vtStan

Call STAN to draw posterior samples of the joint distribution of
immunogenicity rate and toxicity risk for parametric and parametric+ model

Phase I clinical trials are the first step in drug development to test
a new drug or drug combination on humans. Typical designs of Phase I
trials use toxicity as the primary endpoint and aim to find the maximum
tolerable dosage. However, these designs are poorly applicable for the
development of cancer therapeutic vaccines because the expected safety
concerns for these vaccines are not as much as cytotoxic agents. The
primary objectives of a cancer therapeutic vaccine phase I trial thus
often include determining whether the vaccine shows biologic activity
and the minimum dose necessary to achieve a full immune or even clinical
response. This package implements a Bayesian Phase I cancer vaccine
trial design that allows simultaneous evaluation of safety and
immunogenicity outcomes. See Wang et al. (2019) <DOI:10.1002/sim.8021>
for further details.

Chenguang Wang

visit

Vaccine Phase I Design with Simultaneous Evaluation of
Immunogenicity and Toxicity

vtStan function

<dl><dt>obs.y</dt>
<dd>Observed data matrix with \(l\) rows and 4 columns. Row \(k\) in the matrix
 represents the observed data from dose level \(k\). The columns are
<ul>
<li>column 1: number of patient with no DLT, no immune response</li>
<li>column 2: number of patient with no DLT, immune response</li>
<li>column 3: number of patient with DLT, no immune response</li>
<li>column 4: number of patient with DLT, immune response</li>
</ul></dd>
<dt>priors</dt>
<dd>A class <code>VTPRIOR</code> object created by
<code>vtPriorPar</code> for <code>PARA</code> and <code>PARA+</code> model.</dd>
<dt>model</dt>
<dd>option of the probability models:<dl>
 <dt>0:</dt>
<dd>parametric model</dd></dl></dd> <dt>1:</dt>
<dd>parametric+ model</dd>
</dl>See <code>visit</code> for details.
<dt>iter</dt>
<dd>STAN option: number of iterations</dd>
<dt>chains</dt>
<dd>STAN option: number of chains</dd>
<dt>warmup</dt>
<dd>STAN option: number of warmup</dd>
<dt>...</dt>
<dd>additional parameters for package rstan's sampling method. These
options include <code>iter</code>, <code>warmup</code>, <code>thin</code>,
<code>algorithm</code>. See <code>rstan::sampling</code> for details.</dd>

Arguments

Call STAN models for MCMC sampling — vtStan

<dl>

<dt>obs.y</dt>
<dd>Observed data matrix with \(l\) rows and 4 columns. Row \(k\) in the matrix
 represents the observed data from dose level \(k\). The columns are
<ul>
<li>column 1: number of patient with no DLT, no immune response</li>
<li>column 2: number of patient with no DLT, immune response</li>
<li>column 3: number of patient with DLT, no immune response</li>
<li>column 4: number of patient with DLT, immune response</li>
</ul></dd>


<dt>priors</dt>
<dd>A class <code>VTPRIOR</code> object created by
<code>vtPriorPar</code> for <code>PARA</code> and <code>PARA+</code> model.</dd>


<dt>model</dt>
<dd>option of the probability models:<dl>
 <dt>0:</dt>
<dd>parametric model</dd>

 <dt>1:</dt>
<dd>parametric+ model</dd>


</dl>See <code>visit</code> for details.</dd>


<dt>iter</dt>
<dd>STAN option: number of iterations</dd>


<dt>chains</dt>
<dd>STAN option: number of chains</dd>


<dt>warmup</dt>
<dd>STAN option: number of warmup</dd>


<dt>...</dt>
<dd>additional parameters for package rstan's sampling method. These
options include <code>iter</code>, <code>warmup</code>, <code>thin</code>,
<code>algorithm</code>. See <code>rstan::sampling</code> for details.</dd>

</dl>

vtStan: Call STAN models for MCMC sampling

Description

Usage

Value

Arguments