Bayesian Methods for Optimal Threshold Estimation
An S4 class to fit a gamma distribution on a vector of marker values.
An S4 class to fit a logistic distribution on a vector of marker value...
An S4 class to fit a log-normal distribution on a vector of marker val...
An S4 class to fit a normal distribution on a vector of marker values.
An S4 class to fit a Student distribution on a vector of marker values...
An S4 class to fit a user-defined distribution on a vector of marker v...
An S4 class to represent a gamma distribution.
An S4 union class to represent allowed dist object.
An S4 union class to represent allowed fitDist objects.
Cumulative distribution function of a specified distribution
An S4 class to represent a compound distribution.
An S4 class to represent a compound distribution.
An S4 class to represent a compound distribution.
An S4 class to represent a compound distribution.
Credible intervals estimation
Decision curve plot
Density curves plot
An S4 class to describe the optimal threshold of a diagnostic marker.
An S4 class to sum up the results from the decisionCurve methods.
Estimation of the optimal threshold of a diagnostic marker
Indicator estimates
Specify which distribution to fit on the marker values
Probability density function of a specified distribution
Second derivative of the cumulative distribution function of a specifi...
An S4 class to represent a logistic distribution.
An S4 class to represent a log-normal distribution.
An S4 union class to merge mcmc.list and NULL types of object.
An S4 class to represent a normal distribution.
optimalThreshold: Bayesian Methods for Optimal Threshold Estimation
Plot method
Plot the decision curves of a diagnostic marker
Plot the decision curves of a treatment selection marker
Marker-by-treatment predictiveness curves plot
Sample in the posterior distribution of the parameters of a given theo...
Show method
An S4 class to represent a scaled Student distribution.
An S4 method that summarizes the results of a trtSelOpthThresh or a ...
An S4 class to describe the optimal threshold of a treatment selection...
An S4 class to the results from the decisionCurve methods.
Estimation of the optimal threshold of a treatment selection marker
An S4 class to represent an 'undefined' distribution.
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.