beta.posterior.thetasamp

Internal function used in joint approach to group-analysis

internal

Performs a spatial Bayesian general linear model (GLM) for task
functional magnetic resonance imaging (fMRI) data on the cortical surface.
Additional models include group analysis and inference to detect thresholded
areas of activation. Includes direct support for the 'CIFTI' neuroimaging
file format. For more information see A. F. Mejia, Y. R. Yue, D. Bolin, F.
Lindgren, M. A. Lindquist (2020) <doi:10.1080/01621459.2019.1611582> and D.
Spencer, Y. R. Yue, D. Bolin, S. Ryan, A. F. Mejia (2022)
<doi:10.1016/j.neuroimage.2022.118908>.

Amanda Mejia

BayesfMRI

Spatial Bayesian Methods for Task Functional MRI Studies

Daniel Spencer

Damon Pham

David Bolin

Sarah Ryan

Yu (Ryan) Yue

beta.posterior.thetasamp function

<dl><dt>theta</dt>
<dd>A single sample of theta (hyperparameters) from q(theta|y)</dd>
<dt>spde</dt>
<dd>A SPDE object from inla.spde2.matern() function.</dd>
<dt>Xcros</dt>
<dd>A crossproduct of design matrix.</dd>
<dt>Xycros</dt>
<dd>A crossproduct of design matrix and BOLD y.</dd>
<dt>contrasts</dt>
<dd>A list of vectors of length M*K specifying the contrasts of interest.</dd>
<dt>quantiles</dt>
<dd>Vector of posterior quantiles to return in addition to the posterior mean</dd>
<dt>excursion_type</dt>
<dd>Vector of excursion function type ("&gt;", "&lt;", "!=") for each contrast</dd>
<dt>gamma</dt>
<dd>Vector of activation thresholds for each contrast</dd>
<dt>alpha</dt>
<dd>Significance level for activation for the excursion sets</dd>
<dt>nsamp_beta</dt>
<dd>The number of samples to draw from full conditional of beta given the current value of theta (p(beta|theta,y))</dd></dl>

Arguments

This function requires the <code>INLA</code> package, which is not a CRAN package.
See <a href="https://www.r-inla.org/download-install">https://www.r-inla.org/download-install</a> for easy installation instructions.

INLA Requirement

Beta posterior theta sampling — beta.posterior.thetasamp

<dl>

<dt>theta</dt>
<dd>A single sample of theta (hyperparameters) from q(theta|y)</dd>


<dt>spde</dt>
<dd>A SPDE object from inla.spde2.matern() function.</dd>


<dt>Xcros</dt>
<dd>A crossproduct of design matrix.</dd>


<dt>Xycros</dt>
<dd>A crossproduct of design matrix and BOLD y.</dd>


<dt>contrasts</dt>
<dd>A list of vectors of length M*K specifying the contrasts of interest.</dd>


<dt>quantiles</dt>
<dd>Vector of posterior quantiles to return in addition to the posterior mean</dd>


<dt>excursion_type</dt>
<dd>Vector of excursion function type ("&gt;", "&lt;", "!=") for each contrast</dd>


<dt>gamma</dt>
<dd>Vector of activation thresholds for each contrast</dd>


<dt>alpha</dt>
<dd>Significance level for activation for the excursion sets</dd>


<dt>nsamp_beta</dt>
<dd>The number of samples to draw from full conditional of beta given the current value of theta (p(beta|theta,y))</dd>

</dl>

This function requires the <code>INLA</code> package, which is not a CRAN package.
See <a href='https://www.r-inla.org/download-install'>https://www.r-inla.org/download-install</a> for easy installation instructions.

beta.posterior.thetasamp: Beta posterior theta sampling

Description

Usage

Value

Arguments

INLA Requirement