A B C D E F G H I K L M N O P Q R S T U V W X Y Z

A

a0 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
a1 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
a2 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
a3 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
aa - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
acceptance() - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
acceptanceProb(double[], double[]) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
acceptanceProb(double[], double[]) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
acceptanceProb(Object, MultiState, Object, MultiState, int) - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
acceptanceProb(Object, MultiState, Object, MultiState, int) - Method in class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledSampler
 
acceptanceProb(Object, MultiState, Object, MultiState, int) - Method in class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledMaximizer
 
acceptanceProb(Object, Object) - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
acceptanceProb(Object, Object) - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisSampler
 
acceptanceRate - Variable in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
acceptanceRatio() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
AcceptanceWriter - class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter.
 
AcceptanceWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
AcceptanceWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
AcceptanceWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
AcceptanceWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
accepted - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
accepted - Variable in class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
accepted - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
accepted() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
acceptRand - Variable in class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
acceptRate - Variable in class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
accumToVar(MultiDoubleState.CovAccumulator) - Static method in class org.omegahat.Simulation.MCMC.MultiDoubleState
Compute the covariance matrix
adapt(MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalProposal
 
adapt(MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveProposal
modify the state of the enclosed proposal distribution using information from the provided state vector
adapt(MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
 
adapt(MultiState, int) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveKernelProposal
modify the state of the enclosed proposal distribution using information from the provided state vector
adapt(MultiState, int) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
adapt(MultiState, int) - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
adapt(MultiState, int) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
modify the state of the enclosed proposal distribution using information from the provided state vector
adapt(MultiState, int) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalDualKernelProposal
 
adapt(MultiState, int) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
adapt(MultiState, int) - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
AdaptiveKernelProposal - class org.omegahat.Simulation.MCMC.Proposals.AdaptiveKernelProposal.
 
AdaptiveKernelProposal() - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveKernelProposal
 
AdaptiveMultiKernelProposal - class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal.
 
AdaptiveMultiKernelProposal() - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
 
AdaptiveMultiSourceCoupler - class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler.
 
AdaptiveMultiSourceCoupler(int, int, double[][], double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
Constructor for normal increments with specified covariance matrix.
AdaptiveMultiSourceCoupler(int, int, double[][], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
Constructor for normal increment proposal with specified covariance matrix, no variance inflation
AdaptiveMultiSourceCoupler(int, int, int, double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
Constructor for a spherical independent standard normal increments
AdaptiveMultiSourceCoupler(int, int, int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
Constructor for a sperical independent standard normal increments No variance inflation.
AdaptiveNormalDualKernelProposal - class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalDualKernelProposal.
 
AdaptiveNormalDualKernelProposal() - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalDualKernelProposal
 
AdaptiveNormalDualKernelProposal(double[], double[][], double[][], double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalDualKernelProposal
 
AdaptiveNormalDualKernelProposal(int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalDualKernelProposal
 
AdaptiveNormalKernelProposal - class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal.
 
AdaptiveNormalKernelProposal(double[][], double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
Constructor for normal increments with specified covariance matrix.
AdaptiveNormalKernelProposal(double[][], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
Constructor for normal increment proposal with specified covariance matrix, no variance inflation @param var variance matrix
AdaptiveNormalKernelProposal(int, double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
Constructor for a spherical independent standard normal increments
AdaptiveNormalKernelProposal(int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
Constructor for a sperical independent standard normal increments No variance inflation.
AdaptiveNormalMetropolisProposal - class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal.
 
AdaptiveNormalMetropolisProposal(double[][], double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
Constructor for normal increments with specified covariance matrix.
AdaptiveNormalMetropolisProposal(double[][], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
Constructor for normal increment proposal with specified covariance matrix, no variance inflation @param var variance matrix
AdaptiveNormalMetropolisProposal(int, double, double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
Constructor for a spherical normal increments with the same variance for each dimension.
AdaptiveNormalMetropolisProposal(int, double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
Constructor for a independent normal increntens (sam variances for each dimension).
AdaptiveNormalProposal - class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalProposal.
 
AdaptiveNormalProposal(double[], double[][], double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalProposal
Constructor for normal with specified mean and covariance matrix.
AdaptiveNormalProposal(double[], double[][], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalProposal
Constructor for normal with specified mean and covariance matrix, no variance inflation
AdaptiveNormalProposal(int, double, double, double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalProposal
Constructor for a spherical normal with the same mean and variances for each dimension.
AdaptiveNormalProposal(int, double, double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalProposal
Constructor for a spherical normal with the same mean and variances for each dimension.
AdaptiveProposal - class org.omegahat.Simulation.MCMC.Proposals.AdaptiveProposal.
This class implements a generic ``adaptive'' Hastings-Coupled proposal.
AdaptiveProposal() - Constructor for class org.omegahat.Simulation.MCMC.Proposals.AdaptiveProposal
 
add(Object) - Method in class org.omegahat.Simulation.MCMC.MultiState
 
add(Object) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
addListener(PRNGAdministratorListener) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
addListener(PRNGAdministratorListener) - Method in class org.omegahat.Simulation.RandomGenerators.NotifyingPRNG
 
adminName - Variable in class org.omegahat.Simulation.RandomGenerators.TestServer
 
args - Variable in class org.omegahat.Simulation.RandomGenerators.TestServer
 
ArrayListener - class org.omegahat.Simulation.MCMC.Listeners.ArrayListener.
Stores contents of RecordingIndexEvents in an array when one is recieved.
ArrayListener(String[]) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
ArrayListener(String[], int) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
ArrayTools - class org.omegahat.GUtilities.ArrayTools.
 
ArrayTools() - Constructor for class org.omegahat.GUtilities.ArrayTools
 
arrayToString() - Method in class org.omegahat.Simulation.MCMC.ContainerState
 
arrayToString(Object) - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
arrayToString(Object) - Method in class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
 
arrayToString(Object) - Method in class org.omegahat.Simulation.MCMC.Listeners.StepListenerPrinter
 
arrayToString(Object) - Static method in class org.omegahat.GUtilities.ArrayTools
 
arrayToString(Object) - Static method in class org.omegahat.Simulation.MCMC.Utilities
 
arrayToString(Object, String, String, String) - Static method in class org.omegahat.GUtilities.ArrayTools
 
attr(String) - Method in class org.omegahat.Simulation.MCMC.MultiState
 
attr(String, Object) - Method in class org.omegahat.Simulation.MCMC.MultiState
 
attributeNames() - Method in class org.omegahat.Simulation.MCMC.MultiState
 
attributes - Variable in class org.omegahat.Simulation.MCMC.MultiState
 
averageDistance() - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 

B

B_BB_Mixture - class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture.
 
B_BB_Mixture() - Constructor for class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
B_BB_Mixture(String) - Constructor for class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
b1 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
b2 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
b3 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
b4 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
BaseMarkovChain - class org.omegahat.Simulation.MCMC.BaseMarkovChain.
An abstract class providing methods implementing the interface MarkovChain.
BaseMarkovChain() - Constructor for class org.omegahat.Simulation.MCMC.BaseMarkovChain
 
bernoulliRand(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
betaCDF(double, double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Incomplete Beta function.
betaPDF(double, double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
betaQuantile(double, double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
xinbta.f -- translated by f2c and modified
betaRand(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
Binomial_BetaBinomial_Example - class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example.
 
Binomial_BetaBinomial_Example_II - class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_II.
 
Binomial_BetaBinomial_Example_II() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_II
 
Binomial_BetaBinomial_Example_III - class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_III.
 
Binomial_BetaBinomial_Example_III() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_III
 
Binomial_BetaBinomial_Example_NKC - class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_NKC.
 
Binomial_BetaBinomial_Example_NKC_Bimode - class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_NKC_Bimode.
 
Binomial_BetaBinomial_Example_NKC_Bimode() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_NKC_Bimode
 
Binomial_BetaBinomial_Example_NKC() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_NKC
 
Binomial_BetaBinomial_Example() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example
 
Binomial_BetaBinomial_Likelihood - class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood.
 
Binomial_BetaBinomial_Likelihood_Bimode - class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood_Bimode.
 
Binomial_BetaBinomial_Likelihood_Bimode() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood_Bimode
 
Binomial_BetaBinomial_Likelihood() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood
 
Binomial_BetaBinomial_SimpleExample - class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleExample.
 
Binomial_BetaBinomial_SimpleExample_NKC - class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleExample_NKC.
 
Binomial_BetaBinomial_SimpleExample_NKC() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleExample_NKC
 
Binomial_BetaBinomial_SimpleExample() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleExample
 
Binomial_BetaBinomial_SimpleLikelihood - class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleLikelihood.
 
Binomial_BetaBinomial_SimpleLikelihood() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleLikelihood
 
Binomial_BetaBinomialExample - class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomialExample.
 
Binomial_BetaBinomialExample() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomialExample
 
Binomial_Binomial_Likelihood - class org.omegahat.Simulation.MCMC.Examples.Binomial_Binomial_Likelihood.
 
Binomial_Binomial_Likelihood() - Constructor for class org.omegahat.Simulation.MCMC.Examples.Binomial_Binomial_Likelihood
 
binomialCDF(int, int, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
binomialPMF(int, int, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
binomialQuantile(double, int, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
binomialRand(int, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Binomial random generator from Numerical Recipes
bins - Variable in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
Bivariate - interface Bivariate.
 
bivariateDensity(double[]) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
bivariateDensity(double[]) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
bivariateDensity(double[]) - Method in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalDensity
 
BivariateNormalDensity - class org.omegahat.Simulation.MCMC.Targets.BivariateNormalDensity.
A Bivariate normal density
BivariateNormalDensity() - Constructor for class org.omegahat.Simulation.MCMC.Targets.BivariateNormalDensity
 
BivariateNormalDensity(double, double) - Constructor for class org.omegahat.Simulation.MCMC.Targets.BivariateNormalDensity
 
BivariateNormalLikelihood - class org.omegahat.Simulation.MCMC.Targets.BivariateNormalLikelihood.
A Bivariate normal density
BivariateNormalLikelihood(String) - Constructor for class org.omegahat.Simulation.MCMC.Targets.BivariateNormalLikelihood
 
boa - Variable in class org.omegahat.Simulation.RandomGenerators.TestServer
 
BoundedHastingsCoupledMaximizer - class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledMaximizer.
This extends CustomHastingsCoupledSampler by allowing boundaries to be set for each dimension.
BoundedHastingsCoupledMaximizer(MultiState, int, UnnormalizedDensity, HastingsCoupledProposal, double[], double[], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledMaximizer
 
BoundedHastingsCoupledMaximizer(MultiState, int, UnnormalizedDensity, HastingsCoupledProposal, PRNG, double[], double[], boolean) - Constructor for class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledMaximizer
 
BoundedHastingsCoupledSampler - class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledSampler.
This extends CustomHastingsCoupledSampler by allowing boundaries to be set for each dimension.
BoundedHastingsCoupledSampler(MultiState, int, UnnormalizedDensity, HastingsCoupledProposal, double[], double[], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledSampler
 
BoundedHastingsCoupledSampler(MultiState, int, UnnormalizedDensity, HastingsCoupledProposal, PRNG, double[], double[], boolean) - Constructor for class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledSampler
 
bToB(boolean[]) - Static method in class org.omegahat.GUtilities.ArrayTools
 
Btob(Boolean[]) - Static method in class org.omegahat.GUtilities.ArrayTools
 

C

c1 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c10 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c11 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c12 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c13 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c14 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c15 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c16 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c17 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c18 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c19 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c2 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c20 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c21 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c22 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c23 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c24 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c25 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c26 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c27 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c28 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c29 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c3 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c30 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c31 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c32 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c33 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c34 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c35 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c36 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c37 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c38 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c4 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c5 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c6 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c7 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c8 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
c9 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
cacheCov(double[][]) - Static method in class org.omegahat.GUtilities.Distance
 
cachedCovMat - Static variable in class org.omegahat.GUtilities.Distance
 
cachedInverse - Static variable in class org.omegahat.GUtilities.Distance
 
cachedIsLogProb - Variable in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
cachedIsLogProb() - Method in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
cachedMethod - Variable in class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
cachedMethod() - Method in class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
cachedMethod(Method) - Method in class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
cachedObject - Variable in class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
cachedObject() - Method in class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
cachedObject(Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
cacheIndex - Static variable in class org.omegahat.GUtilities.Distance
 
cacheLength - Static variable in class org.omegahat.GUtilities.Distance
 
CachingMethodCall - class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall.
 
CachingMethodCall(ExpressionInt, List) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
CachingMethodCall(ExpressionInt, String, List) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
CachingMethodCall(Name, List) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
CachingMethodCall(String, List) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
CachingMethodCall(String, String[]) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
CachingTarget - class org.omegahat.Simulation.MCMC.Targets.CachingTarget.
 
