Files in luisdamiano/BayesHMM

Full Bayesian Inference for Hidden Markov Models

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

LICENSE.md

NAMESPACE

R/density.R R/densityBernoulli.R R/densityBeta.R R/densityBinomial.R R/densityCategorical.R R/densityCauchy.R R/densityDirichlet.R R/densityExponential.R R/densityGamma.R R/densityGaussian.R R/densityImproperUniform.R R/densityInitialFixed.R R/densityInitialSoftmax.R R/densityInverseWishart.R R/densityLKJCor.R R/densityMVGaussian.R R/densityMVGaussianCholeskyCor.R R/densityMVStudent.R R/densityMultinomial.R R/densityNegativeBinomial.R R/densityNegativeBinomialLocation.R R/densityPoisson.R R/densityRegBernoulliLogit.R R/densityRegBinomialLogit.R R/densityRegBinomialProbit.R R/densityRegCategoricalSoftmax.R R/densityRegGaussian.R R/densityStudent.R R/densityTransitionFixed.R R/densityTransitionSoftmax.R R/densityWishart.R R/diagnose.R R/extract.R R/fit.R R/optimization.R R/optimizationList.R R/parseInitial.R R/parseObservation.R R/parseTransition.R R/plotFeatures.R R/plotPredictive.R R/plotSeries.R R/plotUtils.R R/print.R R/printOptimizing.R R/sortChain.R R/specification.R R/specificationHMM.R R/specificationInternals.R R/specificationMixture.R R/stanfit.R R/theme.R R/utils.R R/validate.R R/write.R R/zzz.R README.md

docs/LICENSE.html

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docs/articles/introduction.html

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inst/examples/compile-sampling.R inst/examples/extract.R inst/examples/hmm-fixed-initial.R inst/examples/hmm-fixed-transition.R inst/examples/hmm-multivariate-gaussian-correlation.R inst/examples/hmm-multivariate-gaussian-covariance.R inst/examples/hmm-multivariate-gaussian-priors.R inst/examples/hmm-multivariate-gaussian.R inst/examples/hmm-multivariate-priors-fixed.R inst/examples/hmm-regression-bernoulli-logit.R inst/examples/hmm-regression-binomial-logit.R inst/examples/hmm-regression-binomial-probit.R inst/examples/hmm-regression-gaussian.R inst/examples/hmm-univariate-bernoulli.R inst/examples/hmm-univariate-binomial.R inst/examples/hmm-univariate-categorical.R inst/examples/hmm-univariate-gaussian-equal-variance.R inst/examples/hmm-univariate-gaussian-fixed-parameters.R inst/examples/hmm-univariate-gaussian-ordered.R inst/examples/hmm-univariate-gaussian.R inst/examples/hmm-univariate-student.R inst/examples/hmm-univariate.poisson.R inst/examples/sampling-optimizing.R inst/examples/simulate-multivariate.R inst/examples/specifications.R inst/examples/tvhmm-initial-softmax.R inst/examples/tvhmm-univariate-gaussian.R inst/examples/visualizations.R

inst/stan/chunks/hmm-forward.stan

inst/stan/chunks/hmm-forwardBackward.stan

inst/stan/chunks/hmm-mappath.stan

inst/stan/chunks/hmm-zpredictive.stan

inst/stan/chunks/mixture.stan

inst/stan/chunks/tvhmm-forward.stan

inst/stan/chunks/tvhmm-forwardBackward.stan

inst/stan/chunks/tvhmm-mappath.stan

inst/stan/chunks/tvhmm-zpredictive.stan

inst/stan/template.stan

inst/tests/compile.RDS

inst/tests/draw_samples.RDS

inst/tests/optimizing_all.RDS

inst/tests/optimizing_best.RDS

inst/tests/sim.RDS

inst/tests/testDensity.R inst/tests/testFit.R inst/tests/testSpecification.R inst/tests/testWorkflow.R

