fitGammaDist-class

fitGammaDist

This class allows to fit a gamma distribution on the marker values <code>x</code>.

Functions to estimate the optimal threshold of diagnostic markers or treatment selection markers. The optimal threshold is the marker value that maximizes the utility of the marker based-strategy (for diagnostic or treatment selection) in a given population. The utility function depends on the type of marker (diagnostic or treatment selection), but always takes into account the preferences of the patients or the physician in the decision process. For estimating the optimal threshold, ones must specify the distributions of the marker in different groups (defined according to the type of marker, diagnostic or treatment selection) and provides data to estimate the parameters of these distributions. Ones must also provide some features of the target populations (disease prevalence or treatment efficacies) as well as the preferences of patients or physicians. The functions rely on Bayesian inference which helps producing several indicators derived from the optimal threshold. See Blangero, Y, Rabilloud, M, Ecochard, R, and Subtil, F (2019) <doi:10.1177/0962280218821394> for the original article that describes the estimation method for treatment selection markers and Subtil, F, and Rabilloud, M (2019) <doi:10.1002/bimj.200900242> for diagnostic markers.

Yoann Blangero

optimalThreshold

Bayesian Methods for Optimal Threshold Estimation

fitGammaDist-class function

<dl class="dl-horizontal">
<dt><code>x</code></dt><dd>This slot takes in argument the marker values. Numeric argument.</dd></dl><dt><code>n</code></dt><dd>Length of x vector (including NA values). Numeric argument.</dd><dt><code>ini</code></dt><dd>This slot is a list of initial values passed to the MCMC algorithm. List argument.</dd><dt><code>thin</code></dt><dd>This slot is a strictly positive integer value that specifies the 'thin' applied to the MCMC algorithm.</dd><dt><code>burnin</code></dt><dd>This slot is a positive integer value that specifies the length of the burnin period in the MCMC algorithm.</dd><dt><code>mcmc</code></dt><dd>This slot allows the main function to k,now whether an MCMC algorithm must be performed to sample the distribution parameters from their posterior distribution.</dd>

fitGammaDist-class: An S4 class to fit a gamma distribution on a vector of marker values.

Description

Arguments

Slots

Details

See Also