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Simulate PP values and true trial outcomes for PP-threshold calibration

run_calibration_grid.Rd

For a single fixed data-generating scenario, simulates n_sims trials, computes the predictive probability (PP) at the futility look, and records what actually happens to each trial if it is allowed to continue through the remaining fixed decision points in future_boundaries. Because the PP value does not depend on the futility threshold \(\kappa\), the output can be summarised over a whole grid of thresholds afterwards via summarize_grid_by_kappa without re-simulating.

Usage

run_calibration_grid(
  n_c,
  n_t,
  control_model,
  effect_model,
  recruitment_model,
  data_generating_model,
  futility_IF,
  total_events,
  future_boundaries,
  analysis_model,
  update_priors_sims = 1000,
  PP_sims = 2000,
  n_sims = 1000,
  n_cores = 1,
  seed = NULL
)

Arguments

n_c, n_t

Planned number of patients in the control / treatment group.

control_model, effect_model

Prior specification used for the interim posterior update (see update_priors). control_model$parameter_mode must be "Distribution".

recruitment_model

Recruitment specification (see add_recruitment_time): method, period, power, rate, duration.

data_generating_model

A named list giving the true scenario used to simulate data: lambda_c, delay_time, post_delay_HR, and optionally gamma_c (Weibull control arm if supplied, exponential otherwise).

futility_IF

Information fraction of the PP futility look.

total_events

Maximum planned number of events.

future_boundaries

List of future fixed decision points, each a list with events and crit (see PP_func).

analysis_model

Analysis specification (see survival_test).

update_priors_sims

Number of posterior samples per interim dataset.

PP_sims

Number of posterior-predictive simulations per interim dataset.

n_sims

Number of simulated trials.

n_cores

Number of cores (uses parallel::mclapply when > 1).

seed

Optional integer seed; replicate i uses seed * 10000 + i.

Value

A list with elements

raw

A data frame with one row per simulated trial and columns PP_val, t_interim, sample_size_interim, continuation_success, continuation_stop_time, continuation_sample_size, converged, P_Z1, P_Z2, P_Z3.

settings

All arguments, plus the package, R, rjags and JAGS versions, the git commit of the working directory, the hostname and a timestamp.

See also

summarize_grid_by_kappa, select_kappa_star