mcmc.control

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

Bayesian and ML Emax model fitting, graphics and simulation for clinical dose
response. The summary data from the dose response meta-analyses in
Thomas, Sweeney, and Somayaji (2014) <doi:10.1080/19466315.2014.924876> and
Thomas and Roy (2016) <doi:10.1080/19466315.2016.1256229>
Wu, Banerjee, Jin, Menon, Martin, and Heatherington(2017) <doi:10.1177/0962280216684528>
are included
in the package. The prior distributions for the Bayesian analyses default to
the posterior predictive distributions derived from these references.

Neal Thomas

clinDR

Simulation and Analysis Tools for Clinical Dose Response
Modeling

Jing Wu

Mike K. Smith

mcmc.control function

<dl> <dt>chains</dt>
<dd>Number of chains</dd> <dt>thin</dt>
<dd>Number of discarded sampled parameter values. <code>warmup</code> and <code>iter</code> include
<code>thin</code>, so for example, to output <code>1000</code> samples, <code>iter</code> must be 
<code>1000</code> times <code>thin</code>.</dd> <dt>warmup</dt>
<dd>See <code>rstan</code> documentation for function <code>sampling</code>.</dd> <dt>iter</dt>
<dd>See <code>rstan</code> documentation for function <code>sampling</code>.</dd> <dt>propInit</dt>
<dd>Initial values for <code>E0</code> and <code>Emax</code> are derived from the prior mean plus/minus
<code>propInit</code> times the prior SD. <code>propInit</code> can be set to a small proportion if
very diffuse prior distributions are specified.</dd> <dt>seed</dt>
<dd>Seed passed to <code>rstan</code>.</dd> <dt>adapt_delta</dt>
<dd>See <code>rstan</code> documentation for function <code>sampling</code>.</dd></dl>

Arguments

Settings for restan execution in function fitEmaxB — mcmc.control

<dl>

 <dt>chains</dt>
<dd>Number of chains</dd>

 <dt>thin</dt>
<dd>Number of discarded sampled parameter values. <code>warmup</code> and <code>iter</code> include
<code>thin</code>, so for example, to output <code>1000</code> samples, <code>iter</code> must be 
<code>1000</code> times <code>thin</code>.</dd>

 <dt>warmup</dt>
<dd>See <code>rstan</code> documentation for function <code>sampling</code>.</dd>

 <dt>iter</dt>
<dd>See <code>rstan</code> documentation for function <code>sampling</code>.</dd>

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

 <dt>seed</dt>
<dd>Seed passed to <code>rstan</code>.</dd>

 <dt>adapt_delta</dt>
<dd>See <code>rstan</code> documentation for function <code>sampling</code>.</dd>

</dl>

mcmc.control: Settings for `restan` execution in function `fitEmaxB`

Description

Usage

Arguments