examples/Rules-method-size-CohortSizeParts.R

In Roche/crmPack: Object-Oriented Implementation of CRM Designs

# 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(
  dlt_start = 0,
  clean_start = 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),
  max_overdose_prob = 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(cohort_sizes = c(1, 3))

# Determine the cohort size for the next cohort
size(mySize, dose = doseRecommendation$value, data = data)

# nolint end