Bayesian Methods for Optimal Threshold Estimation
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Documentation for package ‘optimalThreshold’ version 1.0
Help Pages
-- A --
| allowedDist | An S4 union class to represent allowed dist object. |
| allowedDist-class | An S4 union class to represent allowed dist object. |
| allowedFitDist | An S4 union class to represent allowed fitDist objects. |
| allowedFitDist-class | An S4 union class to represent allowed fitDist objects. |
-- C --
| cdf | Cumulative distribution function of a specified distribution |
| cdf-method | Cumulative distribution function of a specified distribution |
| cdf.compoundEvtInnovDist | Cumulative distribution function of a specified distribution |
| cdf.compoundEvtRefDist | Cumulative distribution function of a specified distribution |
| cdf.compoundNoEvtInnovDist | Cumulative distribution function of a specified distribution |
| cdf.compoundNoEvtRefDist | Cumulative distribution function of a specified distribution |
| cdf.gammaDist | Cumulative distribution function of a specified distribution |
| cdf.logisticDist | Cumulative distribution function of a specified distribution |
| cdf.logNormalDist | Cumulative distribution function of a specified distribution |
| cdf.normalDist | Cumulative distribution function of a specified distribution |
| cdf.studentDist | Cumulative distribution function of a specified distribution |
| compoundEvtInnovDist | An S4 class to represent a compound distribution. |
| compoundEvtInnovDist-class | An S4 class to represent a compound distribution. |
| compoundEvtRefDist | An S4 class to represent a compound distribution. |
| compoundEvtRefDist-class | An S4 class to represent a compound distribution. |
| compoundNoEvtInnovDist | An S4 class to represent a compound distribution. |
| compoundNoEvtInnovDist-class | An S4 class to represent a compound distribution. |
| compoundNoEvtRefDist | An S4 class to represent a compound distribution. |
| compoundNoEvtRefDist-class | An S4 class to represent a compound distribution. |
| credibleIntervals | Credible intervals estimation |
| credibleIntervals-method | Credible intervals estimation |
| credibleIntervals.diagOptThresh | Credible intervals estimation |
| credibleIntervals.trtSelOptThresh | Credible intervals estimation |
-- D --
| decisionCurve | Decision curve plot |
| decisionCurve-method | Decision curve plot |
| decisionCurve.diagOptThresh | Decision curve plot |
| decisionCurve.trtSelOptThresh | Decision curve plot |
| densCurves | Density curves plot |
| diagOptThresh | An S4 class to describe the optimal threshold of a diagnostic marker. |
| diagOptThresh-class | An S4 class to describe the optimal threshold of a diagnostic marker. |
| diagRelUtility | An S4 class to sum up the results from the decisionCurve methods. |
| diagRelUtility-class | An S4 class to sum up the results from the decisionCurve methods. |
| diagThresh | Estimation of the optimal threshold of a diagnostic marker |
-- E --
| estimates | Indicator estimates |
| estimates-method | Indicator estimates |
| estimates.diagOptThresh | Indicator estimates |
| estimates.trtSelOptThresh | Indicator estimates |
-- F --
| fit | Specify which distribution to fit on the marker values |
| fitGammaDist | An S4 class to fit a gamma distribution on a vector of marker values. |
| fitGammaDist-class | An S4 class to fit a gamma distribution on a vector of marker values. |
| fitLogisticDist | An S4 class to fit a logistic distribution on a vector of marker values. |
| fitLogisticDist-class | An S4 class to fit a logistic distribution on a vector of marker values. |
| fitLogNormalDist | An S4 class to fit a log-normal distribution on a vector of marker values. |
| fitLogNormalDist-class | An S4 class to fit a log-normal distribution on a vector of marker values. |
| fitNormalDist | An S4 class to fit a normal distribution on a vector of marker values. |
| fitNormalDist-class | An S4 class to fit a normal distribution on a vector of marker values. |
| fitStudentDist | An S4 class to fit a Student distribution on a vector of marker values. |
| fitStudentDist-class | An S4 class to fit a Student distribution on a vector of marker values. |
| fitUserDefinedDist | An S4 class to fit a user-defined distribution on a vector of marker values. |
| fitUserDefinedDist-class | An S4 class to fit a user-defined distribution on a vector of marker values. |
-- G --
| gammaDist | An S4 class to represent a gamma distribution. |
| gammaDist-class | An S4 class to represent a gamma distribution. |
| gradient | Probability density function of a specified distribution |
| gradient-method | Probability density function of a specified distribution |
| gradient.compoundEvtInnovDist | Probability density function of a specified distribution |
| gradient.compoundEvtRefDist | Probability density function of a specified distribution |
| gradient.compoundNoEvtInnovDist | Probability density function of a specified distribution |
| gradient.compoundNoEvtRefDist | Probability density function of a specified distribution |
