Boom: Bayesian Object Oriented Modeling

A C++ library for Bayesian modeling, with an emphasis on Markov chain Monte Carlo. Although boom contains a few R utilities (mainly plotting functions), its primary purpose is to install the BOOM C++ library on your system so that other packages can link against it.

Install the latest version of this package by entering the following in R:
install.packages("Boom")
AuthorSteven L. Scott is the sole author and creator of the BOOM project. Some code in the BOOM libraries has been modified from other open source projects. These include Cephes (obtained from Netlib, written by Stephen L. Moshier), NEWUOA (M.J.D Powell, obtained from Powell's web site), and a modified version of the R math libraries (R core development team). Original copyright notices have been maintained in all source files. In these cases, copyright claimed by Steven L. Scott is limited to modifications made to the original code.
Date of publication2017-04-07 22:13:43 UTC
MaintainerSteve Scott <stevescott@google.com>
LicenseLGPL-2.1 | file LICENSE
Version0.6

View on CRAN

Man pages

add.segments: Function to add horizontal line segments to an existing plot

ar1.coefficient.prior: Normal prior for an AR1 coefficient

beta.prior: Beta prior for a binomial proportion

boxplot.mcmc.matrix: Plot the distribution of a matrix

boxplot.true: side-by-side boxplots from a matrix, with optional reference...

check.data: Checking data formats

compare.den: Compare several density estimates.

compare.many.densities: Compare several density estimates.

compare.many.ts: Compares several density estimates.

compare.vector.distributions: Boxplots to compare distributions of vectors

dirichlet-distribution: The Dirichlet Distribution

dirichlet.prior: Dirichlet prior for a multinomial distribution

discrete-uniform-prior: Discrete prior distributions

dmvn: Multivariate Normal Density

double.model: Prior distributions for a real valued scalar

external.legend: Add an external legend to an array of plots.

gamma.prior: Gamma prior distribution

generate_factor_data: Generate a data frame of all factor data

histabunch: A Bunch of Histograms

inverse-wishart: Inverse Wishart Distribution

is.even: Check whether a number is even or odd.

lmgamma: Log Multivariate Gamma Function

lognormal.prior: Lognormal Prior Distribution

markov.prior: Prior for a Markov chain

match_data_frame: MatchDataFrame

mscan: Scan a Matrix

mvn.diagonal.prior: diagonal MVN prior

mvn.independent.sigma.prior: Independence prior for the MVN

mvn.prior: Multivariate normal prior

normal.inverse.gamma.prior: Normal inverse gamma prior

normal.inverse.wishart.prior: Normal inverse Wishart prior

normal.prior: Normal (scalar Gaussian) prior distribution

pairs.density: Pairs plot for posterior distributions.

plot.density.contours: Contour plot of a bivariate density.

plot.dynamic.distribution: Plots the pointwise evolution of a distribution over an index...

plot.macf: Plots individual autocorrelation functions for many-valued...

plot.many.ts: Multiple time series plots

regression.coefficient.conjugate.prior: Regression Coefficient Conjugate Prior

rmvn: Multivariate Normal Simulation

sd.prior: Prior for a standard deviation or variance

suggest.burn.log.likelihood: Suggest MCMC Burn-in from Log Likelihood

thin: Thin the rows of a matrix

thin.matrix: Thin a Matrix

ToString: Convert to Character String

traceproduct: Trace of the Product of Two Matrices

uniform.prior: Uniform prior distribution

wishart: Wishart Distribution

Functions

AddExternalLegend Man page
add.segments Man page
AddSegments Man page
Ar1CoefficientPrior Man page
BetaPrior Man page
boxplot.mcmc.matrix Man page
BoxplotMcmcMatrix Man page
boxplot.true Man page
BoxplotTrue Man page
check.data Man page
check.nonnegative.scalar Man page
check.positive.scalar Man page
check.probability.distribution Man page
check.scalar.integer Man page
check.scalar.probability Man page
compare.den Man page
CompareDen Man page
compare.densities Man page
CompareDensities Man page
compare.many.densities Man page
CompareManyDensities Man page
compare.many.ts Man page
CompareManyTs Man page
compare.vector.boxplots Man page
CompareVectorBoxplots Man page
ddirichlet Man page
dInverseWishart Man page
DirichletPrior Man page
DiscreteUniformPrior Man page
dmvn Man page
double.model Man page
DoubleModel Man page
dWishart Man page
ExternalLegendLayout Man page
GammaPrior Man page
GenerateFactorData Man page
histabunch Man page
is.even Man page
IsEven Man page
is.odd Man page
IsOdd Man page
lmgamma Man page
LognormalPrior Man page
MarkovPrior Man page
MatchDataFrame Man page
mscan Man page
MvnDiagonalPrior Man page
MvnIndependentSigmaPrior Man page
MvnPrior Man page
NormalInverseGammaPrior Man page
NormalInverseWishartPrior Man page
NormalPrior Man page
PairsDensity Man page
PlotDensityContours Man page
PlotDynamicDistribution Man page
plot.macf Man page
PlotMacf Man page
plot.many.ts Man page
PlotManyTs Man page
PointMassPrior Man page
PoissonPrior Man page
rdirichlet Man page
RegressionCoefficientConjugatePrior Man page
rmvn Man page
rWishart Man page
SdPrior Man page
SuggestBurnLogLikelihood Man page
thin Man page
ThinMatrix Man page
ToString Man page
ToString.default Man page
ToString.table Man page
TraceProduct Man page
TruncatedGammaPrior Man page
UniformPrior Man page

