examples/Rules-method-stopTrial-StoppingMissingDose.R

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

# Example of usage for `StoppingMissingDose` StopTrial class.

# Create the data.
my_data <- Data(
  x = c(0.01, 0.1, 0.5, 3, 6, 10, 10, 10),
  y = c(0, 1, 1, 0, 0, 0, 0, 1),
  cohort = c(1, 1, 2, 3, 4, 5, 5, 5),
  ID = 1:8,
  doseGrid = c(
    0.01, 0.1, 0.5, 1.5, 3, 6,
    seq(from = 10, to = 80, by = 2)
  ),
  placebo = TRUE
)

# Initialize the CRM model used to model the data.
my_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.
my_options <- McmcOptions(
  burnin = 100,
  step = 2,
  samples = 2000
)

my_samples <- mcmc(my_data, my_model, my_options)

# Define the rule for dose increments and calculate the maximum dose allowed.
my_increments <- IncrementsRelative(
  intervals = c(0, 20),
  increments = c(1, 0.33)
)

next_max_dose <- maxDose(my_increments,
  data = my_data
)

# Define the rule which will be used to select the next best dose based
# on the class 'NextBestNCRM'.
my_next_best <- NextBestNCRM(
  target = c(0.1, 0.25),
  overdose = c(0.2, 1),
  max_overdose_prob = 0.25
)

# Calculate the next best dose.
dose_recommendation <- nextBest(
  my_next_best,
  doselimit = next_max_dose,
  samples = my_samples, model = my_model, data = my_data
)

# Define the stopping rule such that the study would be stopped if there is
# no safe active dose returned from dose_recommendation.
my_stopping <- StoppingMissingDose()
my_stopping <- StoppingAny(
  stop_list = c(
    StoppingMinPatients(nPatients = 16),
    StoppingMissingDose()
  )
)

# Evaluate if to stop the trial.
stopTrial(
  stopping = my_stopping,
  dose = dose_recommendation$value,
  data = my_data,
  model = my_model
)