mcmc.control {clinDR}

Settings for restan execution in function fitEmaxB

Description

Set MCMC controls. Also control spread of initial parameter values.

Usage

mcmc.control(chains = 1, thin = 1, 
	warmup = 1000, iter = 3333* thin+warmup, 
	propInit = 0.50, seed = 12357, adapt_delta = 0.9)

Arguments

chains

Number of chains

thin

Number of discarded sampled parameter values. warmup and iter include thin, so for example, to output 1000 samples, iter must be 1000 times thin.

warmup

See rstan documentation for function sampling.

iter

See rstan documentation for function sampling.

propInit

Initial values for E0 and Emax are derived from the prior mean plus/minus propInit times the prior SD. propInit can be set to a small proportion if very diffuse prior distributions are specified.

seed

Seed passed to rstan.

adapt_delta

See rstan documentation for function sampling.

Note

Some defaults were changed with version>=2.0. For earlier versions, warmup = 500, iter = 5000* thin, and adapt_delta=0.8