size: Determine the size of the next cohort

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

Description

This function determines the size of the next cohort.

Usage

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, ...)

Arguments

cohortSize	The rule, an object of class CohortSize
dose	the next dose
data	The data input, an object of class Data
...	additional arguments

Value

the size as integer value

Functions

• size,CohortSizeRange,ANY,Data-method: Determine the cohort size based on the range into which the next dose falls into

• size,CohortSizeDLT,ANY,Data-method: Determine the cohort size based on the number of DLTs so far

• size,CohortSizeMax,ANY,Data-method: Size based on maximum of multiple cohort size rules

• size,CohortSizeMin,ANY,Data-method: Size based on minimum of multiple cohort size rules

• size,CohortSizeConst,ANY,Data-method: Constant cohort size

• size,CohortSizeParts,ANY,DataParts-method: Cohort size based on the parts

Examples

# nolint start

# 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),
                           ref_dose=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)

# nolint end
# nolint start

# 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),
                           ref_dose=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)

# nolint end
# nolint start

# 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),
                           ref_dose=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)

# nolint end
# nolint start

# 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),
                           ref_dose=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)

# nolint end
# nolint start

# 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),
                           ref_dose=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)

# nolint end
# nolint start

# 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),
                           ref_dose=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)

# nolint end

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