CachingTarget(UnnormalizedDensity) - Constructor for class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
CachingTarget(UnnormalizedDensity, int) - Constructor for class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
calls - Variable in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
cauchyCDF(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
cauchyPDF(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
cauchyQuantile(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
cauchyRand() - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
cc0 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
cc1 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
cc2 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
cc3 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
cdf(double) - Method in class org.omegahat.Probability.Distributions.Normal
 
cdf(double[]) - Method in class org.omegahat.Probability.Distributions.Normal
 
cdf(Object) - Method in class org.omegahat.Probability.Distributions.Normal
 
CDF(Object) - Method in interface org.omegahat.Probability.Distributions.CumulativeDensity
 
CDF(Object) - Method in class org.omegahat.Probability.Distributions.Normal
 
cdf(Object[]) - Method in class org.omegahat.Probability.Distributions.Normal
 
chain - Variable in class org.omegahat.Simulation.MCMC.GenericManagerChainEvent
 
checkConformity() - Method in class org.omegahat.Probability.Distributions.MVNormal
 
checkConformity(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
chisqCDF(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
chisqPDF(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
chisqQuantile(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
ppchi2.f -- translated by f2c and modified
chisqRand(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
chyper(boolean, int, int, int, int) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
This routine has problems.
close() - Method in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
close() - Method in class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter
 
close() - Method in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
close() - Method in class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
 
close() - Method in interface org.omegahat.Simulation.MCMC.Listeners.MCMCListenerWriter
Write out any cached state and then close the output stream.
close() - Method in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
close() - Method in class org.omegahat.Simulation.MCMC.Listeners.QuantileWriter
 
close() - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
close() - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
close() - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter
 
close() - Method in class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
COF1 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
COF2 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
COF3 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
COF4 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
COF5 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
COF6 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
CollingsPRNG - class org.omegahat.Simulation.RandomGenerators.CollingsPRNG.
provide a stream of pseudo-random numbers using Collings Parallel Pseudo Random Number Generator.
CollingsPRNG(int, int, int, int[], int[]) - Constructor for class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Instantiate from state details (needed for CORBA).
CollingsPRNG(PRNGState) - Constructor for class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
instantiate from a specified PRNGState
CollingsPRNGAdministrator - class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator.
creates instances of CollingsPRNG that are garanteed to be mutually independent
CollingsPRNGAdministrator() - Constructor for class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
Default Class Constructor
CollingsPRNGAdministrator(int) - Constructor for class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
Class constructer that allows specification of the seed used to intialize the state of the created PRNG's
CollingsPRNGAdministrator(int, int) - Constructor for class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
Class constructer that allows specification of the seed used to intialize the state of the created PRNG's, and the number of component generators used by each CollingsPRNG created.
CollingsPRNGAdministrator(int, int, int) - Constructor for class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
Class constructer that allows specification of the seed used to intialize the state of the created PRNG's, the number of component generators used by each CollingsPRNG created.
CollingsPRNGConstants - class org.omegahat.Simulation.RandomGenerators.CollingsPRNGConstants.
Contains all of the magic constants necessary to implement Bruce Collings' Pseudorandom Number Generator.
CollingsPRNGConstants() - Constructor for class org.omegahat.Simulation.RandomGenerators.CollingsPRNGConstants
 
CollingsPRNGState - class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState.
Encapsulates the state of a CollingsPRNG
CollingsPRNGState() - Constructor for class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
CollingsPRNGState(int[], int[]) - Constructor for class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
command - Variable in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
command() - Method in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
common(Object, boolean) - Method in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
ComponentMult - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Multiplicative constants for component generators
ComponentMult - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
Multiplier constant for component generators
componentMultiply(double[][], double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
ComponentSeed - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Seeds for component generators
ComponentSeed - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
Seed for component generators
computeDistances(int, int) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
computeEdgePoints(double[], double[], double[], double[]) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
computeFullConditionalExpressions() - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGibbsSampler
; Parse the model specification and create expressions that will compute the full conditional distribution of each component.
computeLikelihood() - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
computeLog(double[][], double, double, double, double) - Method in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalLikelihood
 
computeMinMaxRange() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
computeOptimalAdjust(int, int) - Static method in class org.omegahat.Simulation.MCMC.Proposals.NormalDualKernelProposal
 
computeOptimalAdjust(int, int) - Static method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
computeOptimalAdjust(int, int) - Static method in class org.omegahat.Simulation.MCMC.Proposals.NormalKernelProposal
 
computeOptimalAdjust(int, int) - Static method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalDualKernelProposal
 
computeProposal() - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
computeTerrellAdjust(int, int) - Static method in class org.omegahat.Simulation.MCMC.Proposals.NormalKernelProposal
 
computeWeights(double[][], MultiState, int) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
ConditionalDensity - interface org.omegahat.Probability.Distributions.ConditionalDensity.
 
conditionalDistance() - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
ConditionalDistanceWriter - class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter.
 
ConditionalDistanceWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
ConditionalDistanceWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
ConditionalDistanceWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
ConditionalDistanceWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
ConditionalGenerator - interface org.omegahat.Probability.Distributions.ConditionalGenerator.
 
conditionalPDF(Object, Object) - Method in interface org.omegahat.Probability.Distributions.ConditionalDensity
 
conditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
conditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
conditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
 
conditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalProposal
 
conditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
conditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisProposal
 
conditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
conditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveKernelProposal
 
conditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
conditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
conditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
conditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
conditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
conditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
conditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
conditionalPDF(Object, Object, int, MultiState) - Method in interface org.omegahat.Simulation.MCMC.HastingsCoupledProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
ConditionalSquaredDistanceWriter - class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter.
 
ConditionalSquaredDistanceWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
ConditionalSquaredDistanceWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
ConditionalSquaredDistanceWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
ConditionalSquaredDistanceWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
ContainerState - class org.omegahat.Simulation.MCMC.ContainerState.
A generic MCMCState that can hold arbitrary Objects
ContainerState(Object) - Constructor for class org.omegahat.Simulation.MCMC.ContainerState
 
contents - Variable in class org.omegahat.Simulation.MCMC.ContainerState
 
contents - Variable in class org.omegahat.Simulation.MCMC.MultiState
 
Continuous - interface Continuous.
 
copy() - Method in class org.omegahat.Simulation.MCMC.MultiState
creat a new MultiState object by copying the contents of this one.
copy() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
creat a new MultiState object by copying the contents of this one.
copyFromTo(MultiDoubleState, MultiDoubleState) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
copyFromTo(MultiState, MultiDoubleState) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
copyTo(MultiState) - Method in class org.omegahat.Simulation.MCMC.MultiState
 
correctedVar() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
This function checks if the number of component states used to estimate the covariance matrix is less than or equal to the number of dimensions.
counter - Variable in class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener
 
counter - Variable in class org.omegahat.Simulation.MCMC.Listeners.StepListenerPrinter
 
CovarianceListener - class org.omegahat.Simulation.MCMC.Listeners.CovarianceListener.
 
CovarianceListener() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.CovarianceListener
 
CovarianceWriter - class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter.
 
CovarianceWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter
 
CovarianceWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter
 
CovarianceWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter
 
CovarianceWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter
 
covCacheMat - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
covKey - Static variable in class org.omegahat.GUtilities.Distance
 
createAndAttachDatabases(Database, Database) - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
createDatabase(String) - Method in class org.omegahat.Simulation.MCMC.MCMCStateDatabase
 
createDatabase(String, boolean) - Method in class org.omegahat.Simulation.MCMC.MCMCStateDatabase
Create a new database using another as a template.
createDatabase(String, Database, boolean) - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
; Create a new database using another as a template.
createExpressions() - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget
 
createLikelihood(MultiLineModelFormula) - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
createPath(MCMCStateDatabase) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
cumarray() - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
cumData - Variable in class org.omegahat.Simulation.MCMC.Listeners.CovarianceListener
 
cumExpectedAcceptance - Variable in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
cumExpectedDistance - Variable in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
cummat - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState.CovAccumulator
 
cumsum - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState.CovAccumulator
 
cumsum - Variable in class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
cumsum - Variable in class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
cumsum - Variable in class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
cumsum() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
cumsum(double[]) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
Compute accumulated sums
cumsumAccepted - Variable in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
cumsumAll - Variable in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
cumsums - Variable in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
cumSumSqr() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
cumSumSqr(MultiDoubleState.CovAccumulator) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
cumSumSqrSubset(int[]) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
cumSumSqrSubsetCache(int, int[]) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
cumulative_probs - Variable in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
cumulative_probs - Variable in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
CumulativeConditionalDensity - interface org.omegahat.Probability.Distributions.CumulativeConditionalDensity.
 
cumulativeConditionalDensity(Object, Object) - Method in interface org.omegahat.Probability.Distributions.CumulativeConditionalDensity
 
CumulativeDensity - interface org.omegahat.Probability.Distributions.CumulativeDensity.
 
current - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
current - Variable in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
current - Variable in class org.omegahat.Simulation.MCMC.GenericChainStepEvent
 
CURRENT - Static variable in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
current() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
currentComponent - Variable in class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
 
currentCount - Variable in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
currentCount - Variable in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
currentProposal - Variable in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
currentProposal - Variable in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
CustomGibbsSampler - class org.omegahat.Simulation.MCMC.CustomGibbsSampler.
A Gibbs Sampler that uses an internal FullConditionalProposal to generate the next Markov state.
CustomGibbsSampler.listenerPrinter - class org.omegahat.Simulation.MCMC.CustomGibbsSampler.listenerPrinter.
 
CustomGibbsSampler.listenerPrinter() - Constructor for class org.omegahat.Simulation.MCMC.CustomGibbsSampler.listenerPrinter
 
CustomGibbsSampler.NormalGenerator - class org.omegahat.Simulation.MCMC.CustomGibbsSampler.NormalGenerator.
 
CustomGibbsSampler.NormalGenerator(PRNG) - Constructor for class org.omegahat.Simulation.MCMC.CustomGibbsSampler.NormalGenerator
 
CustomGibbsSampler(ContainerState, FullConditionalProposal) - Constructor for class org.omegahat.Simulation.MCMC.CustomGibbsSampler
 
CustomGibbsSampler(Object, FullConditionalProposal) - Constructor for class org.omegahat.Simulation.MCMC.CustomGibbsSampler
 
CustomHastingsCoupledSampler - class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler.
A Hastings Coupled Sampler that consistes of $C$ component samplers.
CustomHastingsCoupledSampler(MultiState, int, UnnormalizedDensity, HastingsCoupledProposal, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
CustomHastingsCoupledSampler(MultiState, int, UnnormalizedDensity, HastingsCoupledProposal, PRNG, boolean) - Constructor for class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
CustomMarkovChain - class org.omegahat.Simulation.MCMC.CustomMarkovChain.
Markov Chain that uses an internal MarkovProposal to generate the next Markov state.
CustomMarkovChain.listenerPrinter - class org.omegahat.Simulation.MCMC.CustomMarkovChain.listenerPrinter.
 
CustomMarkovChain.listenerPrinter() - Constructor for class org.omegahat.Simulation.MCMC.CustomMarkovChain.listenerPrinter
 
CustomMarkovChain.NormalGenerator - class org.omegahat.Simulation.MCMC.CustomMarkovChain.NormalGenerator.
 
CustomMarkovChain.NormalGenerator(PRNG) - Constructor for class org.omegahat.Simulation.MCMC.CustomMarkovChain.NormalGenerator
 
CustomMarkovChain() - Constructor for class org.omegahat.Simulation.MCMC.CustomMarkovChain
 
CustomMarkovChain(ContainerState, MarkovProposal) - Constructor for class org.omegahat.Simulation.MCMC.CustomMarkovChain
 
CustomMarkovChain(Object, MarkovProposal) - Constructor for class org.omegahat.Simulation.MCMC.CustomMarkovChain
 
CustomMetropolisHastingsSampler - class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler.
A Markov Sampler that uses an internal GenericProposal and UnnormalizedDensity to generate the next Markov state.
CustomMetropolisHastingsSampler() - Constructor for class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
CustomMetropolisHastingsSampler(ContainerState, UnnormalizedDensity, GeneralProposal, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
Generate GenericChainStepEvents at each step
CustomMetropolisHastingsSampler(ContainerState, UnnormalizedDensity, GeneralProposal, PRNG, boolean) - Constructor for class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
Default constructor
CustomMetropolisHastingsSampler(Object, UnnormalizedDensity, GeneralProposal, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
Generate GenericChainStepEvents at each step
CustomMetropolisHastingsSampler(Object, UnnormalizedDensity, GeneralProposal, PRNG, boolean) - Constructor for class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
CustomMetropolisSampler - class org.omegahat.Simulation.MCMC.CustomMetropolisSampler.
A Markov Sampler that uses an internal SymmetricProposal and UnnormalizedDensity to generate the next Markov state.
CustomMetropolisSampler(ContainerState, UnnormalizedDensity, SymmetricProposal, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.CustomMetropolisSampler
 
CustomMetropolisSampler(Object, UnnormalizedDensity, SymmetricProposal, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.CustomMetropolisSampler
 

D

d1 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
d2 - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
data - Variable in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
data - Variable in class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener
 
data() - Method in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
data() - Method in class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener
 
data(int) - Method in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
data(Vector) - Method in class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener
 
databases(Database[]) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionModel
 
databases(Database[]) - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
dataLength - Variable in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood
 
dataLength - Variable in class org.omegahat.Simulation.MCMC.Examples.Binomial_Binomial_Likelihood
 
dataLength - Variable in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
dataN - Variable in class org.omegahat.Simulation.MCMC.Examples.Binomial_Binomial_Likelihood
 
dataN - Variable in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
dataX - Variable in class org.omegahat.Simulation.MCMC.Examples.Binomial_Binomial_Likelihood
 
dataX - Variable in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
dB_B(int[], int[], double, double, double) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_Binomial_Likelihood
 
dB(int, int, double) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_Binomial_Likelihood
 
debug - Variable in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
debug - Variable in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
debug - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
debug - Variable in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGibbsSampler
 
debug - Variable in class org.omegahat.Simulation.MCMC.Expressions.ExpressionMarkovProposal
 
debug - Variable in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
debug - Variable in class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener
 
debug - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
if true, show debugging messages
DEBUG - Variable in class org.omegahat.Probability.Distributions.MVNormal
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveKernelProposal
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalProposal
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.NormalProposal
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisProposal
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
DEBUG - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
debug() - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGibbsSampler
 
debug() - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionMarkovProposal
 
debug() - Method in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
debug() - Method in class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener
 
debug(boolean) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGibbsSampler
 
debug(boolean) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionMarkovProposal
 
debug(boolean) - Method in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
debug(boolean) - Method in class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener
 
DefaultPRNGFactory - class org.omegahat.Simulation.RandomGenerators.DefaultPRNGFactory.
a factory class to create PRNG's from PRNGStates.
DefaultPRNGFactory() - Constructor for class org.omegahat.Simulation.RandomGenerators.DefaultPRNGFactory
 
definitions - Variable in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
delta - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
delta - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
Density - interface org.omegahat.Probability.Distributions.Density.
 
density(double) - Method in class org.omegahat.Probability.Distributions.Normal
 
density(double[]) - Method in class org.omegahat.Probability.Distributions.Normal
 
density(double[]) - Method in class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
density(Object) - Method in class org.omegahat.Probability.Distributions.Normal
 
density(Object[]) - Method in class org.omegahat.Probability.Distributions.Normal
 
description - Variable in class org.omegahat.Simulation.MCMC.GenericMCMCEvent
 
DetailChainStepEvent - class org.omegahat.Simulation.MCMC.DetailChainStepEvent.
 
