objfun

Used for internal optimization. Not intended for users.

Statistical modeling for correlated count data using the beta-binomial distribution, described in Martin et al. (2020) <doi:10.1214/19-AOAS1283>. It allows for both mean and overdispersion covariates.

Amy D Willis

corncob

Count Regression for Correlated Observations with the
Beta-Binomial

Bryan D Martin

Daniela Witten

Sarah Teichman

Thomas W Yee

Xiangjie Xue

objfun function

<dl><dt>theta</dt>
<dd>Numeric vector. Parameters associated with <code>X</code> and <code>X_star</code></dd>
<dt>W</dt>
<dd>Numeric vector of counts</dd>
<dt>M</dt>
<dd>Numeric vector of sequencing depth</dd>
<dt>X</dt>
<dd>Matrix of covariates associated with abundance (including intercept)</dd>
<dt>X_star</dt>
<dd>Matrix of covariates associated with dispersion (including intercept)</dd>
<dt>np</dt>
<dd>Number of covariates associated with abundance (including intercept)</dd>
<dt>npstar</dt>
<dd>Number of covariates associated with dispersion (including intercept)</dd>
<dt>link</dt>
<dd>ink function for abundance covariates</dd>
<dt>phi.link</dt>
<dd>ink function for dispersion covariates</dd></dl>

Arguments

Objective function — objfun

<dl>

<dt>theta</dt>
<dd>Numeric vector. Parameters associated with <code>X</code> and <code>X_star</code></dd>


<dt>W</dt>
<dd>Numeric vector of counts</dd>


<dt>M</dt>
<dd>Numeric vector of sequencing depth</dd>


<dt>X</dt>
<dd>Matrix of covariates associated with abundance (including intercept)</dd>


<dt>X_star</dt>
<dd>Matrix of covariates associated with dispersion (including intercept)</dd>


<dt>np</dt>
<dd>Number of covariates associated with abundance (including intercept)</dd>


<dt>npstar</dt>
<dd>Number of covariates associated with dispersion (including intercept)</dd>


<dt>link</dt>
<dd>ink function for abundance covariates</dd>


<dt>phi.link</dt>
<dd>ink function for dispersion covariates</dd>

</dl>

objfun: Objective function

Description

Usage

Value

Arguments