Files

inst
inst/include
inst/include/Samplers
inst/include/Samplers/UnivariateSliceSampler.hpp
inst/include/Samplers/ScalarLangevinSampler.hpp
inst/include/Samplers/ImportanceResampler.hpp
inst/include/Samplers/Sampler.hpp
inst/include/Samplers/UnivariateLangevinSampler.hpp
inst/include/Samplers/MoveAccounting.hpp
inst/include/Samplers/RejectionSampler.hpp
inst/include/Samplers/ScalarSliceSampler.hpp
inst/include/Samplers/ARMS.hpp
inst/include/Samplers/DirectProposal.hpp
inst/include/Samplers/SliceSampler.hpp
inst/include/Samplers/MetropolisHastings.hpp
inst/include/Samplers/TIM.hpp
inst/include/Samplers/MH_Proposals.hpp
inst/include/Samplers/ScalarAdaptiveRejectionSampler.hpp
inst/include/Samplers/Gilks
inst/include/Samplers/Gilks/arms.hpp
inst/include/distributions
inst/include/distributions/inverse_gaussian.hpp
inst/include/distributions/DoublyBoundedAdaptiveRejectionSampler.hpp
inst/include/distributions/trun_logit.hpp
inst/include/distributions/rng.hpp
inst/include/distributions/BinomialDistribution.hpp
inst/include/distributions/BoundedAdaptiveRejectionSampler.hpp
inst/include/distributions/Rmath_dist.hpp
inst/include/distributions/trun_gamma.hpp
inst/include/distributions/Markov.hpp
inst/include/LinAlg
inst/include/LinAlg/QR.hpp
inst/include/LinAlg/Kronecker.hpp
inst/include/LinAlg/Givens.hpp
inst/include/LinAlg/Array3.hpp
inst/include/LinAlg/SWEEP.hpp
inst/include/LinAlg/VectorView.hpp
inst/include/LinAlg/Selector.hpp
inst/include/LinAlg/DiagonalMatrix.hpp
inst/include/LinAlg/CorrelationMatrix.hpp
inst/include/LinAlg/LU.hpp
inst/include/LinAlg/LinAlgExceptions.hpp
inst/include/LinAlg/MatrixPartition.hpp
inst/include/LinAlg/ArrayIterator.hpp
inst/include/LinAlg/Array.hpp
inst/include/LinAlg/VectorViewIterator.hpp
inst/include/LinAlg/Vector.hpp
inst/include/LinAlg/SVD.hpp
inst/include/LinAlg/SpdMatrix.hpp
inst/include/LinAlg/Eigen.hpp
inst/include/LinAlg/blas.hpp
inst/include/LinAlg/Cholesky.hpp
inst/include/LinAlg/Matrix.hpp
inst/include/LinAlg/stack_columns.hpp
inst/include/LinAlg/SubMatrix.hpp
inst/include/cpputil
inst/include/cpputil/ordering.hpp
inst/include/cpputil/ParamHolder.hpp
inst/include/cpputil/random_element.hpp
inst/include/cpputil/ask_to_continue.hpp
inst/include/cpputil/make_unique_preserve_order.hpp
inst/include/cpputil/str2d.hpp
inst/include/cpputil/date_utils.hpp
inst/include/cpputil/index_table.hpp
inst/include/cpputil/stream.hpp
inst/include/cpputil/ProgramOptions.hpp
inst/include/cpputil/level_iterator.hpp
inst/include/cpputil/permute.hpp
inst/include/cpputil/ParamFileIoManager.hpp
inst/include/cpputil/Ptr.hpp
inst/include/cpputil/OutputTable.hpp
inst/include/cpputil/ThreadTools.hpp
inst/include/cpputil/Redirector.hpp
inst/include/cpputil/file_utils.hpp
inst/include/cpputil/lse.hpp
inst/include/cpputil/DateTime.hpp
inst/include/cpputil/math_utils.hpp
inst/include/cpputil/nyi.hpp
inst/include/cpputil/Date.hpp
inst/include/cpputil/compare_vector_bool.hpp
inst/include/cpputil/apply_permutation.hpp
inst/include/cpputil/scan.hpp
inst/include/cpputil/report_error.hpp
inst/include/cpputil/string_utils.hpp
inst/include/cpputil/seq.hpp
inst/include/cpputil/rep.hpp
inst/include/cpputil/DefaultVnames.hpp
inst/include/cpputil/print.hpp
inst/include/cpputil/Constants.hpp
inst/include/cpputil/ProgressTracker.hpp
inst/include/cpputil/unmap.hpp
inst/include/cpputil/portable_math.hpp
inst/include/cpputil/Split.hpp
inst/include/cpputil/parse_range.hpp
inst/include/cpputil/ThrowException.hpp
inst/include/cpputil/RefCounted.hpp
inst/include/cpputil/Polynomial.hpp
inst/include/cpputil/gll.hpp
inst/include/cpputil/LongString.hpp
inst/include/distributions.hpp
inst/include/TargetFun
inst/include/TargetFun/ScalarLogpostTF.hpp
inst/include/TargetFun/TargetFun.hpp
inst/include/TargetFun/LogPost.hpp
inst/include/TargetFun/JacobianChecker.hpp
inst/include/TargetFun/Loglike.hpp
inst/include/TargetFun/Transformation.hpp
inst/include/stats
inst/include/stats/Design.hpp
inst/include/stats/NaturalSpline.hpp
inst/include/stats/IQagent.hpp
inst/include/stats/ols.hpp
inst/include/stats/moments.hpp
inst/include/stats/logit.hpp
inst/include/stats/compare_binomial_proportions.hpp
inst/include/stats/diff.hpp
inst/include/stats/Resampler.hpp
inst/include/stats/regression.hpp
inst/include/stats/DataTable.hpp
inst/include/stats/Spline.hpp
inst/include/stats/ChiSquareTest.hpp
inst/include/stats/ks_critical_value.hpp
inst/include/stats/Bspline.hpp
inst/include/stats/Mspline.hpp
inst/include/stats/ECDF.hpp
inst/include/stats/FreqDist.hpp
inst/include/stats/simple_random_sample.hpp
inst/include/stats/compare_predictions.hpp
inst/include/Models
inst/include/Models/BernoulliModel.hpp
inst/include/Models/WeightedData.hpp
inst/include/Models/ZeroInflatedPoissonModel.hpp
inst/include/Models/DoubleModel.hpp
inst/include/Models/Glm
inst/include/Models/Glm/Glm.hpp
inst/include/Models/Glm/MultinomialProbitModel.hpp
inst/include/Models/Glm/MvnGivenX.hpp
inst/include/Models/Glm/WeightedRegressionModel.hpp
inst/include/Models/Glm/MultinomialLogitModel.hpp
inst/include/Models/Glm/ZeroInflatedGammaRegression.hpp
inst/include/Models/Glm/ChoiceData.hpp
inst/include/Models/Glm/PoissonRegressionData.hpp
inst/include/Models/Glm/ZeroInflatedPoissonRegression.hpp
inst/include/Models/Glm/ZeroInflatedLognormalRegression.hpp
inst/include/Models/Glm/HierarchicalPoissonRegression.hpp
inst/include/Models/Glm/LogisticRegressionModel.hpp
inst/include/Models/Glm/MvnGivenXandSigma.hpp
inst/include/Models/Glm/TRegression.hpp
inst/include/Models/Glm/BinomialProbitModel.hpp
inst/include/Models/Glm/RegressionModel.hpp
inst/include/Models/Glm/MvtRegModel.hpp
inst/include/Models/Glm/PoissonRegressionModel.hpp
inst/include/Models/Glm/GlmCoefs.hpp
inst/include/Models/Glm/MvReg2.hpp
inst/include/Models/Glm/ProbitRegression.hpp
inst/include/Models/Glm/PosteriorSamplers
inst/include/Models/Glm/PosteriorSamplers/TDataImputer.hpp
inst/include/Models/Glm/PosteriorSamplers/PoissonRegressionRwmSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/draw_logit_lambda.hpp
inst/include/Models/Glm/PosteriorSamplers/DAFE_MLM.hpp
inst/include/Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.hpp
inst/include/Models/Glm/PosteriorSamplers/MnpBetaGivenSigmaSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/MlogitRwm.hpp
inst/include/Models/Glm/PosteriorSamplers/MvtRegSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.hpp
inst/include/Models/Glm/PosteriorSamplers/PoissonDataImputer.hpp
inst/include/Models/Glm/PosteriorSamplers/ZeroInflatedGammaRegressionPosteriorSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.hpp