DetailChainStepEvent() - Constructor for class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
DetailChainStepEvent(Object, MCMCState, MCMCState, MCMCState, double, double, double, double, double, double, boolean, double) - Constructor for class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
detailed - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
detailed - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
detailed() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
detailed(boolean) - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
DetailedMultiState - class org.omegahat.Simulation.MCMC.DetailedMultiState.
MCMCState that can hold several individual states.
DetailedMultiState() - Constructor for class org.omegahat.Simulation.MCMC.DetailedMultiState
 
DetailedMultiState(int) - Constructor for class org.omegahat.Simulation.MCMC.DetailedMultiState
 
DetailedMultiState(int, Object) - Constructor for class org.omegahat.Simulation.MCMC.DetailedMultiState
 
DetailHastingsCoupledStepEvent - class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent.
 
DetailHastingsCoupledStepEvent() - Constructor for class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
only for inheriting classes
DetailHastingsCoupledStepEvent(Object, MCMCState, MCMCState, MCMCState, double, double, double, double, double, double, boolean, double, int, int[], int, Object, Object, Object) - Constructor for class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
 
diagVar() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
Compute the diagonal of the covariance matrix
dim - Variable in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
 
dim - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState.CovAccumulator
 
dim() - Method in class org.omegahat.Probability.Distributions.MVNormal
 
dim() - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalDualKernelProposal
 
dim() - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalKernelProposal
 
dim() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalDualKernelProposal
 
dirichletPDF(double[], double[]) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
dirichletRand(double[]) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
Discrete - interface Discrete.
 
Distance - class org.omegahat.GUtilities.Distance.
 
Distance() - Constructor for class org.omegahat.GUtilities.Distance
 
distance(int, int, int) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
distanceCache(int, int, int) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
distanceCacheMat - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
DistanceListener - class org.omegahat.Simulation.MCMC.Listeners.DistanceListener.
 
DistanceListener() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
DistanceWriter - class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter.
 
DistanceWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter
 
DistanceWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter
 
DistanceWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter
 
DistanceWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter
 
Distribution - interface org.omegahat.Probability.Distributions.Distribution.
 
DistributionFunctions - class org.omegahat.Probability.Distributions.DistributionFunctions.
(C) Copyright B.
DistributionFunctions() - Constructor for class org.omegahat.Probability.Distributions.DistributionFunctions
 
dnorm(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
doParsing() - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
doString(Object) - Method in class org.omegahat.Simulation.MCMC.Listeners.StepListenerPrinter
 
doString(Object) - Method in class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerWriter
 
dToD(double[]) - Static method in class org.omegahat.GUtilities.ArrayTools
 
Dtod(Double[]) - Static method in class org.omegahat.GUtilities.ArrayTools
 
dualKernel - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalDualKernelProposal
 

E

e - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
elementName(String) - Method in class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
environment - Variable in class org.omegahat.Simulation.MCMC.Expressions.ExpressionModel
 
EPSILON - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
EPSILON - Static variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
Euclidean - Static variable in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
euclidean_2(double[], double[]) - Static method in class org.omegahat.GUtilities.Distance
squared euclidean distance
euclidean(double[], double[]) - Static method in class org.omegahat.GUtilities.Distance
euclidean distance
event - Variable in class org.omegahat.Simulation.MCMC.GenericManagerChainEvent
Which chain generated the event
ExpandingPlottingListener - class org.omegahat.Simulation.MCMC.Listeners.ExpandingPlottingListener.
Displays contents and counter of RecordingStepEvents when one is recieved.
ExpandingPlottingListener(String[]) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ExpandingPlottingListener
 
ExpandingPlottingListener(String[], int, int) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ExpandingPlottingListener
 
expectedAcceptance() - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
expectedDistance() - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
exponentialRand() - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Inverse CDF method for generating exponential( 1 ) random number.
exponentialRand(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Inverse CDF method for generating exponential( beta ) random number.
ExpressionGeneralProposal - class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal.
 
ExpressionGeneralProposal(MultiLineModelFormula, Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
ExpressionGeneralProposal(String[], Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
ExpressionGeneralProposal(String, Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
ExpressionGibbsSampler - class org.omegahat.Simulation.MCMC.Expressions.ExpressionGibbsSampler.
; A placeholder for a Gibbs Sampler based on a specified model expression.
ExpressionGibbsSampler(MultiLineModelFormula, Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionGibbsSampler
 
ExpressionGibbsSampler(String[], Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionGibbsSampler
 
ExpressionGibbsSampler(String, Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionGibbsSampler
 
ExpressionMarkovProposal - class org.omegahat.Simulation.MCMC.Expressions.ExpressionMarkovProposal.
 
ExpressionMarkovProposal(MultiLineModelFormula, Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionMarkovProposal
 
ExpressionMarkovProposal(String[], Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionMarkovProposal
 
ExpressionMarkovProposal(String, Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionMarkovProposal
 
ExpressionModel - class org.omegahat.Simulation.MCMC.Expressions.ExpressionModel.
 
ExpressionModel(MultiLineModelFormula, Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionModel
 
ExpressionModel(String[], Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionModel
 
ExpressionModel(String, Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionModel
 
expressions - Variable in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGibbsSampler
 
expressions - Variable in class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget
 
expressions() - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget
 
expressions(List) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget
 
ExpressionTarget - class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget.
 
ExpressionTarget(MultiLineModelFormula, Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget
 
ExpressionTarget(String[], Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget
 
ExpressionTarget(String, Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget
 

F

factoryName - Variable in class org.omegahat.Simulation.RandomGenerators.TestServer
 
fCDF(double, double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
finalize() - Method in class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
Closes the stream when garbage is collected.
findClosest(int, int, int) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
Find closest howmany points to state which using distance method .
findEvalMethod(List, Object, Evaluator, boolean) - Method in class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
five - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
flush() - Method in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
flush() - Method in class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter
 
flush() - Method in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
flush() - Method in class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
 
flush() - Method in interface org.omegahat.Simulation.MCMC.Listeners.MCMCListenerWriter
Write out any cached state
flush() - Method in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
flush() - Method in class org.omegahat.Simulation.MCMC.Listeners.QuantileWriter
 
flush() - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
flush() - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
flush() - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter
 
flush() - Method in class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
flush(double) - Method in class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter
 
flush(double) - Method in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
flush(double) - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
flush(double) - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
flush(double) - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter
 
flush(double) - Method in class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
forwardProb - Variable in class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
four - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
fPDF(double, double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
fQuantile(double, double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
fRand(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
frequency() - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
fromDouble(double) - Static method in class org.omegahat.Simulation.RandomGenerators.Unsigned
Convert a double to an int (treated as unsigned) Note that in the current implementation, long negative values are converted unchanged.
fromLong(long) - Static method in class org.omegahat.Simulation.RandomGenerators.Unsigned
Convert a long to an int (treated as unsigned) Note that in the current implementation, long negative values are converted unchanged.
fToF(float[]) - Static method in class org.omegahat.GUtilities.ArrayTools
 
Ftof(Float[]) - Static method in class org.omegahat.GUtilities.ArrayTools
 
FullConditionalProposal - interface org.omegahat.Simulation.MCMC.FullConditionalProposal.
A full conditional proposal generates the new state using each component's conditional distribution given all other components.

G

gammaCDF(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
gammaPDF(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
gammaQuantile(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
gammaRand(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
gcf(double, double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
compute complementary gamma cdf by its continued fraction expansion
GeneralProposal - interface org.omegahat.Simulation.MCMC.GeneralProposal.
A General proposal distribution generates generates the next state using function of the current state.
generate() - Method in interface org.omegahat.Probability.Distributions.Generator
 
generate() - Method in class org.omegahat.Probability.Distributions.Normal
 
generate() - Method in class org.omegahat.Probability.Distributions.MVNormal
 
generate(double[], double[]) - Method in class org.omegahat.Probability.Distributions.Normal
 
generate(double, double) - Method in class org.omegahat.Probability.Distributions.Normal
 
generate(MCMCState) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
generate(MCMCState) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler
 
generate(MCMCState) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
generate(MCMCState) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain
 
generate(MCMCState) - Method in class org.omegahat.Simulation.MCMC.BaseMarkovChain
Generate the next state from the current one
generate(MCMCState) - Method in class org.omegahat.Simulation.MCMC.CustomMarkovChain
Generate the next state from the current one.
generate(MCMCState) - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
Generate the next state from the current one.
generate(MCMCState) - Method in class org.omegahat.Simulation.MCMC.NotifyingMCMCObject
Generate the next state from the current one
generate(MultiState) - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
generate(Object) - Method in interface org.omegahat.Probability.Distributions.ConditionalGenerator
Generate a single random value conditional on conditionals
generate(Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
generate(Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
generate(Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.IndependenceMultiProposal
 
generate(Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
 
generate(Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalProposal
 
generate(Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
generate(Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisProposal
 
generate(Object) - Method in class org.omegahat.Simulation.MCMC.CustomGibbsSampler.NormalGenerator
 
generate(Object) - Method in class org.omegahat.Simulation.MCMC.CustomMarkovChain.NormalGenerator
 
generate(Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGibbsSampler
 
generate(Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionMarkovProposal
 
generate(Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveKernelProposal
Generate a new component state given the entire state vector
generate(Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
generate(Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveProposal
Generate a new component state given the entire state vector
generate(Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
Generate a new component state given the entire state vector
generate(Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
Generate a new component state given the entire state vector
generate(Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
Generate a new component state given the entire state vector
generate(Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
generate(Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
generate(Object, int, MultiState) - Method in interface org.omegahat.Simulation.MCMC.HastingsCoupledProposal
Generate a new component state given the entire state vector
generateDouble() - Method in class org.omegahat.Probability.Distributions.Normal
 
generateDouble(int) - Method in class org.omegahat.Probability.Distributions.Normal
 
generateDoubleArray() - Method in class org.omegahat.Probability.Distributions.MVNormal
 
generateObject() - Method in class org.omegahat.Probability.Distributions.Normal
 
generateObject(int) - Method in class org.omegahat.Probability.Distributions.Normal
 
generateSample(double[], double[], double[], double[]) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
generateSeveral(int) - Method in interface org.omegahat.Probability.Distributions.Generator
 
generateSeveral(int) - Method in class org.omegahat.Probability.Distributions.Normal
 
generateSeveral(int) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
generateSeveral(int, Object[]) - Method in class org.omegahat.Simulation.MCMC.CustomGibbsSampler.NormalGenerator
 
generateSeveral(int, Object[]) - Method in class org.omegahat.Simulation.MCMC.CustomMarkovChain.NormalGenerator
 
generator - Variable in class org.omegahat.Simulation.MCMC.CustomMarkovChain
 
Generator - interface org.omegahat.Probability.Distributions.Generator.
 
generator() - Method in interface org.omegahat.Simulation.RandomGenerators.PseudoRandomVariableGenerator
 
GenericChainEvent - class org.omegahat.Simulation.MCMC.GenericChainEvent.
 
GenericChainEvent() - Constructor for class org.omegahat.Simulation.MCMC.GenericChainEvent
 
GenericChainStepEvent - class org.omegahat.Simulation.MCMC.GenericChainStepEvent.
 
GenericChainStepEvent() - Constructor for class org.omegahat.Simulation.MCMC.GenericChainStepEvent
 
GenericChainStepEvent(Object, MCMCState) - Constructor for class org.omegahat.Simulation.MCMC.GenericChainStepEvent
 
GenericListenerHandle - class org.omegahat.Simulation.MCMC.GenericListenerHandle.
 
GenericListenerHandle() - Constructor for class org.omegahat.Simulation.MCMC.GenericListenerHandle
 
GenericManagerChainEvent - class org.omegahat.Simulation.MCMC.GenericManagerChainEvent.
 
GenericManagerChainEvent() - Constructor for class org.omegahat.Simulation.MCMC.GenericManagerChainEvent
Default constructor
GenericManagerChainEvent(Object, int, GenericChainEvent) - Constructor for class org.omegahat.Simulation.MCMC.GenericManagerChainEvent
Construct with all details
GenericManagerEvent - class org.omegahat.Simulation.MCMC.GenericManagerEvent.
 
GenericManagerEvent() - Constructor for class org.omegahat.Simulation.MCMC.GenericManagerEvent
 
GenericMCMCEvent - class org.omegahat.Simulation.MCMC.GenericMCMCEvent.
 
