Simulation-class

.simulation_obj

A class for defining Simulation study details. Objects of class
<code>Simulation</code> should not be created directly but by the constructor
<code>create_simulation_obj()</code>.

Bayesian dynamic borrowing is an approach to incorporating external
data to supplement a randomized, controlled trial analysis in which
external data are incorporated in a dynamic way (e.g., based on similarity
of outcomes); see Viele 2013 <doi:10.1002/pst.1589> for an overview.
This package implements the hierarchical commensurate prior approach to dynamic borrowing
as described in Hobbes 2011 <doi:10.1111/j.1541-0420.2011.01564.x>.
There are three main functionalities. First, 'psborrow2' provides a user-friendly
interface for applying dynamic borrowing on the study results handles the Markov Chain
Monte Carlo sampling on behalf of the user. Second, 'psborrow2' provides a
simulation framework to compare different borrowing parameters (e.g. full borrowing, no
borrowing, dynamic borrowing) and other trial and borrowing characteristics
(e.g. sample size, covariates) in a unified way. Third, 'psborrow2' provides
a set of functions to generate data for simulation studies, and also allows
the user to specify their own data generation process. This package is designed to
use the sampling functions from 'cmdstanr' which can be installed from
<https://stan-dev.r-universe.dev>.

Matt Secrest

psborrow2

Bayesian Dynamic Borrowing Analysis and Simulation

Isaac Gravestock

Craig Gower-Page

Manoj Khanal

Mingyang Shan

Kexin Jin

Zhi Yang

Genentech, Inc. 

Simulation-class function

<dl>
<dt><code>data_matrix_list</code></dt>
<dd><code>SimDataList</code>. The list of lists of data matrices created
with <code>sim_data_list()</code>.</dd></dl>
<dt><code>outcome</code></dt>
<dd><code>SimOutcomeList</code>. List of <code>Outcome</code> objects created with
<code>sim_outcome_list()</code>.</dd>
<dt><code>borrowing</code></dt>
<dd><code>SimBorrowingList</code>. List of <code>Borrowing</code> objects created
with <code>sim_borrowing_list()</code>.</dd>
<dt><code>covariate</code></dt>
<dd><code>SimCovariateList</code> or <code>NULL</code>. List of <code>Covariate</code> objects created
with <code>sim_covariate_list()</code> or <code>NULL</code> (no covariate adjustment).</dd>
<dt><code>treatment</code></dt>
<dd><code>SimTreatmentList</code>. List of <code>Treatment</code> objects created
with <code>sim_treatment_list()</code>.</dd>
<dt><code>guide</code></dt>
<dd>data.frame. Data.frame containing information on all
combinations evaluated.</dd>
<dt><code>n_combos</code></dt>
<dd>integer. Number of combinations of parameters to be evaluated.</dd>
<dt><code>n_analyses</code></dt>
<dd>integer. Number of analyses (combos x datasets to be performed).</dd>
<dt><code>`analysis_obj_list`</code></dt>
<dd>list. List of analysis objects indexed according to <code>guide</code>.</dd>

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Simulation Class — Simulation-class

<dl>
<dt><code>data_matrix_list</code></dt>
<dd><code>SimDataList</code>. The list of lists of data matrices created
with <code>sim_data_list()</code>.</dd>


<dt><code>outcome</code></dt>
<dd><code>SimOutcomeList</code>. List of <code>Outcome</code> objects created with
<code>sim_outcome_list()</code>.</dd>


<dt><code>borrowing</code></dt>
<dd><code>SimBorrowingList</code>. List of <code>Borrowing</code> objects created
with <code>sim_borrowing_list()</code>.</dd>


<dt><code>covariate</code></dt>
<dd><code>SimCovariateList</code> or <code>NULL</code>. List of <code>Covariate</code> objects created
with <code>sim_covariate_list()</code> or <code>NULL</code> (no covariate adjustment).</dd>


<dt><code>treatment</code></dt>
<dd><code>SimTreatmentList</code>. List of <code>Treatment</code> objects created
with <code>sim_treatment_list()</code>.</dd>


<dt><code>guide</code></dt>
<dd>data.frame. Data.frame containing information on all
combinations evaluated.</dd>


<dt><code>n_combos</code></dt>
<dd>integer. Number of combinations of parameters to be evaluated.</dd>


<dt><code>n_analyses</code></dt>
<dd>integer. Number of analyses (combos x datasets to be performed).</dd>


<dt><code>`analysis_obj_list`</code></dt>
<dd>list. List of analysis objects indexed according to <code>guide</code>.</dd>


</dl>

<code>Simulation</code> Class

Simulation-class: `Simulation` Class

Description

Arguments

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