inst/include/Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/TRegressionSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/BregVsSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/AggregatedRegressionSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/MLVS.hpp
inst/include/Models/Glm/PosteriorSamplers/BinomialProbitSpikeSlabSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.hpp
inst/include/Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/SpikeSlabSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.hpp
inst/include/Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/ProbitRegressionSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/MLVS_data_imputer.hpp
inst/include/Models/Glm/PosteriorSamplers/NormalMixtureApproximation.hpp
inst/include/Models/Glm/PosteriorSamplers/CumulativeProbitSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/MnpBetaSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/RegressionConjSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/LogitSamplerBma.hpp
inst/include/Models/Glm/PosteriorSamplers/PartRegSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/QuantileRegressionPosteriorSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/LogitSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.hpp
inst/include/Models/Glm/PosteriorSamplers/MLAuxMixSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/NonconjugateRegressionSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/CumulativeLogitSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/VsPriorSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/MvRegSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/BinomialProbitCompositeSpikeSlabSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.hpp
inst/include/Models/Glm/PosteriorSamplers/GammaRegressionPosteriorSampler.hpp
inst/include/Models/Glm/BinomialLogitModel.hpp
inst/include/Models/Glm/GammaRegressionModel.hpp
inst/include/Models/Glm/BinomialRegressionData.hpp
inst/include/Models/Glm/AggregatedRegressionModel.hpp
inst/include/Models/Glm/OrdinalCutpointModel.hpp
inst/include/Models/Glm/VariableSelectionPrior.hpp
inst/include/Models/Glm/CumulativeProbitModel.hpp
inst/include/Models/Glm/ModelSelectionConcepts.hpp
inst/include/Models/Glm/GlmMvnPriorBase.hpp
inst/include/Models/Glm/QuantileRegressionModel.hpp
inst/include/Models/Glm/CumulativeLogitModel.hpp
inst/include/Models/MvnGivenSigma.hpp
inst/include/Models/ZeroMeanMvnModel.hpp
inst/include/Models/WishartModel.hpp
inst/include/Models/ExponentialModel.hpp
inst/include/Models/BinomialModel.hpp
inst/include/Models/MvnModel.hpp
inst/include/Models/ConstrainedVectorParams.hpp
inst/include/Models/MvtModel.hpp
inst/include/Models/MultinomialModel.hpp
inst/include/Models/IndependentMvnModelGivenScalarSigma.hpp
inst/include/Models/FiniteMixtureModel.hpp
inst/include/Models/ProductDirichletModel.hpp
inst/include/Models/SpdParams.hpp
inst/include/Models/Nonparametric
inst/include/Models/Nonparametric/BayesRules.hpp
inst/include/Models/Nonparametric/BayesRulesModel.hpp
inst/include/Models/Nonparametric/DataTableDataPolicy.hpp
inst/include/Models/Nonparametric/GaussianBayesRulesModel.hpp
inst/include/Models/Nonparametric/PosteriorSamplers
inst/include/Models/Nonparametric/PosteriorSamplers/ProposalDistributions.hpp
inst/include/Models/Nonparametric/PosteriorSamplers/GaussianBayesRulesPosteriorSampler.hpp
inst/include/Models/Nonparametric/PosteriorSamplers/BagOfRulesPrior.hpp
inst/include/Models/Nonparametric/PosteriorSamplers/BayesRulesPosteriorSampler.hpp
inst/include/Models/Mixtures
inst/include/Models/Mixtures/DirichletProcessMvnModel.hpp
inst/include/Models/Mixtures/ConditionalFiniteMixtureModel.hpp
inst/include/Models/Mixtures/PosteriorSamplers
inst/include/Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.hpp
inst/include/Models/Mixtures/PosteriorSamplers/ConditionalFiniteMixtureSampler.hpp
inst/include/Models/Policies
inst/include/Models/Policies/IID_DataPolicy.hpp
inst/include/Models/Policies/ParamPolicy_2.hpp
inst/include/Models/Policies/PriorPolicy.hpp
inst/include/Models/Policies/ManyParamPolicy.hpp
inst/include/Models/Policies/DataInfoPolicy.hpp
inst/include/Models/Policies/CompositeParamPolicy.hpp
inst/include/Models/Policies/NullParamPolicy.hpp
inst/include/Models/Policies/ParamPolicy_1.hpp
inst/include/Models/Policies/NullDataPolicy.hpp
inst/include/Models/Policies/SufstatOnlyDataPolicy.hpp
inst/include/Models/Policies/ParamPolicy_4.hpp
inst/include/Models/Policies/SufstatDataPolicy.hpp
inst/include/Models/Policies/NonparametricParamPolicy.hpp
inst/include/Models/Policies/MixtureDataPolicy.hpp
inst/include/Models/Policies/ParamPolicy_3.hpp
inst/include/Models/PoissonModel.hpp
inst/include/Models/ParamTypes.hpp
inst/include/Models/CompositeModel.hpp
inst/include/Models/DataPair.hpp
inst/include/Models/LognormalModel.hpp
inst/include/Models/GaussianModelGivenSigma.hpp
inst/include/Models/HMM
inst/include/Models/HMM/hmm_tools.hpp
inst/include/Models/HMM/HmmFilter.hpp
inst/include/Models/HMM/Clickstream
inst/include/Models/HMM/Clickstream/NestedHmm.hpp
inst/include/Models/HMM/Clickstream/Session.hpp
inst/include/Models/HMM/Clickstream/PosteriorSamplers
inst/include/Models/HMM/Clickstream/PosteriorSamplers/NestedHmmPosteriorSampler.hpp
inst/include/Models/HMM/Clickstream/Stream.hpp
inst/include/Models/HMM/Clickstream/Event.hpp
inst/include/Models/HMM/HmmDataImputer.hpp
inst/include/Models/HMM/PosteriorSamplers
inst/include/Models/HMM/PosteriorSamplers/HmmPosteriorSampler.hpp
inst/include/Models/HMM/HealthStateModel.hpp
inst/include/Models/HMM/HMM2.hpp
inst/include/Models/MarginallyUniformCorrelationModel.hpp
inst/include/Models/MvnGivenScalarSigma.hpp
inst/include/Models/SpdModel.hpp
inst/include/Models/SufstatAbstractCombineImpl.hpp
inst/include/Models/MvnBase.hpp
inst/include/Models/UniformShrinkagePriorModel.hpp
inst/include/Models/DataTypes.hpp
inst/include/Models/SpdData.hpp
inst/include/Models/GaussianModelBase.hpp
inst/include/Models/ZeroInflatedLognormalModel.hpp
inst/include/Models/UniformCorrelationModel.hpp
inst/include/Models/Bart
inst/include/Models/Bart/GaussianBartModel.hpp
inst/include/Models/Bart/Bart.hpp
inst/include/Models/Bart/ResidualRegressionData.hpp
inst/include/Models/Bart/LogitBartModel.hpp
inst/include/Models/Bart/PosteriorSamplers
inst/include/Models/Bart/PosteriorSamplers/BartPosteriorSampler.hpp
inst/include/Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.hpp
inst/include/Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.hpp
inst/include/Models/Bart/PosteriorSamplers/GaussianLinearBartPosteriorSampler.hpp
inst/include/Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.hpp
inst/include/Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.hpp
inst/include/Models/Bart/ProbitBartModel.hpp