GenericMCMCEvent() - Constructor for class org.omegahat.Simulation.MCMC.GenericMCMCEvent
Default constructor
GenericMCMCEvent(Object, String) - Constructor for class org.omegahat.Simulation.MCMC.GenericMCMCEvent
Construct with all details
geometricCDF(int, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
geometricPMF(int, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
geometricQuantile(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
geometricRand_beta - Variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
geometricRand_last_p - Variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
geometricRand(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Generate a geometric random value with trial probability p.
get() - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
get(int) - Method in class org.omegahat.Simulation.MCMC.MultiState
 
getAcceptanceRate() - Method in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
getAdminName() - Method in class org.omegahat.Simulation.RandomGenerators.TestServer
 
getChain() - Method in class org.omegahat.Simulation.MCMC.GenericManagerChainEvent
The event that was generated
getComponentMult() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
getComponentSeed() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
getContents() - Method in class org.omegahat.Simulation.MCMC.ContainerState
 
getCovariance() - Method in class org.omegahat.Probability.Distributions.MVNormal
 
getCovariance() - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalKernelProposal
 
getCovariance() - Method in class org.omegahat.Simulation.MCMC.Listeners.CovarianceListener
 
getCurrent() - Method in class org.omegahat.Simulation.MCMC.GenericChainStepEvent
 
getCurrent() - Method in class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
 
getDataN() - Method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
getDataX() - Method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
getDEBUG() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
getDEBUG() - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
getDEBUG() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
getDEBUG() - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
getDescription() - Method in class org.omegahat.Simulation.MCMC.GenericMCMCEvent
 
getDescription() - Method in interface org.omegahat.Simulation.MCMC.MCMCEvent
 
getDistanceMethod() - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
getDistanceMethod() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
getDistanceMethod() - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
getDoubleEpsilon() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
 
getDoubleEpsilon() - Method in interface org.omegahat.Simulation.RandomGenerators.PRNG
Return the minimum possible difference between two generated double's.
getEvent() - Method in class org.omegahat.Simulation.MCMC.GenericManagerChainEvent
 
getFactoryName() - Method in class org.omegahat.Simulation.RandomGenerators.TestServer
 
getInflationFactor() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
getInflationFactor() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalProposal
 
getInflationFactor() - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
getInflationFactor() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
 
getInflationFactor() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
getInflationFactor() - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
getInputFile() - Method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
getIntegerState() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
getIntegerState() - Method in interface org.omegahat.Simulation.RandomGenerators.PRNGIntegerState
Return an array of ints that fully captures the state of the PRNG represented by this PRNGState.
getIntegerStateHash() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
getIntegerStateHash() - Method in interface org.omegahat.Simulation.RandomGenerators.PRNGIntegerState
Return the hash value for the state of the PRNG represented by this PRNGState.
getIntRange() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
 
getIntRange() - Method in interface org.omegahat.Simulation.RandomGenerators.PRNG
Return the largest int value returned by nextInt<\b>.
getKernel() - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
 
getKernels() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
 
getMaxVals() - Method in class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledSampler
 
getMean() - Method in class org.omegahat.Probability.Distributions.Normal
 
getMean() - Method in class org.omegahat.Probability.Distributions.MVNormal
 
getMean() - Method in interface org.omegahat.Simulation.RandomGenerators.PseudoRandomNormalGenerator
 
getMinVals() - Method in class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledSampler
 
getMixerMult() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
getMixerSeed() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
getMult() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
getMVNorm0() - Method in class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
getMVNorm1() - Method in class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
getNumAccepted() - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
getNumGen() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
getNumGen() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
getNumPoints() - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
getNumProposed() - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
getNumSamplers() - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
getOptimalAdjust() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
getParameterNames() - Method in class org.omegahat.Probability.Distributions.Normal
 
getParameters() - Method in class org.omegahat.Probability.Distributions.Normal
 
getPRNG() - Method in class org.omegahat.Probability.Distributions.PRNGDistributionFunctions
Acessors
getPRNG() - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
 
getPRNG() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
 
getPRNG() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
getPRNGName() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
Returns the name of the class that can be enstantiated from this state.
getPRNGName() - Method in interface org.omegahat.Simulation.RandomGenerators.PRNGState
Return the name of the class that can be enstantiated from this state.
getProposal() - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveProposal
 
getProposal() - Method in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
 
getProposal() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
getProposal() - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
getProposalProbs() - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
getProposalProbs() - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
getProposals() - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
getProposals() - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
getProposalVar() - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
getProposalVar(double[][]) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
getSeed() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
getSource() - Method in class org.omegahat.Simulation.MCMC.GenericMCMCEvent
 
getSource() - Method in interface org.omegahat.Simulation.MCMC.MCMCEvent
 
getStandardDeviation() - Method in class org.omegahat.Probability.Distributions.Normal
 
getState() - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler.BivariateDoubleState
 
getState() - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler.BivariateDoubleState
 
getState() - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler.BivariateDoubleState
 
getState() - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain.doubleState
 
getState() - Method in class org.omegahat.Simulation.MCMC.BaseMarkovChain
Get the current state of the Markov Chain.
getState() - Method in interface org.omegahat.Simulation.MCMC.MarkovChain
Get the current state of the Markov Chain.
getState() - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
getState() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
 
getState() - Method in interface org.omegahat.Simulation.RandomGenerators.PRNG
Return an object describing the state of the PRNG.
getTarget() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
getTarget() - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
getThinningFactor() - Method in class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
getTime() - Method in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
getTime() - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
Get the time
getTime() - Method in interface org.omegahat.Simulation.MCMC.Proposals.TimeDependentProposal
Get the time
getTime() - Method in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
 
getTime() - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
getTime() - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
getTotalEvents() - Method in class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
getUpperWeight() - Method in class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
getVariance() - Method in class org.omegahat.Probability.Distributions.Normal
 
getVariance() - Method in interface org.omegahat.Simulation.RandomGenerators.PseudoRandomNormalGenerator
 
GibbsSampler - interface org.omegahat.Simulation.MCMC.GibbsSampler.
A Gibbs sampler.
gnorm(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Compute gamma cdf by a normal approximation
gser(double, double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
compute gamma cdf by its series representation

H

half - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
HALF_PI - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
hashEquals(int[], int[]) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
HastingsCoupledIteratedProposal - class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal.
 
HastingsCoupledIteratedProposal(HastingsCoupledProposal[], int[]) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
HastingsCoupledIteratedProposal(int) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
HastingsCoupledMixtureProposal - class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal.
 
HastingsCoupledMixtureProposal(HastingsCoupledProposal[], double[], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
HastingsCoupledMixtureProposal(int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
HastingsCoupledProposal - interface org.omegahat.Simulation.MCMC.HastingsCoupledProposal.
This class extends the GeneralProposal interface by adding methods appropriate for generating states for a HastingsCoupledSampler.
HastingsCoupledSampler - interface org.omegahat.Simulation.MCMC.HastingsCoupledSampler.
This file defines an 'marker' interface for a Hastings Coupled Sampler that consistes of $C$ component samplers.
HeavyAndLight_Example_NKC - class org.omegahat.Simulation.MCMC.Examples.HeavyAndLight_Example_NKC.
 
HeavyAndLight_Example_NKC() - Constructor for class org.omegahat.Simulation.MCMC.Examples.HeavyAndLight_Example_NKC
 
histData - Variable in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
Histogram - class org.omegahat.Simulation.MCMC.Listeners.Histogram.
 
Histogram(double[], int) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
Histogram(double, double, double) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
histogram(double, double, int) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
Histogram(double, double, int) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
histogram(Histogram[]) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
HistogramWriter - class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter.
 
HistogramWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
HistogramWriter(String, boolean, boolean, double, double, int) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
HistogramWriter(String, boolean, double, double, int) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
HistogramWriter(String, double, double, int) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
hists - Variable in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
howmany - Variable in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
howmany() - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
hypergeometricCDF(int, int, int, int) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
hypergeometricPMF(int, int, int, int) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 

I

identifier() - Method in class org.omegahat.Probability.Distributions.Normal
 
ignoreRangeErrors - Static variable in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
in - Variable in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
IndependenceMultiProposal - class org.omegahat.Simulation.MCMC.Proposals.IndependenceMultiProposal.
 
IndependenceMultiProposal(GeneralProposal[]) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.IndependenceMultiProposal
 
IndependenceMultiProposal(int) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.IndependenceMultiProposal
 
IndependenceMultiProposal(int, GeneralProposal) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.IndependenceMultiProposal
 
IndependenceProposal - interface org.omegahat.Simulation.MCMC.Proposals.IndependenceProposal.
An independence Markov proposal generates a new state using a distribution that does not depend on the current state.
IndependentHastingsCoupledProposal - class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal.
This class implements an Hastings-Coupled proposal that generates states independently using a common GeneralProposal.
IndependentHastingsCoupledProposal(GeneralProposal) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
 
index - Variable in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
index - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
index - Variable in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
inflationFactor - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
inflationFactor - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalProposal
 
inflationFactor - Variable in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
inflationFactor - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
 
inflationFactor - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
inflationFactor - Variable in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
initCorba() - Method in class org.omegahat.Simulation.RandomGenerators.TestServer
 
initialize() - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
inputFile - Variable in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
instantiate(PRNGState) - Method in class org.omegahat.Simulation.RandomGenerators.DefaultPRNGFactory
Instantiate a PRNG of the correct class
instantiate(PRNGState) - Method in interface org.omegahat.Simulation.RandomGenerators.PRNGFactory
Instantiate a PRNG of the correct class
inT - Variable in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
integerState - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
integerStateHash - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
invalidateCache() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
invalidateCache(int) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
invCache - Static variable in class org.omegahat.GUtilities.Distance
 
isDiagonalCov - Variable in class org.omegahat.Probability.Distributions.MVNormal
 
isOnLine(double[], double[], double[]) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
isValid(Object) - Method in class org.omegahat.Probability.Distributions.Normal
 
isValid(Object[]) - Method in class org.omegahat.Probability.Distributions.Normal
 
iterate(int) - Method in class org.omegahat.Simulation.MCMC.BaseMarkovChain
Perform several steps.
iterate(int) - Method in interface org.omegahat.Simulation.MCMC.MarkovChain
Perform several steps.
iterate(int) - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
IteratedProposal - class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal.
 
IteratedProposal(GeneralProposal[], int[]) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
IteratedProposal(int) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
ITMAX - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
iToI(int[]) - Static method in class org.omegahat.GUtilities.ArrayTools
 
Itoi(Integer[]) - Static method in class org.omegahat.GUtilities.ArrayTools
 

K

kernel - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
 
KernelDirectionSampler - class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler.
 
KernelDirectionSampler(int, double[][], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
KernelProposal - class org.omegahat.Simulation.MCMC.Proposals.KernelProposal.
 
KernelProposal() - Constructor for class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
 
KernelProposal(GeneralProposal, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
 
KernelProposal(PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
 
kernels - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
 

L

LARGE_A - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
last - Variable in class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
lastComponent - Variable in class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
 
lastProb - Variable in class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
LC - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
Multiplicative Congruential Generator used by the administrator to select constants and seeds for the created CollingsPRNG's.
lchoose(int, int) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
lgamma(double) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
lgamma(int) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
LHSarguments - Variable in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
likelihood - Variable in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
likelihood() - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
likelihood(List) - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
likelihoodModel - Variable in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
likelihoodModel() - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
likelihoodModel(MultiLineModelFormula) - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
ListenerGzipWriter - class org.omegahat.Simulation.MCMC.Listeners.ListenerGzipWriter.
 
ListenerGzipWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ListenerGzipWriter
 
ListenerGzipWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ListenerGzipWriter
 
ListenerGzipWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ListenerGzipWriter
 
ListenerPrinter - class org.omegahat.Simulation.MCMC.Listeners.ListenerPrinter.
 
ListenerPrinter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ListenerPrinter
 
listeners - Variable in class org.omegahat.Simulation.MCMC.NotifyingMCMCObject
 
listeners - Variable in class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
listeners - Variable in class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener
 
listeners - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
listeners - Variable in class org.omegahat.Simulation.RandomGenerators.NotifyingPRNG
 
listeners() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
listeners() - Method in class org.omegahat.Simulation.RandomGenerators.NotifyingPRNG
 
listeners(Vector) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
listeners(Vector) - Method in class org.omegahat.Simulation.RandomGenerators.NotifyingPRNG
 
ListenerWriter - class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter.
 
ListenerWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
 
ListenerWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
 
ListenerWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
 
ListenerWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
 
lngamma(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Log gamma function from Numerical Recipes
LocallyAdaptiveNormalKernelProposal - class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal.
 
LocallyAdaptiveNormalKernelProposal(int, int, double[][], double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
Constructor for normal increments with specified covariance matrix.
LocallyAdaptiveNormalKernelProposal(int, int, double[][], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
Constructor for normal increment proposal with specified covariance matrix, no variance inflation
LocallyAdaptiveNormalKernelProposal(int, int, int, double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
Constructor for a spherical independent standard normal increments
LocallyAdaptiveNormalKernelProposal(int, int, int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
Constructor for a sperical independent standard normal increments No variance inflation.
LocallyAdaptiveNormalProposal - class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal.
 