| gradient.gammaDist | Probability density function of a specified distribution |
| gradient.logisticDist | Probability density function of a specified distribution |
| gradient.logNormalDist | Probability density function of a specified distribution |
| gradient.normalDist | Probability density function of a specified distribution |
| gradient.studentDist | Probability density function of a specified distribution |
-- H --
| hessian | Second derivative of the cumulative distribution function of a specified distribution |
| hessian-method | Second derivative of the cumulative distribution function of a specified distribution |
| hessian.compoundEvtInnovDist | Second derivative of the cumulative distribution function of a specified distribution |
| hessian.compoundEvtRefDist | Second derivative of the cumulative distribution function of a specified distribution |
| hessian.compoundNoEvtInnovDist | Second derivative of the cumulative distribution function of a specified distribution |
| hessian.compoundNoEvtRefDist | Second derivative of the cumulative distribution function of a specified distribution |
| hessian.gammaDist | Second derivative of the cumulative distribution function of a specified distribution |
| hessian.logisticDist | Second derivative of the cumulative distribution function of a specified distribution |
| hessian.logNormalDist | Second derivative of the cumulative distribution function of a specified distribution |
| hessian.normalDist | Second derivative of the cumulative distribution function of a specified distribution |
| hessian.studentDist | Second derivative of the cumulative distribution function of a specified distribution |
-- L --
| logisticDist | An S4 class to represent a logistic distribution. |
| logisticDist-class | An S4 class to represent a logistic distribution. |
| logNormalDist | An S4 class to represent a log-normal distribution. |
| logNormalDist-class | An S4 class to represent a log-normal distribution. |
-- M --
| mcmc.listOrNull | An S4 union class to merge mcmc.list and NULL types of object. |
| mcmc.listOrNull-class | An S4 union class to merge mcmc.list and NULL types of object. |
-- N --
| normalDist | An S4 class to represent a normal distribution. |
| normalDist-class | An S4 class to represent a normal distribution. |
-- P --
| plot-method | Plot method |
| plot-method | Plot the decision curves of a diagnostic marker |
| plot-method | Plot the decision curves of a treatment selection marker |
| plot-methods | Plot method |
| plot.diagOptThresh | Plot method |
| plot.diagRelUtility | Plot the decision curves of a diagnostic marker |
| plot.trtSelOptThresh | Plot method |
| plot.trtSelRelUtility | Plot the decision curves of a treatment selection marker |
-- R --
| riskCurves | Marker-by-treatment predictiveness curves plot |
-- S --
| samplePosteriorDist | Sample in the posterior distribution of the parameters of a given theoretical distribution. |
| samplePosteriorDist-method | Sample in the posterior distribution of the parameters of a given theoretical distribution. |
| samplePosteriorDist.fitGammaDist | Sample in the posterior distribution of the parameters of a given theoretical distribution. |
| samplePosteriorDist.fitLogisticDist | Sample in the posterior distribution of the parameters of a given theoretical distribution. |
| samplePosteriorDist.fitLogNormalDist | Sample in the posterior distribution of the parameters of a given theoretical distribution. |
| samplePosteriorDist.fitNormalDist | Sample in the posterior distribution of the parameters of a given theoretical distribution. |
| samplePosteriorDist.fitStudentDist | Sample in the posterior distribution of the parameters of a given theoretical distribution. |
| show-method | Show method |
| show-methods | Show method |
| show.diagOptThresh | Show method |
| show.trtSelOptThresh | Show method |
| studentDist | An S4 class to represent a scaled Student distribution. |
| studentDist-class | An S4 class to represent a scaled Student distribution. |
| summary-method | An S4 method that summarizes the results of a 'trtSelOpthThresh' or a 'diagOpthThresh' object. |
| summary-methods | An S4 method that summarizes the results of a 'trtSelOpthThresh' or a 'diagOpthThresh' object. |
| summary.diagOptThresh | An S4 method that summarizes the results of a 'trtSelOpthThresh' or a 'diagOpthThresh' object. |
| summary.trtSelOptThresh | An S4 method that summarizes the results of a 'trtSelOpthThresh' or a 'diagOpthThresh' object. |
-- T --
| trtSelOptThresh | An S4 class to describe the optimal threshold of a treatment selection marker. |
| trtSelOptThresh-class | An S4 class to describe the optimal threshold of a treatment selection marker. |
| trtSelRelUtility | An S4 class to the results from the decisionCurve methods. |
| trtSelRelUtility-class | An S4 class to the results from the decisionCurve methods. |
| trtSelThresh | Estimation of the optimal threshold of a treatment selection marker |
-- U --
| undefined | An S4 class to represent an 'undefined' distribution. |
| undefined-class | An S4 class to represent an 'undefined' distribution. |