inst/include/Models/Bart/GaussianLinearBartModel.hpp
inst/include/Models/Bart/PoissonBartModel.hpp
inst/include/Models/PosteriorSamplers
inst/include/Models/PosteriorSamplers/ExchangeableDirichletSampler.hpp
inst/include/Models/PosteriorSamplers/FixedSpdSampler.hpp
inst/include/Models/PosteriorSamplers/MultinomialDirichletSampler.hpp
inst/include/Models/PosteriorSamplers/PoissonGammaSampler.hpp
inst/include/Models/PosteriorSamplers/MvnVarSampler.hpp
inst/include/Models/PosteriorSamplers/PosteriorSampler.hpp
inst/include/Models/PosteriorSamplers/ProductDirichletPosteriorSampler.hpp
inst/include/Models/PosteriorSamplers/FixedProbBinomialSampler.hpp
inst/include/Models/PosteriorSamplers/PoissonGammaPosteriorSampler.hpp
inst/include/Models/PosteriorSamplers/SepStratSampler.hpp
inst/include/Models/PosteriorSamplers/MvnMeanSampler.hpp
inst/include/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.hpp
inst/include/Models/PosteriorSamplers/BetaBinomialPosteriorSampler.hpp
inst/include/Models/PosteriorSamplers/IndependentMvnVarSampler.hpp
inst/include/Models/PosteriorSamplers/ExponentialGammaSampler.hpp
inst/include/Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.hpp
inst/include/Models/PosteriorSamplers/MarkovConjSampler.hpp
inst/include/Models/PosteriorSamplers/GaussianConjSampler.hpp
inst/include/Models/PosteriorSamplers/ZeroInflatedPoissonSampler.hpp
inst/include/Models/PosteriorSamplers/FiniteMixturePosteriorSampler.hpp
inst/include/Models/PosteriorSamplers/BetaBinomialSampler.hpp
inst/include/Models/PosteriorSamplers/CompositeModelSampler.hpp
inst/include/Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.hpp
inst/include/Models/PosteriorSamplers/SharedSigsqSampler.hpp
inst/include/Models/PosteriorSamplers/CorrelationSampler.hpp
inst/include/Models/PosteriorSamplers/FixedUnivariateSampler.hpp
inst/include/Models/PosteriorSamplers/DirichletPosteriorSampler.hpp
inst/include/Models/PosteriorSamplers/GaussianVarSampler.hpp
inst/include/Models/PosteriorSamplers/CompositeSampler.hpp
inst/include/Models/PosteriorSamplers/GaussianMeanSampler.hpp
inst/include/Models/PosteriorSamplers/GammaPosteriorSampler.hpp
inst/include/Models/PosteriorSamplers/MarkovConjShrinkageSampler.hpp
inst/include/Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.hpp
inst/include/Models/PosteriorSamplers/IndependentMvnConjSampler.hpp
inst/include/Models/PosteriorSamplers/Imputer.hpp
inst/include/Models/PosteriorSamplers/MvnConjSampler.hpp
inst/include/Models/PosteriorSamplers/MvnIndependentVarianceSampler.hpp
inst/include/Models/PosteriorSamplers/ZeroMeanMvnConjSampler.hpp
inst/include/Models/PosteriorSamplers/BetaPosteriorSampler.hpp
inst/include/Models/PosteriorSamplers/AbsorbingMarkovConjSampler.hpp
inst/include/Models/PosteriorSamplers/GenericGaussianVarianceSampler.hpp
inst/include/Models/StateSpace
inst/include/Models/StateSpace/StateSpacePoissonModel.hpp
inst/include/Models/StateSpace/StateSpaceModelBase.hpp
inst/include/Models/StateSpace/StateSpaceNormalMixture.hpp
inst/include/Models/StateSpace/AggregatedStateSpaceRegression.hpp
inst/include/Models/StateSpace/StateSpaceStudentRegressionModel.hpp
inst/include/Models/StateSpace/StateSpaceRegressionModel.hpp
inst/include/Models/StateSpace/PosteriorSamplers
inst/include/Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.hpp
inst/include/Models/StateSpace/PosteriorSamplers/SufstatManager.hpp
inst/include/Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.hpp
inst/include/Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.hpp
inst/include/Models/StateSpace/PosteriorSamplers/StateSpaceRegressionSampler.hpp
inst/include/Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.hpp
inst/include/Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.hpp
inst/include/Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.hpp
inst/include/Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.hpp
inst/include/Models/StateSpace/StateSpaceLogitModel.hpp
inst/include/Models/StateSpace/StateSpaceModel.hpp
inst/include/Models/StateSpace/Filters
inst/include/Models/StateSpace/Filters/SparseVector.hpp
inst/include/Models/StateSpace/Filters/SparseMatrix.hpp
inst/include/Models/StateSpace/Filters/ScalarKalmanStorage.hpp
inst/include/Models/StateSpace/Filters/SparseKalmanTools.hpp
inst/include/Models/StateSpace/Filters/KalmanTools.hpp
inst/include/Models/StateSpace/StateModels
inst/include/Models/StateSpace/StateModels/Holiday.hpp
inst/include/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.hpp
inst/include/Models/StateSpace/StateModels/StudentLocalLinearTrend.hpp
inst/include/Models/StateSpace/StateModels/ArStateModel.hpp
inst/include/Models/StateSpace/StateModels/DynamicRegressionStateModel.hpp
inst/include/Models/StateSpace/StateModels/RegressionStateModel.hpp
inst/include/Models/StateSpace/StateModels/TrigStateModel.hpp
inst/include/Models/StateSpace/StateModels/LocalLinearTrend.hpp
inst/include/Models/StateSpace/StateModels/SeasonalStateModel.hpp
inst/include/Models/StateSpace/StateModels/SemilocalLinearTrend.hpp
inst/include/Models/StateSpace/StateModels/StateModel.hpp
inst/include/Models/StateSpace/StateModels/LocalLevelStateModel.hpp
inst/include/Models/EmMixtureComponent.hpp
inst/include/Models/UniformModel.hpp
inst/include/Models/WeightedGaussianSuf.hpp
inst/include/Models/PointProcess
inst/include/Models/PointProcess/MarkovModulatedPoissonProcess.hpp
inst/include/Models/PointProcess/PoissonClusterProcess.hpp
inst/include/Models/PointProcess/PoissonProcess.hpp
inst/include/Models/PointProcess/HomogeneousPoissonProcess.hpp
inst/include/Models/PointProcess/BoundedPoissonProcessSimulator.hpp
inst/include/Models/PointProcess/PosteriorSamplers
inst/include/Models/PointProcess/PosteriorSamplers/WeeklyCyclePoissonProcessSampler.hpp
inst/include/Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.hpp
inst/include/Models/PointProcess/PosteriorSamplers/PoissonClusterPosteriorSampler.hpp
inst/include/Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.hpp
inst/include/Models/PointProcess/WeeklyCyclePoissonProcess.hpp
inst/include/Models/PointProcess/PointProcess.hpp
inst/include/Models/PointProcess/CosinePoissonProcess.hpp
inst/include/Models/ModelTypes.hpp
inst/include/Models/ZeroInflatedGammaModel.hpp
inst/include/Models/IndependentMvnModel.hpp
inst/include/Models/PoissonGammaModel.hpp
inst/include/Models/ProductVectorModel.hpp
inst/include/Models/Sufstat.hpp
inst/include/Models/GaussianModel.hpp
inst/include/Models/BetaBinomialModel.hpp
inst/include/Models/TruncatedGammaModel.hpp
inst/include/Models/BetaModel.hpp
inst/include/Models/IRT
inst/include/Models/IRT/SubjectPrior.hpp
inst/include/Models/IRT/PcrNid.hpp
inst/include/Models/IRT/PartialCreditModel.hpp
