R: Bayesian Methods for Optimal Threshold Estimation

# Bayesian Methods for Optimal Threshold Estimation

## Documentation for package ‘optimalThreshold’ version 1.0

- DESCRIPTION file

## Help Pages

A C D E F G H L M N P R S T U

## -- 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.