LocallyAdaptiveNormalProposal(int, int, double[][], double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
Constructor for normal increments with specified covariance matrix.
LocallyAdaptiveNormalProposal(int, int, double[][], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
Constructor for normal increment proposal with specified covariance matrix, no variance inflation
LocallyAdaptiveNormalProposal(int, int, int, double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
Constructor for a spherical independent standard normal increments
LocallyAdaptiveNormalProposal(int, int, int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
Constructor for a sperical independent standard normal increments No variance inflation.
log_dnorm(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
log_mixture_binom_beta_binom(int, int, double, double, double, double) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
log_normalizing_constant - Variable in class org.omegahat.Probability.Distributions.MVNormal
 
log_p_X - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
log_p_X - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
log_p_X() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
log_p_Y - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
log_p_Y - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
log_p_Y() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
log_q_X_to_Y - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
log_q_X_to_Y - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
log_q_X_to_Y() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
log_q_Y_to_X - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
log_q_Y_to_X - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
log_q_Y_to_X() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
logAcceptanceProb(Object, MultiState, Object, MultiState, int) - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
logAcceptanceProb(Object, MultiState, Object, MultiState, int) - Method in class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledSampler
 
logAcceptanceProb(Object, MultiState, Object, MultiState, int) - Method in class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledMaximizer
 
logAcceptanceProb(Object, Object) - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
logAcceptanceProb(Object, Object) - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisSampler
 
logAcceptProb - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
logAcceptProb - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
logAcceptProb() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
logbeta(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Log Beta function.
logCDF(Object) - Method in interface org.omegahat.Probability.Distributions.CumulativeDensity
 
logCDF(Object) - Method in class org.omegahat.Probability.Distributions.Normal
 
logConditionalPDF(Object, Object) - Method in interface org.omegahat.Probability.Distributions.ConditionalDensity
 
logConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
logConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
logConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.IndependenceMultiProposal
 
logConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
 
logConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalProposal
 
logConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
logConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisProposal
 
logConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
logConditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveKernelProposal
 
logConditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
logConditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
logConditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
logConditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
logConditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
logConditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
logConditionalPDF(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
logConditionalPDF(Object, Object, int, MultiState) - Method in interface org.omegahat.Simulation.MCMC.HastingsCoupledProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
logCumulativeConditionalDensity(Object, Object) - Method in interface org.omegahat.Probability.Distributions.CumulativeConditionalDensity
 
logPDF(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
logPDF(double, double, double) - Method in class org.omegahat.Probability.Distributions.Normal
 
logPDF(Object) - Method in interface org.omegahat.Probability.Distributions.Density
 
logPDF(Object) - Method in class org.omegahat.Probability.Distributions.Normal
 
logPDF(Object) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
logTransitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
Convenience method for computing the log probability of proposing a move.
logTransitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
Convenience method for computing the log probability of proposing a move.
logTransitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
Convenience method for computing the log probability of proposing a move.
logTransitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalProposal
 
logTransitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
logTransitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisProposal
 
logTransitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
logTransitionProbability(Object, Object) - Method in interface org.omegahat.Simulation.MCMC.GeneralProposal
Convenience method for computing the log probability of proposing a move.
logTransitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveKernelProposal
 
logTransitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
Convenience method for computing the log probability of proposing a move.
logTransitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
logTransitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
logTransitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
logTransitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
logTransitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
Convenience method for computing the log probability of proposing a move.
logTransitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
logTransitionProbability(Object, Object, int, MultiState) - Method in interface org.omegahat.Simulation.MCMC.HastingsCoupledProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
logUnnormalezedDensity(Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget
 
logUnnormalizedConditionalPDF(Object, Object) - Method in interface org.omegahat.Probability.Distributions.UnnormalizedConditionalDensity
 
logUnnormalizedConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
 
logUnnormalizedConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
logUnnormalizedPDF(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
logUnnormalizedPDF(double[], double, double) - Method in class org.omegahat.Probability.Distributions.Normal
 
logUnnormalizedPDF(double, double, double) - Method in class org.omegahat.Probability.Distributions.Normal
 
logUnnormalizedPDF(Object) - Method in interface org.omegahat.Probability.Distributions.UnnormalizedDensity
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Probability.Distributions.Normal
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_Binomial_Likelihood
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleLikelihood
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood_Bimode
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalDensity
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalLikelihood
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget
 
logUnnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.MultiTarget
 
loh - Variable in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood
 
loh - Variable in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleLikelihood
 
lowerEdge - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 

M

macheps() - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Virtual Machine Epsilon.
Mahalanobis - Static variable in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
mahalanobis_2(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
mahalanobis_2(double[], double[], double[][]) - Static method in class org.omegahat.GUtilities.Distance
squared Mahalanobis distance
mahalanobis(double[], double[], double[][]) - Static method in class org.omegahat.GUtilities.Distance
Mahalanobis distance
main(String[]) - Static method in class org.omegahat.Probability.Distributions.Normal
 
main(String[]) - Static method in class org.omegahat.Probability.Distributions.MVNormal
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.SimpleExample
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_III
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleExample
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_NKC
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomialExample
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleExample_NKC
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.HeavyAndLight_Example_NKC
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_II
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Example_NKC_Bimode
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalProposal
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Proposals.NormalProposal
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisProposal
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.CustomGibbsSampler
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.CustomMarkovChain
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.CustomMetropolisSampler
 
main(String[]) - Static method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
main(String[]) - Static method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
To test, generate 10 integers
main(String[]) - Static method in class org.omegahat.Simulation.RandomGenerators.DefaultPRNGFactory
Test PRNGFactory class by creating a CollingsPRNGState, instantiating it using the Factory, and then generating 10 random integers with the result.
main(String[]) - Static method in class org.omegahat.Simulation.RandomGenerators.TestCollingsPRNG
Compute a batch of double pseudo-random variates using the PRNGAdmin setup.
main(String[]) - Static method in class org.omegahat.Simulation.RandomGenerators.TestCollingsPRNG_Batch
Compute a batch of double pseudo-random variates using the PRNGAdmin setup.
main(String[]) - Static method in class org.omegahat.Simulation.RandomGenerators.TestServer
 
main(String[]) - Static method in class org.omegahat.GUtilities.ReadData
 
makeGeneratorState() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
makeIntegerStateHash(int[]) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
MarkovChain - interface org.omegahat.Simulation.MCMC.MarkovChain.
A Markov Chain.
MarkovProposal - interface org.omegahat.Simulation.MCMC.MarkovProposal.
A Markov proposal distribution generates a new state based only on information from the current state
MASK - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
matCache - Static variable in class org.omegahat.GUtilities.Distance
 
max - Variable in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
max - Variable in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
max() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
max() - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
maxCache - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
maxRanges - Variable in class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener
 
maxsize - Variable in class org.omegahat.Simulation.MCMC.Listeners.ExpandingPlottingListener
 
maxsize() - Method in class org.omegahat.Simulation.MCMC.Listeners.ExpandingPlottingListener
 
maxsize(int) - Method in class org.omegahat.Simulation.MCMC.Listeners.ExpandingPlottingListener
 
maxVals - Variable in class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledSampler
 
maxVar - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
 
MCMCEvent - interface org.omegahat.Simulation.MCMC.MCMCEvent.
 
MCMCListener - interface org.omegahat.Simulation.MCMC.MCMCListener.
 
MCMCListenerHandle - interface org.omegahat.Simulation.MCMC.MCMCListenerHandle.
 
MCMCListenerWriter - interface org.omegahat.Simulation.MCMC.Listeners.MCMCListenerWriter.
 
MCMCState - interface org.omegahat.Simulation.MCMC.MCMCState.
Marker for objects representing the current state of an MCMC Chain.
MCMCStateDatabase - class org.omegahat.Simulation.MCMC.MCMCStateDatabase.
 
MCMCStateDatabase() - Constructor for class org.omegahat.Simulation.MCMC.MCMCStateDatabase
 
MCMCStateDatabase(String) - Constructor for class org.omegahat.Simulation.MCMC.MCMCStateDatabase
 
mean - Static variable in interface org.omegahat.Simulation.RandomGenerators.PseudoRandomNormalGenerator
 
mean() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
Compute the mean
Mean() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
meanCacheVec - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
MeanWriter - class org.omegahat.Simulation.MCMC.Listeners.MeanWriter.
 
MeanWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
MeanWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
MeanWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
MeanWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
method - Variable in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
method - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
method - Variable in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
MetropolisHastingsSampler - interface org.omegahat.Simulation.MCMC.MetropolisHastingsSampler.
A Metropolis-Hastings Markov Chain sampler.
MetropolisSampler - interface org.omegahat.Simulation.MCMC.MetropolisSampler.
A Metropolis Markov Chain sampler.
min - Variable in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
min - Variable in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
min() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
Compute the minimum 2-way variance vector between a specified state and the other states
min() - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
minCache - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
minRanges - Variable in class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener
 
minVals - Variable in class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledSampler
 
minVar - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
 
MixerMult - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Multiplicative constant for mixing generator
MixerMult - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
Multiplier constant for mixing generator
MixerSeed - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Seed for mixing generator
MixerSeed - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
Seed for mixing generator
MixtureProposal - class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal.
 
MixtureProposal(GeneralProposal[], double[], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
MixtureProposal(GeneralProposal[], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
MixtureProposal(int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
mod - Variable in class org.omegahat.Simulation.RandomGenerators.MultiplicativeCongruentialPRNG
Modulus constant
Mod - Static variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Modulus constant for all generators
Mod - Static variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
Modulus constant for the congruential generator used to pick the multiplicative constants and to intialize the seeds for each component generator.
model - Variable in class org.omegahat.Simulation.MCMC.Expressions.ExpressionModel
 
model() - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionModel
 
model(MultiLineModelFormula) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionModel
 
ModelEvaluator - class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator.
 
ModelEvaluator(MultiLineModelFormula, MultiLineModelFormula, Database, Database) - Constructor for class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
Modulus - Static variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGConstants
Prime Modulus Constant = 2^32-1
mu - Variable in class org.omegahat.Probability.Distributions.Normal
Mean
mu - Variable in class org.omegahat.Probability.Distributions.MVNormal
Mean
mult - Variable in class org.omegahat.Simulation.RandomGenerators.MultiplicativeCongruentialPRNG
Multiplicative constant
Mult - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
Multiplicative constant for the congruential generator used to pick the multiplicative constants and to intialize the seeds for each component generator.
multCong(int, int, int) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Compute next value using multiplicative congruential formula.
MultiDoubleState - class org.omegahat.Simulation.MCMC.MultiDoubleState.
MCMCState that can hold several Double[] states.
MultiDoubleState.CovAccumulator - class org.omegahat.Simulation.MCMC.MultiDoubleState.CovAccumulator.
 
MultiDoubleState.CovAccumulator(MultiDoubleState, int) - Constructor for class org.omegahat.Simulation.MCMC.MultiDoubleState.CovAccumulator
 
MultiDoubleState() - Constructor for class org.omegahat.Simulation.MCMC.MultiDoubleState
 
MultiDoubleState(int) - Constructor for class org.omegahat.Simulation.MCMC.MultiDoubleState
 
MultiDoubleState(int, double[]) - Constructor for class org.omegahat.Simulation.MCMC.MultiDoubleState
 
MultiDoubleState(int, Double[]) - Constructor for class org.omegahat.Simulation.MCMC.MultiDoubleState
 
MultiDoubleState(MultiState) - Constructor for class org.omegahat.Simulation.MCMC.MultiDoubleState
This constructor creates a new MultDoubleState by duplicating the contents of the provided MultiState, checking that each non-null component is a Double[].
MultiplicativeCongruentialPRNG - class org.omegahat.Simulation.RandomGenerators.MultiplicativeCongruentialPRNG.
Compute pseudo-random number using multiplicative congruential formula.
MultiplicativeCongruentialPRNG() - Constructor for class org.omegahat.Simulation.RandomGenerators.MultiplicativeCongruentialPRNG
Create a Multiplicative Congruential Generator using the default seed, multiplier and modulus constants.
MultiplicativeCongruentialPRNG(int) - Constructor for class org.omegahat.Simulation.RandomGenerators.MultiplicativeCongruentialPRNG
Create A Multiplicative Congruential Generator using a specified seed.
MultiplicativeCongruentialPRNG(int, int) - Constructor for class org.omegahat.Simulation.RandomGenerators.MultiplicativeCongruentialPRNG
Create A Multiplicative Congruential Generator using a specified seed and multiplicative constant.
MultiplicativeCongruentialPRNG(int, int, int) - Constructor for class org.omegahat.Simulation.RandomGenerators.MultiplicativeCongruentialPRNG
Create A Multiplicative Congruential Generator using a specified seed and multiplicative constant.
MultiProposal - class org.omegahat.Simulation.MCMC.Proposals.MultiProposal.
 
MultiProposal() - Constructor for class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
 
MultiState - class org.omegahat.Simulation.MCMC.MultiState.
MCMCState that can hold several individual states.
MultiState() - Constructor for class org.omegahat.Simulation.MCMC.MultiState
 
MultiState(int) - Constructor for class org.omegahat.Simulation.MCMC.MultiState
 
MultiState(int, Object) - Constructor for class org.omegahat.Simulation.MCMC.MultiState
 
MultiTarget - class org.omegahat.Simulation.MCMC.MultiTarget.
 
MultiTarget(int) - Constructor for class org.omegahat.Simulation.MCMC.MultiTarget
 
MultiTarget(int, UnnormalizedDensity) - Constructor for class org.omegahat.Simulation.MCMC.MultiTarget
 
MultiTarget(UnnormalizedDensity[]) - Constructor for class org.omegahat.Simulation.MCMC.MultiTarget
 
mvnorm0 - Variable in class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
mvnorm1 - Variable in class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
MVNormal - class org.omegahat.Probability.Distributions.MVNormal.
 
MVNormal(double[][], PRNG) - Constructor for class org.omegahat.Probability.Distributions.MVNormal
 
MVNormal(double[], double[][], PRNG) - Constructor for class org.omegahat.Probability.Distributions.MVNormal
 
MVNormal(int, PRNG) - Constructor for class org.omegahat.Probability.Distributions.MVNormal
 

N

n - Variable in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood
 
n - Variable in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleLikelihood
 
name() - Method in class org.omegahat.Probability.Distributions.Normal
 
nearestNeighborDiagVar(int, int, int) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
nearestNeighborMean(int, int, int) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
nearestNeighborVar(int, int, int) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
Compute the (local) covariance matrix at one state using a specified number of nearest neighbors
nextComponentDouble(int) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Generate a double on [0,1] using pool generator which.
nextComponentInt(int) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Generate an int using pool generator which.
nextDouble() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Generate a single pseudo-random double on [0,1)
nextDouble() - Method in interface org.omegahat.Simulation.RandomGenerators.PRNG
Generate a pseudo-random double value from a uniforml distribion on [0,1)
nextDouble() - Method in class org.omegahat.Simulation.RandomGenerators.MultiplicativeCongruentialPRNG
Generate a random double in [0,1)
nextDouble() - Method in interface org.omegahat.Simulation.RandomGenerators.PseudoRandomUnivariateGenerator
Generate a single pseudo-random value.
nextDouble(int) - Method in interface org.omegahat.Simulation.RandomGenerators.PseudoRandomUnivariateGenerator
Generate several pseudo-random values.
nextDoubleArray(int) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Generate num pseudo-random doubles on (0,1]
nextDoubleArray(int) - Method in interface org.omegahat.Simulation.RandomGenerators.PRNG
Generate several pseudo-random doubles from a uniforml distribion on [0,1)
nextInt() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Generate a single pseudo-random integer
nextInt() - Method in interface org.omegahat.Simulation.RandomGenerators.PRNG
Generate a pseudo-random integer from a uniforml distribion on [0,intRange)
nextInt() - Method in class org.omegahat.Simulation.RandomGenerators.MultiplicativeCongruentialPRNG
Generate a random integer in [1,Mod]
nextIntArray(int) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Generate num pseudo-random integers
nextIntArray(int) - Method in interface org.omegahat.Simulation.RandomGenerators.PRNG
Generate several pseudo-random integers from a uniforml distribion on [0,intRange)
nextMixerDouble() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Generate a double on [0,1) using the mixing generator.
nextMixerInt() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Generate an int using the mixing generator.
nextVariable() - Method in interface org.omegahat.Simulation.RandomGenerators.PseudoRandomVariableGenerator
Generate a single pseudo-random variable
nextVariable(int) - Method in interface org.omegahat.Simulation.RandomGenerators.PseudoRandomVariableGenerator
Generate a set of pseudo-random variables
niter - Variable in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
niter - Variable in class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
niter - Variable in class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
niter - Variable in class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
niterAccepted - Variable in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
niterAll - Variable in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
nobs - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState.CovAccumulator
 
norm - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
norm - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler
 
norm - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
norm - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain
 
norm - Variable in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalDensity
 
norm - Variable in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalLikelihood
 
normal - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
Normal - class org.omegahat.Probability.Distributions.Normal.
 