inst/include/Models/IRT/SubjectSliceSampler.hpp
inst/include/Models/IRT/IRT.hpp
inst/include/Models/IRT/Subject.hpp
inst/include/Models/IRT/ItemDataPolicy.hpp
inst/include/Models/IRT/IrtModel.hpp
inst/include/Models/IRT/multisubscale_logit_cutpoint_model.hpp
inst/include/Models/IRT/Item.hpp
inst/include/Models/IRT/DafePcrRwm.hpp
inst/include/Models/IRT/DafePcr.hpp
inst/include/Models/IRT/ItemSliceSampler.hpp
inst/include/Models/IRT/Subject_prior.hpp
inst/include/Models/GammaModel.hpp
inst/include/Models/ChisqModel.hpp
inst/include/Models/WeightedMvnModel.hpp
inst/include/Models/ZeroMeanGaussianModel.hpp
inst/include/Models/Hierarchical
inst/include/Models/Hierarchical/HierarchicalZeroInflatedGammaModel.hpp
inst/include/Models/Hierarchical/HierarchicalDirichletModel.hpp
inst/include/Models/Hierarchical/HierarchicalPoissonModel.hpp
inst/include/Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.hpp
inst/include/Models/Hierarchical/PosteriorSamplers
inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalGammaSampler.hpp
inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalDirichletPosteriorSampler.hpp
inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedPoissonSampler.hpp
inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedGammaSampler.hpp
inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.hpp
inst/include/Models/Hierarchical/HierarchicalGammaModel.hpp
inst/include/Models/Hierarchical/HierarchicalModel.hpp
inst/include/Models/CompositeData.hpp
inst/include/Models/ScaledChisqModel.hpp
inst/include/Models/DirichletModel.hpp
inst/include/Models/TimeSeries
inst/include/Models/TimeSeries/ArModel.hpp
inst/include/Models/TimeSeries/AugmentedTimeSeriesDataPolicy.hpp
inst/include/Models/TimeSeries/TimeSeriesSufstatDataPolicy.hpp
inst/include/Models/TimeSeries/TimeSeries.hpp
inst/include/Models/TimeSeries/TimeSeriesDataPolicy.hpp
inst/include/Models/TimeSeries/MarkovLink.hpp
inst/include/Models/TimeSeries/AugmentedTimeSeries.hpp
inst/include/Models/TimeSeries/PosteriorSamplers
inst/include/Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.hpp
inst/include/Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.hpp
inst/include/Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.hpp
inst/include/Models/TimeSeries/NonzeroMeanAr1Model.hpp
inst/include/Models/DiscreteUniformModel.hpp
inst/include/Models/VectorModel.hpp
inst/include/Models/CategoricalData.hpp
inst/include/Models/MarkovModel.hpp
inst/include/r_interface
inst/include/r_interface/create_mixture_component.hpp
inst/include/r_interface/determine_nthreads.hpp
inst/include/r_interface/create_poisson_cluster_components.hpp
inst/include/r_interface/print_R_timestamp.hpp
inst/include/r_interface/boom_r_tools.hpp
inst/include/r_interface/handle_exception.hpp
inst/include/r_interface/create_point_process.hpp
inst/include/r_interface/create_poisson_process.hpp
inst/include/r_interface/seed_rng_from_R.hpp
inst/include/r_interface/create_state_model.hpp
inst/include/r_interface/parse_model_formula.hpp
inst/include/r_interface/list_io.hpp
inst/include/r_interface/prior_specification.hpp
inst/include/numopt.hpp
inst/include/uint.hpp
inst/include/numopt
inst/include/numopt/NumericalDerivatives.hpp
inst/include/numopt/Powell.hpp
inst/include/numopt/ScalarNewtonMax.hpp
inst/include/numopt/Integral.hpp
inst/include/numopt/Brent.hpp
inst/include/numopt/NelderMead.hpp
inst/include/numopt/ScalarLaplaceApproximation.hpp
inst/include/numopt/initialize_derivatives.hpp
inst/include/BOOM.hpp
src
src/create_mixture_component.cpp
src/Makevars
src/spike_slab_prior.cpp
src/math
src/math/special_functions.hpp
src/math/cephes
src/math/cephes/zetac.cpp
src/math/cephes/sici.cpp
src/math/cephes/zeta.cpp
src/math/cephes/planck.cpp
src/math/cephes/fresnl.cpp
src/math/cephes/powi.cpp
src/math/cephes/ei.cpp
src/math/cephes/polevl.cpp
src/math/cephes/expn.cpp
src/math/cephes/chbevl.cpp
src/math/cephes/polylog.cpp
src/math/cephes/fac.cpp
src/math/cephes/dawsn.cpp
src/math/cephes/rgamma.cpp
src/math/cephes/shichi.cpp
src/math/cephes/cephes_impl.hpp
src/math/cephes/spence.cpp
src/math/lmultigamma.cpp
src/create_poisson_process.cpp
src/print_R_timestamp.cpp
src/handle_exception.cpp
src/install.libs.R
src/Samplers
src/Samplers/ScalarLangevinSampler.cpp
src/Samplers/MH_Proposals.cpp
src/Samplers/MoveAccounting.cpp
src/Samplers/Sampler.cpp
src/Samplers/MetropolisHastings.cpp
src/Samplers/RejectionSampler.cpp
src/Samplers/UnivariateLangevinSampler.cpp
src/Samplers/TIM.cpp
src/Samplers/ARMS.cpp
src/Samplers/SliceSampler.cpp
src/Samplers/ScalarAdaptiveRejectionSampler.cpp
src/Samplers/ImportanceResampler.cpp
src/Samplers/DirectProposal.cpp
src/Samplers/ScalarSliceSampler.cpp
src/Samplers/Gilks
src/Samplers/Gilks/arms.cpp
src/Samplers/UnivariateSliceSampler.cpp
src/create_poisson_cluster_components.cpp
src/distributions
src/distributions/Markov.cpp
src/distributions/rmulti.cpp
src/distributions/mvn.cpp
src/distributions/BinomialDistribution.cpp
src/distributions/Tn2Sampler.cpp
src/distributions/trun_logit.cpp
src/distributions/trun_norm.cpp
src/distributions/trun_exp.cpp
src/distributions/random_int.cpp
src/distributions/Rmath_dist.cpp
src/distributions/student_fix.cpp
src/distributions/rlexp.cpp
src/distributions/BoundedAdaptiveRejectionSampler.cpp
src/distributions/matrix_normal.cpp
src/distributions/usp.cpp
src/distributions/DoublyBoundedAdaptiveRejectionSampler.cpp
src/distributions/dirichlet.cpp
src/distributions/random_cor.cpp
src/distributions/trun_gamma.cpp
src/distributions/Wishart.cpp
src/distributions/extreme_value.cpp
src/distributions/rtriangle.cpp
src/distributions/rng.cpp
src/distributions/inverse_gaussian.cpp
src/distributions/mvt.cpp
src/list_io.cpp
src/LinAlg
src/LinAlg/Selector.cpp
src/LinAlg/QR.cpp
src/LinAlg/VectorView.cpp
src/LinAlg/Eigen.cpp
src/LinAlg/SubMatrix.cpp
src/LinAlg/Cholesky.cpp
src/LinAlg/Matrix.cpp
src/LinAlg/LinAlgExceptions.cpp
src/LinAlg/MatrixPartition.cpp
src/LinAlg/stack_columns.cpp
src/LinAlg/Givens.cpp
src/LinAlg/blas.cpp
src/LinAlg/SVD.cpp
src/LinAlg/Kronecker.cpp
src/LinAlg/Array.cpp
src/LinAlg/SWEEP.cpp
src/LinAlg/ArrayIterator.cpp
src/LinAlg/Vector.cpp
src/LinAlg/DiagonalMatrix.cpp
src/LinAlg/CorrelationMatrix.cpp
src/LinAlg/SpdMatrix.cpp
src/LinAlg/LU.cpp
src/LinAlg/Array3.cpp
src/create_state_model.cpp
src/cpputil
src/cpputil/is_numeric.cpp
src/cpputil/split_string.cpp
src/cpputil/is_all_white.cpp
src/cpputil/strip_path.cpp
src/cpputil/LongString.cpp
src/cpputil/strip.cpp
src/cpputil/report_error.cpp
src/cpputil/ParamHolder.cpp
src/cpputil/infinity.cpp
src/cpputil/strip_white_space.cpp
src/cpputil/split.cpp
src/cpputil/gll.cpp
src/cpputil/DateTime.cpp
src/cpputil/DefaultVnames.cpp
