EpiNow2 (version 1.3.2)

rstan_sampling_opts: Rstan Sampling Options

Description

Defines a list specifying the arguments passed to rstan::sampling. Custom settings can be supplied which override the defaults.

Usage

rstan_sampling_opts(
  cores = getOption("mc.cores", 1L),
  warmup = 250,
  samples = 2000,
  chains = 4,
  control = list(),
  save_warmup = FALSE,
  seed = as.integer(runif(1, 1, 1e+08)),
  future = FALSE,
  max_execution_time = Inf,
  ...
)

Arguments

cores

Number of cores to use when executing the chains in parallel, which defaults to 1 but it is recommended to set the mc.cores option to be as many processors as the hardware and RAM allow (up to the number of chains).

warmup

Numeric, defaults to 250. Number of warmup samples per chain.

samples

Numeric, default 2000. Overall number of posterior samples. When using multiple chains iterations per chain is samples / chains.

chains

Numeric, defaults to 4. Number of MCMC chains to use.

control

List, defaults to empty. control parameters to pass to underlying rstan function. By default adapt_delta = 0.98 and max_treedepth = 15 though these settings can be overwritten.

save_warmup

Logical, defaults to FALSE. Should warmup progress be saved.

seed

Numeric, defaults uniform random number between 1 and 1e8. Seed of sampling process.

future

Logical, defaults to FALSE. Should stan chains be run in parallel using future. This allows users to have chains fail gracefully (i.e when combined with max_execution_time). Should be combined with a call to future::plan

max_execution_time

Numeric, defaults to Inf (seconds). If set will kill off processing of each chain if not finished within the specified timeout. When more than 2 chains finish successfully estimates will still be returned. If less than 2 chains return within the allowed time then estimation will fail with an informative error.

...

Additional parameters to pass to rstan::sampling.

Value

A list of arguments to pass to rstan::sampling

Examples

# NOT RUN {
rstan_sampling_opts(samples = 2000)
# }