Normal(PRNG) - Constructor for class org.omegahat.Probability.Distributions.Normal
 
Normal(PRNG, Object[]) - Constructor for class org.omegahat.Probability.Distributions.Normal
 
normalCDF(double) - Static method in class org.omegahat.Probability.Distributions.DistributionFunctions
Normal Distribution Cumulative Distribution function.
NormalDualKernelProposal - class org.omegahat.Simulation.MCMC.Proposals.NormalDualKernelProposal.
 
NormalDualKernelProposal() - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalDualKernelProposal
 
NormalDualKernelProposal(double[], double[][], double[][], double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalDualKernelProposal
 
NormalDualKernelProposal(int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalDualKernelProposal
 
normalize() - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
normalize() - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
normalized_probs - Variable in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
normalized_probs - Variable in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
normalizing_constant - Variable in class org.omegahat.Probability.Distributions.MVNormal
 
NormalKernelProposal - class org.omegahat.Simulation.MCMC.Proposals.NormalKernelProposal.
 
NormalKernelProposal() - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalKernelProposal
 
NormalKernelProposal(double[][], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalKernelProposal
 
NormalKernelProposal(int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalKernelProposal
 
normalLogPDF(double, double, double) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
NormalMetropolisComponentProposal - class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal.
 
NormalMetropolisComponentProposal(double[], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
Constructor for normal increments with specified covariance matrix.
NormalMetropolisComponentProposal(int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
Constructor for normal increments with identity covariance matrix.
NormalMetropolisProposal - class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisProposal.
 
NormalMetropolisProposal(double[][], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisProposal
Constructor for normal increments with specified covariance matrix.
NormalMetropolisProposal(int, double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisProposal
Constructor for a spherical normal increments with variances for each dimension.
NormalMetropolisProposal(int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisProposal
Constructor for normal increments with identity covariance matrix.
normalPDF(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
normalPDF(double, double, double) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
NormalProposal - class org.omegahat.Simulation.MCMC.Proposals.NormalProposal.
 
NormalProposal(double[], double[][], PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalProposal
Constructor for normal with specified mean and covariance matrix.
NormalProposal(int, double, double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalProposal
Constructor for a spherical normal with the same mean and variances for each dimension.
NormalProposal(int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Proposals.NormalProposal
Constructor for a (standard) spherical normal with mean 0 and identity covariance matrix
normalQuantile(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Standard-Normal Quantile Function
normalRand() - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Normal Random Generator
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler.listenerPrinter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler.listenerPrinter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler.listenerPrinter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain.listenerPrinter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.CustomGibbsSampler.listenerPrinter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.CustomMarkovChain.listenerPrinter
 
notify(MCMCEvent) - Method in interface org.omegahat.Simulation.MCMC.MCMCListener
Function to be called for notification
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.ExpandingPlottingListener
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.ListenerPrinter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.PlottingListener
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.StepListenerPrinter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerWriter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
Function to be called for notification
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.PosteriorProbWriter
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.CovarianceListener
 
notify(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener
Function to be called for notification
notifyAll(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.NotifyingMCMCObject
 
notifyAll(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
notifyAll(MCMCEvent) - Method in class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener
 
NotifyingMCMCObject - class org.omegahat.Simulation.MCMC.NotifyingMCMCObject.
A simple class providing methods implementing the interface NotifyingObject
NotifyingMCMCObject.MyHandle - class org.omegahat.Simulation.MCMC.NotifyingMCMCObject.MyHandle.
 
NotifyingMCMCObject.MyHandle(NotifyingMCMCObject) - Constructor for class org.omegahat.Simulation.MCMC.NotifyingMCMCObject.MyHandle
 
NotifyingMCMCObject() - Constructor for class org.omegahat.Simulation.MCMC.NotifyingMCMCObject
 
NotifyingObject - interface org.omegahat.Simulation.MCMC.NotifyingObject.
Indicates that this MCMC Object can register and unregister listeners and will notify them of events.
NotifyingPRNG - class org.omegahat.Simulation.RandomGenerators.NotifyingPRNG.
 
NotifyingPRNG() - Constructor for class org.omegahat.Simulation.RandomGenerators.NotifyingPRNG
 
notifyListeners(PRNGState) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
numAccepted - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
numAccepted - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
numAccepted - Variable in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
numAccepted() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
numBins() - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
numChain - Variable in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
numChain - Variable in class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
numChain - Variable in class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
numChain - Variable in class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
numChain - Variable in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
numChains() - Method in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
numChains() - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
numChains() - Method in class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
 
numChains() - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
numChains() - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
numChains() - Method in class org.omegahat.Simulation.MCMC.MultiTarget
 
numComputed - Variable in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
numComputed() - Method in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
numEvents - Variable in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
NumGen - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNG
Number of generators in the pool
NumGen - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
Number of generators that each CollingsPRNG will use
NumGen - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
Number of component generators
numNeighbors - Variable in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
numNeighbors - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
numNeighbors - Variable in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
numPoints - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
numProposed - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
numProposed - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
numProposed() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
numSamplers - Variable in class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
 
numSamplers - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 

O

objectCache - Variable in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
objectCache() - Method in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
one - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
optimalAdjust - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
orb - Variable in class org.omegahat.Simulation.RandomGenerators.TestServer
 
order - Variable in class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
 
order - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
Random Number Generator
Otob(Object) - Static method in class org.omegahat.GUtilities.ArrayTools
 
Otod(Object) - Static method in class org.omegahat.GUtilities.ArrayTools
 
Otof(Object) - Static method in class org.omegahat.GUtilities.ArrayTools
 
Otoi(Object) - Static method in class org.omegahat.GUtilities.ArrayTools
 
out - Variable in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
out - Variable in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
out - Variable in class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter
 
out - Variable in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
out - Variable in class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
 
out - Variable in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
out - Variable in class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
out - Variable in class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
out - Variable in class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter
 
out - Variable in class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 

P

PDF(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
PDF(double, double, double) - Method in class org.omegahat.Probability.Distributions.Normal
 
PDF(Object) - Method in interface org.omegahat.Probability.Distributions.Density
 
PDF(Object) - Method in class org.omegahat.Probability.Distributions.Normal
 
PDF(Object) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
permute() - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
PipeLikelihood - class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood.
 
PipeLikelihood(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
PipeLikelihood(String, String[], boolean) - Constructor for class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
plots - Variable in class org.omegahat.Simulation.MCMC.Listeners.PlottingListener
 
plots() - Method in class org.omegahat.Simulation.MCMC.Listeners.PlottingListener
 
PlottingListener - class org.omegahat.Simulation.MCMC.Listeners.PlottingListener.
Displays contents and counter of RecordingIndexEvents when one is recieved.
PlottingListener(String[]) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.PlottingListener
 
PlottingListener(String[], int) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.PlottingListener
 
plotWindows - Variable in class org.omegahat.Simulation.MCMC.Listeners.PlottingListener
 
plotWindows() - Method in class org.omegahat.Simulation.MCMC.Listeners.PlottingListener
 
pmax - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
pmin - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
poissonCDF(int, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
poissonPMF(int, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
poissonQuantile(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
poissonRand(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
Poisson random generator from Numerical Recipes
pool - Static variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGConstants
Pool of (empirically) good multiplicative constants
PosteriorProbWriter - class org.omegahat.Simulation.MCMC.Listeners.PosteriorProbWriter.
 
PosteriorProbWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.PosteriorProbWriter
 
PosteriorProbWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.PosteriorProbWriter
 
PosteriorProbWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.PosteriorProbWriter
 
PosteriorProbWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.PosteriorProbWriter
 
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter
 
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
 
print(String) - Method in interface org.omegahat.Simulation.MCMC.Listeners.MCMCListenerWriter
Write arbitrary text to the output stream.
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.QuantileWriter
 
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerWriter
 
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter
 
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
print(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.PosteriorProbWriter
 
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter
 
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
 
println(String) - Method in interface org.omegahat.Simulation.MCMC.Listeners.MCMCListenerWriter
Write arbitrary text to the output stream.
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.QuantileWriter
 
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerWriter
 
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter
 
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
println(String) - Method in class org.omegahat.Simulation.MCMC.Listeners.PosteriorProbWriter
 
prng - Variable in class org.omegahat.Probability.Distributions.Normal
Pseudo-Random Number Generator to Use
prng - Variable in class org.omegahat.Probability.Distributions.PRNGDistributionFunctions
 
prng - Variable in class org.omegahat.Probability.Distributions.MVNormal
Pseudo-Random Number Generator to Use
prng - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
prng - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler
 
prng - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
prng - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain
 
prng - Variable in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
prng - Variable in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
prng - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveProposal
 
prng - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
 
prng - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
 
prng - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
prng - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
prng - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
the current state
PRNG - interface org.omegahat.Simulation.RandomGenerators.PRNG.
Interface to Pseudo-random number generators.
PRNGAdministrator - interface org.omegahat.Simulation.RandomGenerators.PRNGAdministrator.
The administrator interface provides methods to define successive PRNG's intended to be used in parallel simulations.
PRNGAdministratorEvent - class org.omegahat.Simulation.RandomGenerators.PRNGAdministratorEvent.
 
PRNGAdministratorEvent() - Constructor for class org.omegahat.Simulation.RandomGenerators.PRNGAdministratorEvent
 
PRNGAdministratorEvent(PRNGState, PRNGAdministrator) - Constructor for class org.omegahat.Simulation.RandomGenerators.PRNGAdministratorEvent
 
PRNGAdministratorListener - interface org.omegahat.Simulation.RandomGenerators.PRNGAdministratorListener.
 
PRNGDistributionFunctions - class org.omegahat.Probability.Distributions.PRNGDistributionFunctions.
 
PRNGDistributionFunctions(PRNG) - Constructor for class org.omegahat.Probability.Distributions.PRNGDistributionFunctions
Constructor
PRNGFactory - interface org.omegahat.Simulation.RandomGenerators.PRNGFactory.
interface for factories that create PRNG's from PRNGStates.
PRNGIntegerState - interface org.omegahat.Simulation.RandomGenerators.PRNGIntegerState.
Extends PRNGState to provide methods for obtaining and setting state details for PRNG's that can represent thier state as a sequence of ints.
PRNGName - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
Class this State corresponds to.
PRNGParameters - interface org.omegahat.Simulation.RandomGenerators.PRNGParameters.
 
PRNGState - interface org.omegahat.Simulation.RandomGenerators.PRNGState.
Enapsulates all of the state information of a PRNG.
PRNGStateRegistered(PRNGAdministratorEvent) - Method in interface org.omegahat.Simulation.RandomGenerators.PRNGAdministratorListener
 
prob - Variable in class org.omegahat.Probability.Distributions.Normal
Pull all the probability functions out of ' package
prob - Variable in class org.omegahat.Probability.Distributions.MVNormal
Pull all the probability functions out of package
prob - Variable in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
probability() - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
probAccept - Variable in class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
probCache - Variable in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
probCache() - Method in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
proposal - Variable in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveProposal
 
proposal - Variable in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
 
proposal - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
proposal - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
PROPOSAL - Static variable in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
proposal_probs - Variable in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
proposal_probs - Variable in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
proposalDetails - Variable in class org.omegahat.Simulation.MCMC.DetailedMultiState
 
ProposalDetails - interface org.omegahat.Simulation.MCMC.ProposalDetails.
 
proposalDetails() - Method in class org.omegahat.Simulation.MCMC.DetailedMultiState
 
proposalDetails(ProposalDetails) - Method in class org.omegahat.Simulation.MCMC.DetailedMultiState
 
proposalFreqs - Variable in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
proposalFreqs - Variable in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
proposalModel - Variable in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
proposalModel() - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
proposalModel(MultiLineModelFormula) - Method in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
proposals - Variable in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
proposals - Variable in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
proposals - Variable in class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
 
proposals - Variable in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
proposals - Variable in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
proposalVar - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
proposed - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
proposed - Variable in class org.omegahat.Simulation.MCMC.Expressions.ModelEvaluator
 
proposed - Variable in class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
proposed() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
proposedComponent - Variable in class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
 
proposedProb - Variable in class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
PseudoRandomNormalGenerator - interface org.omegahat.Simulation.RandomGenerators.PseudoRandomNormalGenerator.
Interface definition for classes that generate univariate pseudo-random normals.
PseudoRandomUnivariateGenerator - interface org.omegahat.Simulation.RandomGenerators.PseudoRandomUnivariateGenerator.
Pseudo-random variable generators for univariate variables representable by double's.
PseudoRandomVariableGenerator - interface org.omegahat.Simulation.RandomGenerators.PseudoRandomVariableGenerator.
Interface to Pseudo-random variable generators.