src/cpputil/get_date.cpp
src/cpputil/lse.cpp
src/cpputil/ThreadTools.cpp
src/cpputil/print_columns.cpp
src/cpputil/Constants.cpp
src/cpputil/read_file.cpp
src/cpputil/safelog.cpp
src/cpputil/rep.cpp
src/cpputil/str2d.cpp
src/cpputil/trim_white_space.cpp
src/cpputil/Date.cpp
src/cpputil/split_delimited.cpp
src/cpputil/OutputTable.cpp
src/cpputil/legalize_file_name.cpp
src/cpputil/parse_range.cpp
src/cpputil/Polynomial.cpp
src/cpputil/compare_vector_bool.cpp
src/cpputil/Redirector.cpp
src/cpputil/apply_permutation.cpp
src/cpputil/replace_all.cpp
src/cpputil/substring_delimited.cpp
src/cpputil/cat_string.cpp
src/boom_r_tools.cpp
src/TargetFun
src/TargetFun/ScalarLogpostTF.cpp
src/TargetFun/LogPost.cpp
src/TargetFun/JacobianChecker.cpp
src/TargetFun/TargetFun.cpp
src/TargetFun/Transformation.cpp
src/determine_nthreads.cpp
src/stats
src/stats/NaturalSpline.cpp
src/stats/diff.cpp
src/stats/ChiSquareTest.cpp
src/stats/regression.cpp
src/stats/Mspline.cpp
src/stats/compare_predictions.cpp
src/stats/Design.cpp
src/stats/DataTable.cpp
src/stats/Resampler.cpp
src/stats/IQagent.cpp
src/stats/Spline.cpp
src/stats/simple_random_sample.cpp
src/stats/Bspline.cpp
src/stats/ECDF.cpp
src/stats/moments.cpp
src/stats/FreqDist.cpp
src/stats/compare_binomial_proportions.cpp
src/Models
src/Models/TruncatedGammaModel.cpp
src/Models/ScaledChisqModel.cpp
src/Models/ZeroInflatedGammaModel.cpp
src/Models/FiniteMixtureModel.cpp
src/Models/LognormalModel.cpp
src/Models/MvtModel.cpp
src/Models/Glm
src/Models/Glm/ZeroInflatedGammaRegression.cpp
src/Models/Glm/MvnGivenX.cpp
src/Models/Glm/PoissonRegressionModel.cpp
src/Models/Glm/GlmCoefs.cpp
src/Models/Glm/HierarchicalPoissonRegression.cpp
src/Models/Glm/MvtRegModel.cpp
src/Models/Glm/GammaRegressionModel.cpp
src/Models/Glm/Glm.cpp
src/Models/Glm/ZeroInflatedPoissonRegression.cpp
src/Models/Glm/BinomialLogitModel.cpp
src/Models/Glm/LogisticRegressionModel.cpp
src/Models/Glm/ChoiceData.cpp
src/Models/Glm/BinomialRegressionData.cpp
src/Models/Glm/MvReg2.cpp
src/Models/Glm/OrdinalCutpointModel.cpp
src/Models/Glm/WeightedRegressionModel.cpp
src/Models/Glm/MvnGivenXandSigma.cpp
src/Models/Glm/BinomialProbitModel.cpp
src/Models/Glm/PosteriorSamplers
src/Models/Glm/PosteriorSamplers/GammaRegressionPosteriorSampler.cpp
src/Models/Glm/PosteriorSamplers/PoissonRegressionRwmSampler.cpp
src/Models/Glm/PosteriorSamplers/CumulativeProbitSampler.cpp
src/Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.cpp
src/Models/Glm/PosteriorSamplers/VsPriorSampler.cpp
src/Models/Glm/PosteriorSamplers/LogitSampler.cpp
src/Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.cpp
src/Models/Glm/PosteriorSamplers/TDataImputer.cpp
src/Models/Glm/PosteriorSamplers/draw_logit_lambda.cpp
src/Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.cpp
src/Models/Glm/PosteriorSamplers/BregVsSampler.cpp
src/Models/Glm/PosteriorSamplers/TRegressionSampler.cpp
src/Models/Glm/PosteriorSamplers/LogitSamplerBma.cpp
src/Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.cpp
src/Models/Glm/PosteriorSamplers/NormalMixtureApproximation.cpp
src/Models/Glm/PosteriorSamplers/PoissonDataImputer.cpp
src/Models/Glm/PosteriorSamplers/RegressionConjSampler.cpp
src/Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.cpp
src/Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_1.cpp
src/Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.cpp
src/Models/Glm/PosteriorSamplers/DAFE_MLM.cpp
src/Models/Glm/PosteriorSamplers/MlogitRwm.cpp
src/Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.cpp
src/Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.cpp
src/Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.cpp
src/Models/Glm/PosteriorSamplers/PartRegSampler.cpp
src/Models/Glm/PosteriorSamplers/BinomialProbitCompositeSpikeSlabSampler.cpp
src/Models/Glm/PosteriorSamplers/MnpBetaSampler.cpp
src/Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.cpp
src/Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.cpp
src/Models/Glm/PosteriorSamplers/AggregatedRegressionSampler.cpp
src/Models/Glm/PosteriorSamplers/BinomialProbitSpikeSlabSampler.cpp
src/Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.cpp
src/Models/Glm/PosteriorSamplers/MLVS.cpp
src/Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.cpp
src/Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.cpp
src/Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.cpp
src/Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.cpp
src/Models/Glm/PosteriorSamplers/QuantileRegressionPosteriorSampler.cpp
src/Models/Glm/PosteriorSamplers/SpikeSlabSampler.cpp
src/Models/Glm/PosteriorSamplers/ProbitRegressionSampler.cpp
src/Models/Glm/PosteriorSamplers/MvRegSampler.cpp
src/Models/Glm/PosteriorSamplers/MvtRegSampler.cpp
src/Models/Glm/PosteriorSamplers/MLVS_data_imputer.cpp
src/Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.cpp
src/Models/Glm/PosteriorSamplers/CumulativeLogitSampler.cpp
src/Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.cpp
src/Models/Glm/PosteriorSamplers/MLAuxMixSampler.cpp
src/Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.cpp
src/Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.cpp
src/Models/Glm/PosteriorSamplers/NonconjugateRegressionSampler.cpp
src/Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.cpp
src/Models/Glm/PosteriorSamplers/MnpBetaGivenSigmaSampler.cpp
src/Models/Glm/VariableSelectionPrior.cpp
src/Models/Glm/PoissonRegressionData.cpp
src/Models/Glm/CumulativeLogitModel.cpp
src/Models/Glm/ZeroInflatedLognormalRegression.cpp
src/Models/Glm/MultinomialProbitModel.cpp
src/Models/Glm/CumulativeProbitModel.cpp
src/Models/Glm/ProbitRegression.cpp
src/Models/Glm/MultinomialLogitModel.cpp
src/Models/Glm/QuantileRegressionModel.cpp
src/Models/Glm/AggregatedRegressionModel.cpp
src/Models/Glm/RegressionModel.cpp
src/Models/Glm/TRegression.cpp
src/Models/WeightedMvnModel.cpp
src/Models/WeightedGaussianSuf.cpp
src/Models/MvnGivenScalarSigma.cpp
src/Models/MvnBase.cpp
src/Models/IndependentMvnModelGivenScalarSigma.cpp
src/Models/ChisqModel.cpp
src/Models/GaussianModelGivenSigma.cpp
src/Models/PoissonGammaModel.cpp
src/Models/CompositeModel.cpp
src/Models/SpdParams.cpp
src/Models/BetaBinomialModel.cpp
src/Models/MvnGivenSigma.cpp
src/Models/DataTypes.cpp
src/Models/MvnModel.cpp
src/Models/IndependentMvnModel.cpp
src/Models/UniformModel.cpp
src/Models/GaussianModel.cpp
src/Models/Mixtures
src/Models/Mixtures/ConditionalFiniteMixtureModel.cpp
src/Models/Mixtures/PosteriorSamplers
src/Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.cpp
src/Models/Mixtures/PosteriorSamplers/ConditionalFiniteMixtureSampler.cpp
src/Models/Mixtures/DirichletProcessMvnModel.cpp
src/Models/Policies
