, 10), y=c(0, 0, 0, 0, 0, 0, 1, 0), cohort=c(0, 1, 2, 3, 4, 5, 5, 5), doseGrid= c(0.1, 0.5, 1.5, 3, 6, seq(from=10, to=80, by=2))) # Initialize the CRM model used to model the data model <- LogisticLogNormal(mean=c(-0.85, 1), cov= matrix(c(1, -0.5, -0.5, 1), nrow=2), refDose=56) # Set-up some MCMC parameters and generate samples from the posterior options <- McmcOptions(burnin=100, step=2, samples=2000) set.seed(94) samples <- mcmc(data, model, options) # Define the rule for dose increments and calculate the maximum dose allowed myIncrements <- IncrementsRelative(intervals=c(0, 20), increments=c(1, 0.33)) nextMaxDose <- maxDose(myIncrements, data=data) # Define the rule which will be used to select the next best dose # based on the class 'NextBestNCRM' myNextBest <- NextBestNCRM(target=c(0.2, 0.35), overdose=c(0.35, 1), maxOverdoseProb=0.25) # Calculate the next best dose doseRecommendation <- nextBest(myNextBest, doselimit=nextMaxDose, samples=samples, model=model, data=data) # Rule for having cohort of size 1 for doses <30 # and having cohort of size 3 for doses >=30 mySize1 <- CohortSizeRange(intervals = c(0, 30), cohortSize = c(1, 3)) # Rule for having cohort of size 1 until no DLT were observed # and having cohort of size 3 as soon as 1 DLT is observed mySize2 <- CohortSizeDLT(DLTintervals=c(0, 1), cohortSize=c(1, 3)) # Combining the two rules for cohort size by taking the minimum of the sample sizes # of the single rules mySize <- minSize(mySize1, mySize2) # Determine the cohort size for the next cohort size(mySize, dose=doseRecommendation$value, data = data) # Create the data data <- Data(x=c(0.1, 0.5, 1.5, 3, 6, 10, 10, 10), y=c(0, 0, 0, 0, 0, 0, 1, 0), cohort=c(0, 1, 2, 3, 4, 5, 5, 5), doseGrid= c(0.1, 0.5, 1.5, 3, 6, seq(from=10, to=80, by=2))) # Initialize the CRM model used to model the data model <- LogisticLogNormal(mean=c(-0.85, 1), cov= matrix(c(1, -0.5, -0.5, 1), nrow=2), refDose=56) # Set-up some MCMC parameters and generate samples from the posterior options <- McmcOptions(burnin=100, step=2, samples=2000) set.seed(94) samples <- mcmc(data, model, options) # Define the rule for dose increments and calculate the maximum dose allowed myIncrements <- IncrementsRelative(intervals=c(0, 20), increments=c(1, 0.33)) nextMaxDose <- maxDose(myIncrements, data=data) # Define the rule which will be used to select the next best dose # based on the class 'NextBestNCRM' myNextBest <- NextBestNCRM(target=c(0.2, 0.35), overdose=c(0.35, 1), maxOverdoseProb=0.25) # Calculate the next best dose doseRecommendation <- nextBest(myNextBest, doselimit=nextMaxDose, samples=samples, model=model, data=data) # Rule for having cohorts with constant cohort size of 3 mySize <- CohortSizeConst(size=3) # Determine the cohort size for the next cohort size(mySize, dose=doseRecommendation$value, data = data) # create an object of class 'DataParts' data <- DataParts(x=c(0.1,0.5,1.5), y=c(0,0,0), doseGrid=c(0.1,0.5,1.5,3,6, seq(from=10,to=80,by=2)), part=c(1L,1L,1L), nextPart=1L, part1Ladder=c(0.1,0.5,1.5,3,6,10)) # Initialize the CRM model used to model the data model <- LogisticLogNormal(mean=c(-0.85, 1), cov= matrix(c(1, -0.5, -0.5, 1), nrow=2), refDose=56) # Set-up some MCMC parameters and generate samples from the posterior options <- McmcOptions(burnin=100, step=2, samples=2000) set.seed(94) samples <- mcmc(data, model, options) myIncrements <- IncrementsRelativeParts(dltStart=0, cleanStart=1) nextMaxDose <- maxDose(myIncrements, data=data) # Define the rule which will be used to select the next best dose # based on the class 'NextBestNCRM' myNextBest <- NextBestNCRM(target=c(0.2, 0.35), overdose=c(0.35, 1), maxOverdoseProb=0.25) # Calculate the next best dose doseRecommendation <- nextBest(myNextBest, doselimit=nextMaxDose, samples=samples, model=model, data=data) # Rule for the cohort size: mySize <- CohortSizeParts(sizes=c(1,3)) # Determine the cohort size for the next cohort size(mySize, dose=doseRecommendation$value, data = data)
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