Q

qualifier(ExpressionInt) - Method in class org.omegahat.Simulation.MCMC.Expressions.CachingMethodCall
 
quantileDouble(double) - Method in class org.omegahat.Probability.Distributions.Normal
 
quantileDouble(double[]) - Method in class org.omegahat.Probability.Distributions.Normal
 
quantileObject(double) - Method in class org.omegahat.Probability.Distributions.Normal
 
quantileObject(double[]) - Method in class org.omegahat.Probability.Distributions.Normal
 
quantiles - Variable in class org.omegahat.Simulation.MCMC.Listeners.QuantileWriter
 
quantiles(double[]) - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
QuantileWriter - class org.omegahat.Simulation.MCMC.Listeners.QuantileWriter.
 
QuantileWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.QuantileWriter
 
QuantileWriter(String, boolean, boolean, double, double, int, double[]) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.QuantileWriter
 
QuantileWriter(String, boolean, double, double, int, double[]) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.QuantileWriter
 
QuantileWriter(String, double, double, int, double[]) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.QuantileWriter
 

R

range() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
rangeCache - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
ReadData - class org.omegahat.GUtilities.ReadData.
 
ReadData() - Constructor for class org.omegahat.GUtilities.ReadData
 
readData(String) - Method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
readData(String) - Method in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalLikelihood
 
readDataAsColumnMatrix(String, int, boolean, boolean) - Static method in class org.omegahat.GUtilities.ReadData
Read numeric data from a file and return as a square matrix;
readDataAsColumnMatrix(String, int, int, boolean, boolean) - Static method in class org.omegahat.GUtilities.ReadData
Read numeric data from a file and return as a square matrix;
readDataAsRowMatrix(String, int, boolean, boolean) - Static method in class org.omegahat.GUtilities.ReadData
Read numeric data from a file and return as a square matrix;
readDataAsSquareMatrix(String, boolean, boolean) - Static method in class org.omegahat.GUtilities.ReadData
Read numeric data from a file and return as a square matrix;
readDataAsVector(String, boolean) - Static method in class org.omegahat.GUtilities.ReadData
Read numeric data from a file and return as a java.util.Vector;
RecordingStepListener - class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener.
Displays contents and counter of RecordingStepEvents when one is recieved.
RecordingStepListener() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener
 
RecordingStepListener(int) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener
 
refreshInterval - Variable in class org.omegahat.Simulation.MCMC.Listeners.PlottingListener
 
refreshInterval() - Method in class org.omegahat.Simulation.MCMC.Listeners.PlottingListener
 
refreshInterval(int) - Method in class org.omegahat.Simulation.MCMC.Listeners.PlottingListener
 
registerCorbaServer(String, Object) - Method in class org.omegahat.Simulation.RandomGenerators.TestServer
 
registerListener(MCMCListener) - Method in interface org.omegahat.Simulation.MCMC.NotifyingObject
Register a listener to be notified of events.
registerListener(MCMCListener) - Method in class org.omegahat.Simulation.MCMC.NotifyingMCMCObject
 
registerListener(MCMCListener) - Method in class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
registerListener(MCMCListener) - Method in class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener
 
registerPRNGState() - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
registerPRNGState() - Method in interface org.omegahat.Simulation.RandomGenerators.PRNGAdministrator
 
registerPRNGState(Object) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
registerPRNGState(Object) - Method in interface org.omegahat.Simulation.RandomGenerators.PRNGAdministrator
 
remove(int) - Method in class org.omegahat.Simulation.MCMC.MultiState
 
remove(int) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
removeListener(PRNGAdministratorListener) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
 
removeListener(PRNGAdministratorListener) - Method in class org.omegahat.Simulation.RandomGenerators.NotifyingPRNG
 
reset() - Method in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
reset() - Method in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
reset() - Method in class org.omegahat.Simulation.MCMC.Listeners.ListenerPrinter
 
reset() - Method in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
reset() - Method in class org.omegahat.Simulation.MCMC.Listeners.DistanceListener
 
reset() - Method in class org.omegahat.Simulation.MCMC.Listeners.CovarianceListener
 
reset() - Method in interface org.omegahat.Simulation.MCMC.Listeners.ResettableListener
Reset any stored state to the initial condition
resetCounters() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
resetNumAccepted() - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
resetNumProposed() - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
ResettableListener - interface org.omegahat.Simulation.MCMC.Listeners.ResettableListener.
This interface indicates that the listener has some stored state that can be reset by calling the notify() method.
resetTime() - Method in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
resetTime() - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
Reset time to 0
resetTime() - Method in interface org.omegahat.Simulation.MCMC.Proposals.TimeDependentProposal
Reset time to 0
resetTime() - Method in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
 
resetTime() - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
resetTime() - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
resetTotalEvents() - Method in class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
returnsLogLikelihood - Variable in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
returnsLogLikelihood() - Method in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
reverseProb - Variable in class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
rho - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
rho - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler
 
rho - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
rho - Variable in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalDensity
 
RHSarguments - Variable in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
rnorm() - Method in class org.omegahat.Probability.Distributions.MVNormal
 
run() - Method in class org.omegahat.Simulation.MCMC.BaseMarkovChain
 
run() - Method in class org.omegahat.Simulation.RandomGenerators.NotifyingPRNG
 

S

sae - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
sample - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
seed - Variable in class org.omegahat.Simulation.RandomGenerators.MultiplicativeCongruentialPRNG
Seed value in [1, 2^31-1]
Seed - Variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGAdministrator
Seed for the congruential generator used to pick the multiplicative constants and to intialize the seeds for each component generator.
seedi - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
seedj - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
set(int, Object) - Method in class org.omegahat.Simulation.MCMC.MultiState
 
set(int, Object) - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
setAdminName(String) - Method in class org.omegahat.Simulation.RandomGenerators.TestServer
 
setChain(int) - Method in class org.omegahat.Simulation.MCMC.GenericManagerChainEvent
 
setCovariance(double[]) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
setCovariance(double[][]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
setCovariance(double[][]) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
setCovariance(double[][]) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalKernelProposal
 
setCurrent(MCMCState) - Method in class org.omegahat.Simulation.MCMC.GenericChainStepEvent
 
setDataN(int[]) - Method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
setDataX(int[]) - Method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
setDEBUG(boolean) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
setDEBUG(boolean) - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
setDEBUG(boolean) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
setDEBUG(boolean) - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
setDescription(String) - Method in class org.omegahat.Simulation.MCMC.GenericMCMCEvent
 
setDistanceMethod(int) - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
setDistanceMethod(int) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
setDistanceMethod(int) - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
setEvent(GenericChainEvent) - Method in class org.omegahat.Simulation.MCMC.GenericManagerChainEvent
 
setFactoryName(String) - Method in class org.omegahat.Simulation.RandomGenerators.TestServer
 
setInflationFactor(double) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
setInflationFactor(double) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalProposal
 
setInflationFactor(double) - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalKernelProposal
 
setInflationFactor(double) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
 
setInflationFactor(double) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiSourceCoupler
 
setInflationFactor(double) - Method in class org.omegahat.Simulation.MCMC.Proposals.LocallyAdaptiveNormalProposal
 
setIntegerState(int[], int[]) - Method in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGState
 
setIntegerState(int[], int[]) - Method in interface org.omegahat.Simulation.RandomGenerators.PRNGIntegerState
Set the internal state using an array of ints provided by another PRNGIntegerState.
setKernel(GeneralProposal) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
 
setKernels(GeneralProposal[]) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
 
setMaxVals(double[]) - Method in class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledSampler
 
setMaxVar(double[][]) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
 
setMean(double) - Method in class org.omegahat.Probability.Distributions.Normal
 
setMean(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
setMean(Object) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
setMinVals(double[]) - Method in class org.omegahat.Simulation.MCMC.BoundedHastingsCoupledSampler
 
setMinVar(double[][]) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalMetropolisProposal
 
setNumPoints(int) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
setNumSamplers(int) - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
setOptimalAdjust(double) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveNormalKernelProposal
 
setParameters(Object[]) - Method in class org.omegahat.Probability.Distributions.Normal
 
setPRNG(PRNG) - Method in class org.omegahat.Probability.Distributions.PRNGDistributionFunctions
 
setPRNG(PRNG) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
 
setPRNG(PRNG) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
 
setProposal(HastingsCoupledProposal) - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
setProposal(int, GeneralProposal) - Method in class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
 
setProposal(int, GeneralProposal, double) - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
setProposal(int, GeneralProposal, int) - Method in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
setProposal(int, HastingsCoupledProposal, double) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
setProposal(int, HastingsCoupledProposal, int) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
setProposals(GeneralProposal[]) - Method in class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
 
setProposals(GeneralProposal[], double[]) - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
 
setProposals(GeneralProposal[], int[]) - Method in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
setProposals(HastingsCoupledProposal[], double[]) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
 
setProposals(HastingsCoupledProposal[], int[]) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
setRange(MCMCListenerHandle, double[], double[]) - Method in class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener
 
setSource(Object) - Method in class org.omegahat.Simulation.MCMC.GenericMCMCEvent
 
setStandardDeviation(double) - Method in class org.omegahat.Probability.Distributions.Normal
 
setState(MultiState) - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
setTarget(int, UnnormalizedDensity) - Method in class org.omegahat.Simulation.MCMC.MultiTarget
 
setTarget(UnnormalizedDensity) - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
setTargets(UnnormalizedDensity[]) - Method in class org.omegahat.Simulation.MCMC.MultiTarget
 
setThinningFactor(int) - Method in class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
setupTransMat() - Method in class org.omegahat.Probability.Distributions.MVNormal
 
setVariance(double) - Method in class org.omegahat.Probability.Distributions.Normal
 
showAllStates - Variable in class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
 
sigma - Variable in class org.omegahat.Probability.Distributions.Normal
Standard Deviation
sigma - Variable in class org.omegahat.Probability.Distributions.MVNormal
Covariance Matrix
sigma - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
sigma - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler
 
sigma - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
sigma - Variable in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
sigma - Variable in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalDensity
 
sigmaDet - Variable in class org.omegahat.Probability.Distributions.MVNormal
 
sigmaInv - Variable in class org.omegahat.Probability.Distributions.MVNormal
 
sigmaSqrt - Variable in class org.omegahat.Probability.Distributions.MVNormal
 
sigmaSVD - Variable in class org.omegahat.Probability.Distributions.MVNormal
 
SimpleExample - class org.omegahat.Simulation.MCMC.Examples.SimpleExample.
 
SimpleExample() - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleExample
 
SimpleGibbsSampler - class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler.
A simple Markov Chain example.
SimpleGibbsSampler.BivariateDoubleState - class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler.BivariateDoubleState.
 
SimpleGibbsSampler.BivariateDoubleState(SimpleGibbsSampler, double[]) - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler.BivariateDoubleState
 
SimpleGibbsSampler.listenerPrinter - class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler.listenerPrinter.
 
SimpleGibbsSampler.listenerPrinter() - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler.listenerPrinter
 
SimpleGibbsSampler(PRNG, double, double) - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler
 
SimpleMarkovChain - class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain.
A simple Markov Chain example.
SimpleMarkovChain.doubleState - class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain.doubleState.
 
SimpleMarkovChain.doubleState(SimpleMarkovChain, double) - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain.doubleState
 
SimpleMarkovChain.listenerPrinter - class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain.listenerPrinter.
 
SimpleMarkovChain.listenerPrinter() - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain.listenerPrinter
 
SimpleMarkovChain(PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain
 
SimpleMetropolisHastingsSampler - class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler.
A simple Markov Chain example.
SimpleMetropolisHastingsSampler.BivariateDoubleState - class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler.BivariateDoubleState.
 
SimpleMetropolisHastingsSampler.BivariateDoubleState(SimpleMetropolisHastingsSampler, double[]) - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler.BivariateDoubleState
 
SimpleMetropolisHastingsSampler.listenerPrinter - class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler.listenerPrinter.
 
SimpleMetropolisHastingsSampler.listenerPrinter() - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler.listenerPrinter
 
SimpleMetropolisHastingsSampler(PRNG, double, double, double) - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
SimpleMetropolisSampler - class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler.
A simple Markov Chain example.
SimpleMetropolisSampler.BivariateDoubleState - class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler.BivariateDoubleState.
 
SimpleMetropolisSampler.BivariateDoubleState(SimpleMetropolisSampler, double[]) - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler.BivariateDoubleState
 
SimpleMetropolisSampler.listenerPrinter - class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler.listenerPrinter.
 
SimpleMetropolisSampler.listenerPrinter() - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler.listenerPrinter
 
SimpleMetropolisSampler(PRNG, double, double, double) - Constructor for class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
six - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
SIZE - Static variable in class org.omegahat.Simulation.RandomGenerators.CollingsPRNGConstants
Number of good multiplier constants in the pool
size() - Method in class org.omegahat.Simulation.MCMC.MultiState
 
source - Variable in class org.omegahat.Simulation.MCMC.GenericMCMCEvent
 
source - Variable in class org.omegahat.Simulation.RandomGenerators.PRNGAdministratorEvent
 
split - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
SplittingProxyListener - class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener.
This object serves as a proxy MCMCListener that only forwards 1 out of every thinningFactor events to its subscribers
SplittingProxyListener.MyHandle - class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener.MyHandle.
 
SplittingProxyListener.MyHandle(SplittingProxyListener) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener.MyHandle
 
SplittingProxyListener() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener
 
sqrtMat(double[][]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
sqrtVec(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
square(double) - Static method in class org.omegahat.Probability.Distributions.MVNormal
 
square(double) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
square(double) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
square(double) - Method in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalDensity
 
square(double) - Method in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalLikelihood
 
SquaredDistanceWriter - class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter.
 
SquaredDistanceWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
SquaredDistanceWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
SquaredDistanceWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
SquaredDistanceWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
startProcess(String[]) - Method in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
state - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
state - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler.BivariateDoubleState
 
state - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler
 
state - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler.BivariateDoubleState
 
state - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler
 
state - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler.BivariateDoubleState
 
state - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain.doubleState
 
state - Variable in class org.omegahat.Simulation.MCMC.BaseMarkovChain
 
state - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
target distribution
state - Variable in class org.omegahat.Simulation.RandomGenerators.PRNGAdministratorEvent
 
state() - Method in class org.omegahat.Simulation.RandomGenerators.PRNGAdministratorEvent
 
state(PRNGState) - Method in class org.omegahat.Simulation.RandomGenerators.PRNGAdministratorEvent
 
step - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler.listenerPrinter
 
step - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler.listenerPrinter
 
step - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler.listenerPrinter
 
step - Variable in class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain.listenerPrinter
 
step - Variable in class org.omegahat.Simulation.MCMC.CustomGibbsSampler.listenerPrinter
 
step - Variable in class org.omegahat.Simulation.MCMC.CustomMarkovChain.listenerPrinter
 
step - Variable in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
step - Variable in class org.omegahat.Simulation.MCMC.Listeners.RecordingStepListener
 
step - Variable in class org.omegahat.Simulation.MCMC.Listeners.StepListenerPrinter
 
step() - Method in class org.omegahat.Simulation.MCMC.BaseMarkovChain
Generate the next state from the current state.
step() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
Generate the next state from the current state.
step() - Method in interface org.omegahat.Simulation.MCMC.MarkovChain
Generate the next state from the current state.
step() - Method in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
Generate the next state from the current state.
step() - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
StepListenerPrinter - class org.omegahat.Simulation.MCMC.Listeners.StepListenerPrinter.
Displays contents and counter of ChainStepEvents when one is recieved.
StepListenerPrinter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.StepListenerPrinter
 
storeTime - Variable in class org.omegahat.Simulation.MCMC.Listeners.AcceptanceWriter
 
storeTime - Variable in class org.omegahat.Simulation.MCMC.Listeners.CovarianceWriter
 
storeTime - Variable in class org.omegahat.Simulation.MCMC.Listeners.HistogramWriter
 
storeTime - Variable in class org.omegahat.Simulation.MCMC.Listeners.ListenerWriter
 
storeTime - Variable in class org.omegahat.Simulation.MCMC.Listeners.MeanWriter
 
storeTime - Variable in class org.omegahat.Simulation.MCMC.Listeners.ConditionalDistanceWriter
 
storeTime - Variable in class org.omegahat.Simulation.MCMC.Listeners.ConditionalSquaredDistanceWriter
 
storeTime - Variable in class org.omegahat.Simulation.MCMC.Listeners.DistanceWriter
 
storeTime - Variable in class org.omegahat.Simulation.MCMC.Listeners.SquaredDistanceWriter
 
StrippedListenerGzipWriter - class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerGzipWriter.
 
StrippedListenerGzipWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerGzipWriter
 
StrippedListenerGzipWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerGzipWriter
 
StrippedListenerGzipWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerGzipWriter
 
StrippedListenerWriter - class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerWriter.
 
StrippedListenerWriter() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerWriter
 
StrippedListenerWriter(String) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerWriter
 
StrippedListenerWriter(String, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerWriter
 
StrippedListenerWriter(String, boolean, boolean) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.StrippedListenerWriter
 
sumSqrSubsetCache - Variable in class org.omegahat.Simulation.MCMC.MultiDoubleState
 
SymmetricProposal - interface org.omegahat.Simulation.MCMC.SymmetricProposal.
A symmetric proposal distribution generates a new state based only on information from the current state and has the property that

T

target - Variable in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
target - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
target - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
proposal method
target() - Method in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
targets - Variable in class org.omegahat.Simulation.MCMC.MultiTarget
 
tCDF(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
CACM Algorithm 395, by G.
TestCollingsPRNG - class org.omegahat.Simulation.RandomGenerators.TestCollingsPRNG.
Test/Demo the Collings PRNG classes.
TestCollingsPRNG_Batch - class org.omegahat.Simulation.RandomGenerators.TestCollingsPRNG_Batch.
Test/Demo the Collings PRNG classes.
TestCollingsPRNG_Batch() - Constructor for class org.omegahat.Simulation.RandomGenerators.TestCollingsPRNG_Batch
 
TestCollingsPRNG() - Constructor for class org.omegahat.Simulation.RandomGenerators.TestCollingsPRNG
 
TestServer - class org.omegahat.Simulation.RandomGenerators.TestServer.
 
TestServer(String[]) - Constructor for class org.omegahat.Simulation.RandomGenerators.TestServer
 
thinningFactor - Variable in class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
ThinningProxyListener - class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener.
This object serves as a proxy MCMCListener that only forwards 1 out of every thinningFactor events to its subscribers
ThinningProxyListener.MyHandle - class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener.MyHandle.
 
ThinningProxyListener.MyHandle(ThinningProxyListener) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener.MyHandle
 
ThinningProxyListener() - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
ThinningProxyListener(int) - Constructor for class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
three - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
time - Variable in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
time - Variable in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
 
time - Variable in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
time - Variable in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
time - Variable in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
time() - Method in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
timeCalls - Variable in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
 
TimeDependentProposal - interface org.omegahat.Simulation.MCMC.Proposals.TimeDependentProposal.
 
timeInc() - Method in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
 
timeInc() - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
Increment time
timeInc() - Method in interface org.omegahat.Simulation.MCMC.Proposals.TimeDependentProposal
Increment time
timeInc() - Method in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
 
timeInc() - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
timeInc() - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
 
toDouble(int) - Static method in class org.omegahat.Simulation.RandomGenerators.Unsigned
Convert an int (treated as unsigned) to a double
TOL - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
toLong(int) - Static method in class org.omegahat.Simulation.RandomGenerators.Unsigned
Convert an int (treated as unsigned) to a long
toString() - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler.BivariateDoubleState
 
toString() - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleGibbsSampler.BivariateDoubleState
 
toString() - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisSampler.BivariateDoubleState
 
toString() - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMarkovChain.doubleState
 
toString() - Method in class org.omegahat.Simulation.MCMC.ContainerState
 
toString() - Method in class org.omegahat.Simulation.MCMC.DetailChainStepEvent
 
toString() - Method in class org.omegahat.Simulation.MCMC.DetailedMultiState
 
toString() - Method in class org.omegahat.Simulation.MCMC.GenericChainStepEvent
 
toString() - Method in class org.omegahat.Simulation.MCMC.GenericManagerChainEvent
 
toString() - Method in class org.omegahat.Simulation.MCMC.MCMCStateDatabase
 
toString() - Method in class org.omegahat.Simulation.MCMC.MultiState
 
toString() - Method in class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
 
toString() - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
toString(String, String, String, String, String, String) - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
totalEvents - Variable in class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
tPDF(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
tQuantile(double, double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
CACM Algorithm 396, by G.
tRand(double) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
transitionDensity(double[], double[]) - Method in class org.omegahat.Simulation.MCMC.Examples.SimpleMetropolisHastingsSampler
 
transitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.IteratedProposal
Convenience method for computing the probability of proposing a move.
transitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MixtureProposal
Convenience method for computing the probability of proposing a move.
transitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
Convenience method for computing the probability of proposing a move.
transitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalProposal
 
transitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
transitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisProposal
 
transitionProbability(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
transitionProbability(Object, Object) - Method in interface org.omegahat.Simulation.MCMC.GeneralProposal
Convenience method for computing the probability of proposing a move.
transitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveKernelProposal
 
transitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledMixtureProposal
Convenience method for computing the probability of proposing a move.
transitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
transitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
transitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.IndependentHastingsCoupledProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
transitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.AdaptiveMultiKernelProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
transitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.HastingsCoupledIteratedProposal
Convenience method for computing the probability of proposing a move.
transitionProbability(Object, Object, int, MultiState) - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
transitionProbability(Object, Object, int, MultiState) - Method in interface org.omegahat.Simulation.MCMC.HastingsCoupledProposal
Computes the HastingsCoupled transition probability for one sub-state given the entire state vector
transMat - Variable in class org.omegahat.Probability.Distributions.MVNormal
 
two - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 
TwoMultivariateNormalMixture - class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture.
A UpperWeight of Two Unit Multivariate normal densities
TwoMultivariateNormalMixture(double[], double[][], double[], double[][], double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
TwoMultivariateNormalMixture(double, int, double, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
TwoMultivariateNormalMixture(double, int, PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
TwoMultivariateNormalMixture(PRNG) - Constructor for class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
TWOVRPI - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 

U

ud_b_bb(int[], int[], double, double, double, double) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleLikelihood
 
udb(int, int, double) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleLikelihood
 
udbb(int, int, double, double) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleLikelihood
 
uniformRand - Variable in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
uniformRand - Variable in class org.omegahat.Simulation.MCMC.CustomHastingsCoupledSampler
 
uniformRand() - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
uniformRand() - Method in class org.omegahat.Probability.Distributions.PRNGDistributionFunctions
 
uniformRand() - Method in class org.omegahat.Simulation.MCMC.CustomMetropolisHastingsSampler
 
uniformSeeds(long, long) - Method in class org.omegahat.Probability.Distributions.DistributionFunctions
 
Univariate - interface Univariate.
 
unnorm_beta_binom(int, int, double, double) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
unnorm_binom(int, int, double) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
unnorm_dnorm(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
unnorm_log_beta_binom(int, int, double, double) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
unnorm_log_binom(int, int, double) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
unnorm_log_dnorm(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
unnorm_log_mixture_binom_beta_binom(int[], int[], double, double, double, double) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
unnorm_log_mixture_binom_beta_binom(int, int, double, double, double, double) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
unnorm_mixture_binom_beta_binom(int[], int[], double, double, double, double) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
unnorm_mixture_binom_beta_binom(int, int, double, double, double, double) - Static method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
unnormalized_density_betabinomial(int, int, double, double) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood
 
unnormalized_density_binomial(int, int, double) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood
 
unnormalized_density_loh(double, double, double, double) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood
 
UnnormalizedConditionalDensity - interface org.omegahat.Probability.Distributions.UnnormalizedConditionalDensity.
 
unnormalizedConditionalPDF(Object, Object) - Method in interface org.omegahat.Probability.Distributions.UnnormalizedConditionalDensity
 
unnormalizedConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Proposals.MultiProposal
 
unnormalizedConditionalPDF(Object, Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionGeneralProposal
 
UnnormalizedDensity - interface org.omegahat.Probability.Distributions.UnnormalizedDensity.
 
unnormalizedDensity(Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget
 
unnormalizedPDF(double[]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
unnormalizedPDF(double[], double, double) - Method in class org.omegahat.Probability.Distributions.Normal
 
unnormalizedPDF(double, double, double) - Method in class org.omegahat.Probability.Distributions.Normal
 
unnormalizedPDF(Object) - Method in interface org.omegahat.Probability.Distributions.UnnormalizedDensity
 
unnormalizedPDF(Object) - Method in class org.omegahat.Probability.Distributions.Normal
 
unnormalizedPDF(Object) - Method in class org.omegahat.Probability.Distributions.MVNormal
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_Binomial_Likelihood
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Examples.B_BB_Mixture
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_SimpleLikelihood
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood_Bimode
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalDensity
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalLikelihood
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Targets.PipeLikelihood
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Targets.CachingTarget
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.Expressions.ExpressionTarget
 
unnormalizedPDF(Object) - Method in class org.omegahat.Simulation.MCMC.MultiTarget
 
unormalized_density_binomial_betabinomial_mixture(int[], int[], int, double, double, double, double) - Method in class org.omegahat.Simulation.MCMC.Examples.Binomial_BetaBinomial_Likelihood
 
unregisterListener(MCMCListenerHandle) - Method in interface org.omegahat.Simulation.MCMC.NotifyingObject
Unregister a listener to be notified of events.
unregisterListener(MCMCListenerHandle) - Method in class org.omegahat.Simulation.MCMC.NotifyingMCMCObject
 
unregisterListener(MCMCListenerHandle) - Method in class org.omegahat.Simulation.MCMC.Listeners.ThinningProxyListener
 
unregisterListener(MCMCListenerHandle) - Method in class org.omegahat.Simulation.MCMC.Listeners.SplittingProxyListener
 
Unsigned - class org.omegahat.Simulation.RandomGenerators.Unsigned.
Package to provide conversion from/to integer values treated as unsigned.
Unsigned() - Constructor for class org.omegahat.Simulation.RandomGenerators.Unsigned
 
update(double) - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
update(Double) - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
update(double[]) - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
update(Double[]) - Method in class org.omegahat.Simulation.MCMC.Listeners.Histogram
 
upperEdge - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
upperWeight - Variable in class org.omegahat.Simulation.MCMC.Targets.TwoMultivariateNormalMixture
 
Utilities - class org.omegahat.Simulation.MCMC.Utilities.
 
Utilities() - Constructor for class org.omegahat.Simulation.MCMC.Utilities
 

V

var() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
Compute the covariance matrix
Var() - Method in class org.omegahat.Simulation.MCMC.MultiDoubleState
Compute the covariance matrix
variance - Static variable in interface org.omegahat.Simulation.RandomGenerators.PseudoRandomNormalGenerator
 
varNames - Variable in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
varNames() - Method in class org.omegahat.Simulation.MCMC.Listeners.ArrayListener
 
vm_epsilon - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 

W

weightsWithoutX1 - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
weightsWithX1 - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
weightsWithY - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
which - Variable in class org.omegahat.Simulation.MCMC.Proposals.NormalMetropolisComponentProposal
 
which - Variable in class org.omegahat.Simulation.MCMC.DetailHastingsCoupledStepEvent
 
wipeFields() - Method in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 

X

X - Variable in class org.omegahat.Simulation.MCMC.Targets.BivariateNormalLikelihood
 
X1 - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
X2 - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
xVx(double[], double[][]) - Method in class org.omegahat.Probability.Distributions.MVNormal
 

Y

Y - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 
Yindex - Variable in class org.omegahat.Simulation.MCMC.Proposals.KernelDirectionSampler
 

Z

zero - Static variable in class org.omegahat.Probability.Distributions.DistributionFunctions
 

A B C D E F G H I K L M N O P Q R S T U V W X Y Z