src/Models/Policies/MixtureDataPolicy.cpp
src/Models/Policies/ManyParamPolicy.cpp
src/Models/Policies/CompositeParamPolicy.cpp
src/Models/Policies/PriorPolicy.cpp
src/Models/Policies/NullParamPolicy.cpp
src/Models/ExponentialModel.cpp
src/Models/UniformShrinkagePriorModel.cpp
src/Models/CompositeData.cpp
src/Models/DiscreteUniformModel.cpp
src/Models/GaussianModelBase.cpp
src/Models/ModelTypes.cpp
src/Models/ParamTypes.cpp
src/Models/SpdModel.cpp
src/Models/MultinomialModel.cpp
src/Models/BetaModel.cpp
src/Models/HMM
src/Models/HMM/HmmFilter.cpp
src/Models/HMM/HMM2.cpp
src/Models/HMM/hmm_tools.cpp
src/Models/HMM/Clickstream
src/Models/HMM/Clickstream/NestedHmm.cpp
src/Models/HMM/Clickstream/Event.cpp
src/Models/HMM/Clickstream/Session.cpp
src/Models/HMM/Clickstream/Stream.cpp
src/Models/HMM/Clickstream/PosteriorSamplers
src/Models/HMM/Clickstream/PosteriorSamplers/NestedHmmPosteriorSampler.cpp
src/Models/HMM/PosteriorSamplers
src/Models/HMM/PosteriorSamplers/HmmPosteriorSampler.cpp
src/Models/HMM/HmmDataImputer.cpp
src/Models/HMM/HealthStateModel.cpp
src/Models/ZeroMeanGaussianModel.cpp
src/Models/ConstrainedVectorParams.cpp
src/Models/ProductDirichletModel.cpp
src/Models/CategoricalData.cpp
src/Models/UniformCorrelationModel.cpp
src/Models/GammaModel.cpp
src/Models/Bart
src/Models/Bart/PoissonBartModel.cpp
src/Models/Bart/GaussianBartModel.cpp
src/Models/Bart/ProbitBartModel.cpp
src/Models/Bart/Bart.cpp
src/Models/Bart/GaussianLinearBartModel.cpp
src/Models/Bart/PosteriorSamplers
src/Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.cpp
src/Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.cpp
src/Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.cpp
src/Models/Bart/PosteriorSamplers/GaussianLinearBartPosteriorSampler.cpp
src/Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.cpp
src/Models/Bart/PosteriorSamplers/BartPosteriorSampler.cpp
src/Models/Bart/ResidualRegressionData.cpp
src/Models/Bart/LogitBartModel.cpp
src/Models/PosteriorSamplers
src/Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.cpp
src/Models/PosteriorSamplers/FixedProbBinomialSampler.cpp
src/Models/PosteriorSamplers/BetaPosteriorSampler.cpp
src/Models/PosteriorSamplers/SepStratSampler.cpp
src/Models/PosteriorSamplers/GammaPosteriorSampler.cpp
src/Models/PosteriorSamplers/ExponentialGammaSampler.cpp
src/Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.cpp
src/Models/PosteriorSamplers/ZeroInflatedPoissonSampler.cpp
src/Models/PosteriorSamplers/GaussianVarSampler.cpp
src/Models/PosteriorSamplers/IndependentMvnConjSampler.cpp
src/Models/PosteriorSamplers/ExchangeableDirichletSampler.cpp
src/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.cpp
src/Models/PosteriorSamplers/SharedSigsqSampler.cpp
src/Models/PosteriorSamplers/CompositeModelSampler.cpp
src/Models/PosteriorSamplers/BetaBinomialSampler.cpp
src/Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.cpp
src/Models/PosteriorSamplers/MarkovConjSampler.cpp
src/Models/PosteriorSamplers/PoissonGammaSampler.cpp
src/Models/PosteriorSamplers/MvnVarSampler.cpp
src/Models/PosteriorSamplers/MvnIndependentVarianceSampler.cpp
src/Models/PosteriorSamplers/MarkovConjShrinkageSampler.cpp
src/Models/PosteriorSamplers/ProductDirichletPosteriorSampler.cpp
src/Models/PosteriorSamplers/GaussianConjSampler.cpp
src/Models/PosteriorSamplers/CompositeSampler.cpp
src/Models/PosteriorSamplers/ZeroMeanMvnConjSampler.cpp
src/Models/PosteriorSamplers/CorrelationSampler.cpp
src/Models/PosteriorSamplers/PoissonGammaPosteriorSampler.cpp
src/Models/PosteriorSamplers/IndependentMvnVarSampler.cpp
src/Models/PosteriorSamplers/MultinomialDirichletSampler.cpp
src/Models/PosteriorSamplers/MvnConjSampler.cpp
src/Models/PosteriorSamplers/AbsorbingMarkovConjSampler.cpp
src/Models/PosteriorSamplers/PosteriorSampler.cpp
src/Models/PosteriorSamplers/BetaBinomialPosteriorSampler.cpp
src/Models/PosteriorSamplers/GenericGaussianVarianceSampler.cpp
src/Models/PosteriorSamplers/MvnMeanSampler.cpp
src/Models/PosteriorSamplers/GaussianMeanSampler.cpp
src/Models/PosteriorSamplers/DirichletPosteriorSampler.cpp
src/Models/Sufstat.cpp
src/Models/StateSpace
src/Models/StateSpace/StateSpaceLogitModel.cpp
src/Models/StateSpace/StateSpaceNormalMixture.cpp
src/Models/StateSpace/StateSpaceModel.cpp
src/Models/StateSpace/StateSpacePoissonModel.cpp
src/Models/StateSpace/AggregatedStateSpaceRegression.cpp
src/Models/StateSpace/PosteriorSamplers
src/Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.cpp
src/Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.cpp
src/Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.cpp
src/Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.cpp
src/Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.cpp
src/Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.cpp
src/Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.cpp
src/Models/StateSpace/StateSpaceStudentRegressionModel.cpp
src/Models/StateSpace/Filters
src/Models/StateSpace/Filters/KalmanTools.cpp
src/Models/StateSpace/Filters/SparseKalmanTools.cpp
src/Models/StateSpace/Filters/SparseMatrix.cpp
src/Models/StateSpace/Filters/SparseVector.cpp
src/Models/StateSpace/StateSpaceRegressionModel.cpp
src/Models/StateSpace/StateModels
src/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.cpp
src/Models/StateSpace/StateModels/TrigStateModel.cpp
src/Models/StateSpace/StateModels/DynamicRegressionStateModel.cpp
src/Models/StateSpace/StateModels/SemilocalLinearTrend.cpp
src/Models/StateSpace/StateModels/LocalLevelStateModel.cpp
src/Models/StateSpace/StateModels/LocalLinearTrend.cpp
src/Models/StateSpace/StateModels/SeasonalStateModel.cpp
src/Models/StateSpace/StateModels/StudentLocalLinearTrend.cpp
src/Models/StateSpace/StateModels/Holiday.cpp
src/Models/StateSpace/StateModels/StateModel.cpp
src/Models/StateSpace/StateModels/RegressionStateModel.cpp
src/Models/StateSpace/StateModels/ArStateModel.cpp
src/Models/StateSpace/StateSpaceModelBase.cpp
src/Models/WishartModel.cpp
src/Models/PointProcess
src/Models/PointProcess/WeeklyCyclePoissonProcess.cpp
src/Models/PointProcess/MarkovModulatedPoissonProcess.cpp
src/Models/PointProcess/PoissonClusterProcess.cpp
src/Models/PointProcess/HomogeneousPoissonProcess.cpp
src/Models/PointProcess/BoundedPoissonProcessSimulator.cpp
src/Models/PointProcess/PosteriorSamplers
src/Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.cpp
src/Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.cpp
src/Models/PointProcess/PosteriorSamplers/WeeklyCyclePoissonProcessSampler.cpp
src/Models/PointProcess/CosinePoissonProcess.cpp
src/Models/PointProcess/PointProcess.cpp
src/Models/ZeroInflatedLognormalModel.cpp
src/Models/SpdData.cpp
src/Models/DirichletModel.cpp
