Sample from Stan model — mcmc_sample • psborrow2

Method to sample from compiled Stan model and return a CmdStanMCMC object with draws.

Usage

mcmc_sample(x, ...)

# S4 method for ANY
mcmc_sample(x, ...)

# S4 method for Analysis
mcmc_sample(
  x,
  iter_warmup = 1000L,
  iter_sampling = 10000L,
  chains = 4L,
  verbose = FALSE,
  ...
)

Arguments

x: object to sample, such as Analysis (created with create_analysis_obj()) or Simulation.
...: additional arguments passed to the $sample() method of a cmdstanr Stan model. See https://mc-stan.org/cmdstanr/reference/model-method-sample.html
iter_warmup: The number of warm up iterations to run per chain. The default is 1000.
iter_sampling: The number of post-warm up iterations to run per chain. The default is 10000.
chains: The number of Markov chains to run. The default is 4.
verbose: logical. Whether to print sampler updates (TRUE) or not (FALSE)

Value

An object of class CmdStanMCMC

Examples

## Analysis objects
anls <- create_analysis_obj(
  data_matrix = example_matrix,
  covariates = add_covariates(
    covariates = c("cov1", "cov2"),
    priors = normal_prior(0, 1000)
  ),
  outcome = weib_ph_surv_dist(
    "time",
    "cnsr",
    shape_prior = normal_prior(0, 1000)
  ),
  borrowing = borrowing_details(
    "BDB",
    "ext",
    exponential_prior(.001),
    baseline_prior = normal_prior(0, 1000)
  ),
  treatment = treatment_details("trt", normal_prior(0, 1000))
)
#> Inputs look good.
#> Error: CmdStan path has not been set yet. See ?set_cmdstan_path.

mcmc_results <- mcmc_sample(anls)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'mcmc_sample': object 'anls' not found