Package org.broadinstitute.hellbender.utils.mcmc

Interface Summary

Interface	Description
DataCollection	Interface for tagging any class that represents a collection of datasets required to update posterior samples for Markov-Chain Monte Carlo sampling using samplers implementing the ParameterSampler interface.
ParameterEnum	Interface for tagging an enum that represents the name of every Parameter comprising a ParameterizedState.
ParameterSampler<U,V extends java.lang.Enum<V> & ParameterEnum,S extends ParameterizedState<V>,T extends DataCollection>	Interface for generating random samples of a Parameter value, given an ParameterizedState and a DataCollection.

Class Summary

Class	Description
AdaptiveMetropolisSampler	Metropolis MCMC sampler using an adaptive step size that increases / decreases in order to decrease / increase acceptance rate to some desired value.
DecileCollection	Represents a set of deciles.
GibbsSampler<V extends java.lang.Enum<V> & ParameterEnum,S extends ParameterizedState<V>,T extends DataCollection>	Implements Gibbs sampling of a multivariate probability density function.
Parameter<T extends java.lang.Enum<T> & ParameterEnum,U>	Represents a parameter value with a named ParameterEnum key.
ParameterizedModel<V1 extends java.lang.Enum<V1> & ParameterEnum,S1 extends ParameterizedState<V1>,T1 extends DataCollection>	Represents a parameterized model.
ParameterizedModel.GibbsBuilder<V2 extends java.lang.Enum<V2> & ParameterEnum,S2 extends ParameterizedState<V2>,T2 extends DataCollection>	Builder for constructing a ParameterizedModel to be Gibbs sampled using GibbsSampler.
ParameterizedState<T extends java.lang.Enum<T> & ParameterEnum>	Represents a mapped collection of Parameter objects, i.e., named, ordered, enumerated keys associated with values of mixed type via a key -> key, value map.
ParameterReader<T extends java.lang.Enum<T> & ParameterEnum>	Table reader for reading a PosteriorSummary for each global parameter in a ParameterEnum.
ParameterWriter<T extends java.lang.Enum<T> & ParameterEnum>	Table writer for ouputting a PosteriorSummary for each global parameter in a ParameterEnum.
PosteriorSummary	Represents central tendency and upper/lower credible-interval bounds of the posterior of a univariate model parameter, along with optional deciles.
PosteriorSummaryUtils	Contains methods for computing summary statistics for the posterior of a univariate model parameter.
SliceSampler	Implements slice sampling of a continuous, univariate, unnormalized probability density function, which is assumed to be unimodal.

Enum Summary

Enum	Description
Decile	Enumerates individual deciles.
ParameterizedModel.UpdateMethod
ParameterTableColumn