src/Models/ProductVectorModel.cpp
src/Models/IRT
src/Models/IRT/DafePcrItemSampler.cpp
src/Models/IRT/PartialCreditModel.cpp
src/Models/IRT/SubjectSliceSampler.cpp
src/Models/IRT/DafePcrRwmItemSampler.cpp
src/Models/IRT/DafePcrDataImputer.cpp
src/Models/IRT/IrtModel.cpp
src/Models/IRT/SubjectPrior.cpp
src/Models/IRT/Item.cpp
src/Models/IRT/DafePcrSubject.cpp
src/Models/IRT/Subject.cpp
src/Models/IRT/DafePcrRwmSubject.cpp
src/Models/IRT/IRT.cpp
src/Models/PoissonModel.cpp
src/Models/MarginallyUniformCorrelationModel.cpp
src/Models/Hierarchical
src/Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.cpp
src/Models/Hierarchical/HierarchicalZeroInflatedGammaModel.cpp
src/Models/Hierarchical/PosteriorSamplers
src/Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedPoissonSampler.cpp
src/Models/Hierarchical/PosteriorSamplers/HierarchicalDirichletPosteriorSampler.cpp
src/Models/Hierarchical/PosteriorSamplers/HierarchicalGammaSampler.cpp
src/Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.cpp
src/Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedGammaSampler.cpp
src/Models/Hierarchical/HierarchicalGammaModel.cpp
src/Models/Hierarchical/HierarchicalDirichletModel.cpp
src/Models/Hierarchical/HierarchicalPoissonModel.cpp
src/Models/MarkovModel.cpp
src/Models/ZeroInflatedPoissonModel.cpp
src/Models/ZeroMeanMvnModel.cpp
src/Models/TimeSeries
src/Models/TimeSeries/NonzeroMeanAr1Model.cpp
src/Models/TimeSeries/PosteriorSamplers
src/Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.cpp
src/Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.cpp
src/Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.cpp
src/Models/TimeSeries/ArModel.cpp
src/Models/BinomialModel.cpp
src/prior_specification.cpp
src/numopt
src/numopt/newton.cpp
src/numopt/ScalarNewtonMax.cpp
src/numopt/NelderMead.cpp
src/numopt/simulated_annealing.cpp
src/numopt/initialize_derivatives.cpp
src/numopt/NumericalDerivatives.cpp
src/numopt/Negate.cpp
src/numopt/nelder_mead.cpp
src/numopt/bfgs.cpp
src/numopt/ScalarLaplaceApproximation.cpp
src/numopt/conj_grad.cpp
src/numopt/Integral.cpp
src/numopt/Powell.cpp
src/numopt/Brent.cpp
src/numopt/max_nd.cpp
src/parse_model_formula.cpp
src/Bmath
src/Bmath/mlutils.cpp
src/Bmath/rnchisq.cpp
src/Bmath/gammalims.cpp
src/Bmath/dhyper.cpp
src/Bmath/ptukey.cpp
src/Bmath/sexp.cpp
src/Bmath/rhyper.cpp
src/Bmath/qbinom.cpp
src/Bmath/fsign.cpp
src/Bmath/dcauchy.cpp
src/Bmath/dnbinom.cpp
src/Bmath/qweibull.cpp
src/Bmath/toms708.cpp
src/Bmath/ftrunc.cpp
src/Bmath/dpq.hpp
src/Bmath/dnorm.cpp
src/Bmath/bd0.cpp
src/Bmath/rnbinom.cpp
src/Bmath/snorm.cpp
src/Bmath/qf.cpp
src/Bmath/qnorm.cpp
src/Bmath/fround.cpp
src/Bmath/phyper.cpp
src/Bmath/pbeta.cpp
src/Bmath/qbeta.cpp
src/Bmath/nmath.hpp
src/Bmath/rexp.cpp
src/Bmath/dlogis.cpp
src/Bmath/pgeom.cpp
src/Bmath/rnorm.cpp
src/Bmath/rt.cpp
src/Bmath/rbinom.cpp
src/Bmath/pweibull.cpp
src/Bmath/qnchisq.cpp
src/Bmath/pt.cpp
src/Bmath/rweibull.cpp
src/Bmath/unif_rand.cpp
src/Bmath/rlnorm.cpp
src/Bmath/Random.hpp
src/Bmath/stirlerr.cpp
src/Bmath/dgamma.cpp
src/Bmath/rgeom.cpp
src/Bmath/sign.cpp
src/Bmath/pexp.cpp
src/Bmath/mathlib_error.cpp
src/Bmath/pf.cpp
src/Bmath/rloggamma_small_alpha.cpp
src/Bmath/qnbinom.cpp
src/Bmath/choose.cpp
src/Bmath/polygamma.cpp
src/Bmath/qtukey.cpp
src/Bmath/pnt.cpp
src/Bmath/plogis.cpp
src/Bmath/lbeta.cpp
src/Bmath/dpois.cpp
src/Bmath/gamma_cody.cpp
src/Bmath/rmultinom.cpp
src/Bmath/pchisq.cpp
src/Bmath/dnbeta.cpp
src/Bmath/pnbeta.cpp
src/Bmath/pcauchy.cpp
src/Bmath/pnbinom.cpp
src/Bmath/qexp.cpp
src/Bmath/qhyper.cpp
src/Bmath/rgamma.cpp
src/Bmath/fprec.cpp
src/Bmath/punif.cpp
src/Bmath/Bmath.hpp
src/Bmath/dt.cpp
src/Bmath/runif.cpp
src/Bmath/dunif.cpp
src/Bmath/qgamma.cpp
src/Bmath/i1mach.cpp
src/Bmath/dchisq.cpp
src/Bmath/qlnorm.cpp
src/Bmath/qgeom.cpp
src/Bmath/lgammacor.cpp
src/Bmath/rlogis.cpp
src/Bmath/rchisq.cpp
src/Bmath/d1mach.cpp
src/Bmath/pnorm.cpp
src/Bmath/qlogis.cpp
src/Bmath/qcauchy.cpp
src/Bmath/beta.cpp
src/Bmath/df.cpp
src/Bmath/dweibull.cpp
src/Bmath/dlnorm.cpp
src/Bmath/ppois.cpp
src/Bmath/plnorm.cpp
src/Bmath/dbeta.cpp
src/Bmath/dnchisq.cpp
src/Bmath/qt.cpp
src/Bmath/dbinom.cpp
src/Bmath/qunif.cpp
src/Bmath/rf.cpp
src/Bmath/pnchisq.cpp
src/Bmath/pnf.cpp
src/Bmath/qchisq.cpp
src/Bmath/pbinom.cpp
src/Bmath/dgeom.cpp
src/Bmath/rpois.cpp
src/Bmath/qpois.cpp
src/Bmath/pgamma.cpp
src/Bmath/rcauchy.cpp
src/Bmath/rbeta.cpp
src/Bmath/chebyshev.cpp
src/Bmath/dexp.cpp
src/Interfaces
src/Interfaces/R
src/Interfaces/R/BoomInterface
src/Interfaces/R/BoomInterface/test
src/Interfaces/R/BoomInterface/test/generate_factor_data_test.R src/Interfaces/R/BoomInterface/test/mvn_test.R src/Interfaces/R/BoomInterface/test/match_data_frame_test.R src/Interfaces/R/BoomInterface/test/dmvn_test.R src/Interfaces/R/BoomInterface/test/testdriver.R src/Interfaces/R/BoomInterface/test/dirichlet_test.R src/Interfaces/R/BoomInterface/test/format_test.R src/Interfaces/R/BoomInterface/test/wishart_test.R
src/create_point_process.cpp
src/extract_mixture_data.cpp
src/seed_rng_from_R.cpp
NAMESPACE
R
R/histabunch.R R/compare.vector.distribution.R R/lmgamma.R R/match_data_frame.R R/pairs.density.R R/boxplot.mcmc.matrix.R R/inverse.wishart.R R/suggest_burn_log_likelihood.R R/compare.many.ts.R R/boxplot.true.R R/add.segments.R R/compare.many.densities.R R/plot.macf.R R/external.legend.R R/format.R R/rmvn.R R/dmvn.R R/dirichlet.R R/plot.many.ts.R R/compare.den.R R/plot.dynamic.distribution.R R/check.data.R R/prior_specification.R R/mscan.R R/generate_factor_data.R R/thin.matrix.R R/thin.R R/is.even.R
MD5
DESCRIPTION
man
man/histabunch.Rd man/traceproduct.Rd man/check.data.Rd man/ToString.Rd man/plot.macf.Rd man/mvn.diagonal.prior.Rd man/double.model.Rd man/regression.coefficient.conjugate.prior.Rd man/normal.inverse.gamma.prior.Rd man/mvn.independent.sigma.prior.Rd man/normal.inverse.wishart.prior.Rd man/compare.vector.distributions.Rd man/plot.density.contours.Rd man/lmgamma.Rd man/compare.many.densities.Rd man/generate_factor_data.Rd man/boxplot.true.Rd man/beta.prior.Rd man/boxplot.mcmc.matrix.Rd man/ar1.coefficient.prior.Rd man/inverse-wishart.Rd man/gamma.prior.Rd man/pairs.density.Rd man/wishart.Rd man/dirichlet.prior.Rd man/dirichlet-distribution.Rd man/lognormal.prior.Rd man/plot.dynamic.distribution.Rd man/add.segments.Rd man/compare.den.Rd man/thin.Rd man/external.legend.Rd man/suggest.burn.log.likelihood.Rd man/mvn.prior.Rd man/compare.many.ts.Rd man/discrete-uniform-prior.Rd man/thin.matrix.Rd man/sd.prior.Rd man/mscan.Rd man/match_data_frame.Rd man/rmvn.Rd man/markov.prior.Rd man/is.even.Rd man/dmvn.Rd man/plot.many.ts.Rd man/normal.prior.Rd man/uniform.prior.Rd
LICENSE

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