label_switch_2stage

Fix Label Switching in MCMC Results from a Binary Outcome Misclassification Model

Use frequentist and Bayesian methods to estimate parameters from a
binary outcome misclassification model. These methods correct for the problem
of "label switching" by assuming that the sum of outcome sensitivity and
specificity is at least 1. A description of the analysis methods is
available in Hochstedler and Wells (2023) <doi:10.48550/arXiv.2303.10215>.

Kimberly Hochstedler

COMBO

Correcting Misclassified Binary Outcomes in Association Studies

Kimberly Hochstedler Webb

label_switch_2stage function

<dl><dt>chain_matrix</dt>
<dd>A numeric matrix containing the posterior samples for all
parameters in a given MCMC chain. <code>chain_matrix</code> must be a named
object (i.e. each parameter must be named as <code>beta[j, p]</code>, <code>gamma[k,j,p]</code>,
or <code>delta[l,k,j,p]</code>).</dd>
<dt>dim_x</dt>
<dd>An integer specifying the number of columns of the design matrix of the true outcome mechanism, <code>X</code>.</dd>
<dt>dim_z</dt>
<dd>An integer specifying the number of columns of the design matrix of the first-stage observation mechanism, <code>Z</code>.</dd>
<dt>dim_v</dt>
<dd>An integer specifying the number of columns of the design matrix of the second-stage observation mechanism, <code>V</code>.</dd>
<dt>n_cat</dt>
<dd>An integer specifying the number of categorical values that the true outcome, \(Y\),
the first-stage observed outcome, \(Y^*\), and the second-stage observed
outcome \(\tilde{Y}\) can take.</dd></dl>

Arguments

Fix Label Switching in MCMC Results from a Binary Outcome Misclassification Model — label_switch_2stage

<dl>

<dt>chain_matrix</dt>
<dd>A numeric matrix containing the posterior samples for all
parameters in a given MCMC chain. <code>chain_matrix</code> must be a named
object (i.e. each parameter must be named as <code>beta[j, p]</code>, <code>gamma[k,j,p]</code>,
or <code>delta[l,k,j,p]</code>).</dd>


<dt>dim_x</dt>
<dd>An integer specifying the number of columns of the design matrix of the true outcome mechanism, <code>X</code>.</dd>


<dt>dim_z</dt>
<dd>An integer specifying the number of columns of the design matrix of the first-stage observation mechanism, <code>Z</code>.</dd>


<dt>dim_v</dt>
<dd>An integer specifying the number of columns of the design matrix of the second-stage observation mechanism, <code>V</code>.</dd>


<dt>n_cat</dt>
<dd>An integer specifying the number of categorical values that the true outcome, \(Y\),
the first-stage observed outcome, \(Y^*\), and the second-stage observed
outcome \(\tilde{Y}\) can take.</dd>

</dl>

label_switch_2stage: Fix Label Switching in MCMC Results from a Binary Outcome Misclassification Model

Description

Usage

Value

Arguments