###
### NAMESPACE
###


## Imported methods
import(methods)
import(stats)
importFrom(BimodalIndex, bimodalIndex)
importFrom(mc2d, rdirichlet)

## Public classes
exportClasses(BlockHyperParameters)
exportClasses(CancerEngine)
exportClasses(CancerModel)
exportClasses(Engine)
exportClasses(EngineWithActivity)
exportClasses(IndependentLogNormal)
exportClasses(IndependentNormal)
exportClasses(MVN)
exportClasses(NoiseModel)
exportClasses(SurvivalModel)

## S4 methods made from existing functions or S3 methods
exportMethods(ncol)
exportMethods(nrow)
exportMethods(summary)

## S4 methods for new generic functions
exportMethods(nComponents)
exportMethods(alterMean)
exportMethods(alterSD)
exportMethods(blur)
exportMethods(rand)
exportMethods(addControl)

## Public functions
export(nComponents)  # of an Engine
export(covar)        # gets the covariance matrix of an MVN object
export(correl)       # gets the correlation matrix of an MVN object
export(normalOffset)     # example of an "alterMean transformation"
export(invGammaMultiple) # example of an "alterSD tansformation"
export(nPatterns)            # part of cancer model
export(nPossibleHits)        # part of cancer model
export(nHitsPerPattern)      # part of cancer model
export(survivalCoefficients) # part of cancer model
export(outcomeCoefficients)  # part of cancer model

## Public generator functions
export(BlockHyperParameters)
export(CancerEngine)
export(CancerModel)
export(Engine)
export(EngineWithActivity)
export(IndependentLogNormal)
export(IndependentNormal)
export(MVN)
export(NoiseModel)
export(SurvivalModel)

## Public functions that construct classes
export(makeBlockStructure)
export(NormalVsCancerModel)
export(NormalVsCancerEngine)

## clinical stuff
exportClasses(MixedTypeEngine)
export("makeDataTypes", "getDataTypes", "getDaisyTypes",
       "ClinicalNoiseModel", "ClinicalEngine", "MixedTypeEngine")