inst/tests/validate_calibration.RDS

man/BayesHMM-package.Rd man/Bernoulli.Rd man/Beta.Rd man/Binomial.Rd man/Categorical.Rd man/Cauchy.Rd man/CholeskyLKJCor.Rd man/Density.Rd man/Dirichlet.Rd man/DiscreteDensity.Rd man/Exponential.Rd man/GammaDensity.Rd man/Gaussian.Rd man/ImproperUniform.Rd man/InitialFixed.Rd man/InitialSoftmax.Rd man/InverseWishart.Rd man/LinkDensity.Rd man/MVGaussian.Rd man/MVGaussianCholeskyCor.Rd man/MVStudent.Rd man/Multinomial.Rd man/MultivariateDensity.Rd man/MultivariateDiscreteDensity.Rd man/NegativeBinomial.Rd man/NegativeBinomialLocation.Rd man/Poisson.Rd man/PriorOnlyDensity.Rd man/PriorOnlyMultivariateDensity.Rd man/RegBernoulliLogit.Rd man/RegBinomialLogit.Rd man/RegBinomialProbit.Rd man/RegCategoricalSoftmax.Rd man/RegGaussian.Rd man/Student.Rd man/TransitionFixed.Rd man/TransitionSoftmax.Rd man/Wishart.Rd man/block_data.Density.Rd man/block_data.DiscreteDensity.Rd man/block_data.Rd man/block_data.RegBernoulliLogit.Rd man/block_data.RegBinomialLogit.Rd man/block_data.RegBinomialProbit.Rd man/block_data.RegCategoricalSoftmax.Rd man/block_data.RegGaussian.Rd man/block_data.Specification.Rd man/block_functions.Rd man/block_functions.Specification.Rd man/block_generated.Rd man/block_generated.Specification.Rd man/block_parameters.Rd man/block_parameters.Specification.Rd man/block_target.Rd man/block_target.Specification.Rd man/block_tdata.Rd man/block_tdata.Specification.Rd man/block_tparameters.Rd man/block_tparameters.Specification.Rd man/browse_model.Optimization.Rd man/browse_model.Rd man/browse_model.Specification.Rd man/browse_model.stanfit.Rd man/browse_model.stanmodel.Rd man/classify_alpha.Optimization.Rd man/classify_alpha.Rd man/classify_alpha.stanfit.Rd man/classify_gamma.Optimization.Rd man/classify_gamma.Rd man/classify_gamma.stanfit.Rd man/classify_quantity.Rd man/classify_zstar.Optimization.Rd man/classify_zstar.Rd man/classify_zstar.stanfit.Rd man/compile.Rd man/compile.Specification.Rd man/constants.Binomial.Rd man/constants.Categorical.Rd man/constants.Density.Rd man/constants.Multinomial.Rd man/constants.Rd man/constants.RegBinomialLogit.Rd man/constants.RegBinomialProbit.Rd man/constants.RegCategoricalSoftmax.Rd man/draw_samples.Optimization.Rd man/draw_samples.Rd man/draw_samples.Specification.Rd man/draw_samples.stanfit.Rd man/draw_samples.stanmodel.Rd man/explain.Rd man/explain.Specification.Rd man/explain_density.Density.Rd man/explain_density.DensityList.Rd man/explain_density.InitialFixed.Rd man/explain_density.InitialSoftmax.Rd man/explain_density.Rd man/explain_density.TransitionFixed.Rd man/explain_density.TransitionSoftmax.Rd man/explain_initial.Rd man/explain_initial.Specification.Rd man/explain_observation.Rd man/explain_observation.Specification.Rd man/explain_transition.Rd man/explain_transition.Specification.Rd man/extract.Rd man/extract_K.Rd man/extract_R.Rd man/extract_T.Rd man/extract_alpha.Rd man/extract_best.Rd man/extract_data.Rd man/extract_date.Optimization.Rd man/extract_date.Rd 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man/extract_time.Rd man/extract_time.stanfit.Rd man/extract_y.Rd man/extract_ypred.Rd man/extract_ysim.Rd man/extract_zpred.Rd man/extract_zsim.Rd man/extract_zstar.Rd man/fit.Optimization.Rd man/fit.Rd man/fit.Specification.Rd man/fit.stanfit.Rd man/fit.stanmodel.Rd man/fixedParameters.Bernoulli.Rd man/fixedParameters.Beta.Rd man/fixedParameters.Binomial.Rd man/fixedParameters.Categorical.Rd man/fixedParameters.Cauchy.Rd man/fixedParameters.Dirichlet.Rd man/fixedParameters.Exponential.Rd man/fixedParameters.GammaDensity.Rd man/fixedParameters.Gaussian.Rd man/fixedParameters.InitialFixed.Rd man/fixedParameters.InitialSoftmax.Rd man/fixedParameters.MVGaussian.Rd man/fixedParameters.MVGaussianCholeskyCor.Rd man/fixedParameters.MVStudent.Rd man/fixedParameters.Multinomial.Rd man/fixedParameters.NegativeBinomial.Rd man/fixedParameters.NegativeBinomialLocation.Rd man/fixedParameters.Poisson.Rd man/fixedParameters.PriorOnlyDensity.Rd man/fixedParameters.Rd 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man/generated.Student.Rd man/getFixedParameters.Density.Rd man/getFixedParameters.Rd man/getFreeParameters.Density.Rd man/getFreeParameters.PriorOnlyDensity.Rd man/getFreeParameters.Rd man/getParameterNames.Bernoulli.Rd man/getParameterNames.Beta.Rd man/getParameterNames.Binomial.Rd man/getParameterNames.Categorical.Rd man/getParameterNames.Cauchy.Rd man/getParameterNames.Density.Rd man/getParameterNames.Dirichlet.Rd man/getParameterNames.Exponential.Rd man/getParameterNames.GammaDensity.Rd man/getParameterNames.Gaussian.Rd man/getParameterNames.InitialFixed.Rd man/getParameterNames.InitialSoftmax.Rd man/getParameterNames.MVGaussian.Rd man/getParameterNames.MVGaussianCholeskyCor.Rd man/getParameterNames.MVStudent.Rd man/getParameterNames.Multinomial.Rd man/getParameterNames.NegativeBinomial.Rd man/getParameterNames.NegativeBinomialLocation.Rd man/getParameterNames.Poisson.Rd man/getParameterNames.PriorOnlyDensity.Rd man/getParameterNames.Rd man/getParameterNames.RegBernoulliLogit.Rd 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man/is.discrete.Density.Rd man/is.discrete.DensityList.Rd man/is.discrete.DiscreteDensity.Rd man/is.discrete.Rd man/is.discrete.Specification.Rd man/is.equal.Density.Rd man/is.equal.Rd man/is.link.Density.Rd man/is.link.LinkDensity.Rd man/is.link.Rd man/is.multivariate.Density.Rd man/is.multivariate.DensityList.Rd man/is.multivariate.MultivariateDensity.Rd man/is.multivariate.Rd man/is.multivariate.Specification.Rd man/is.ordered.Density.Rd man/is.ordered.Rd man/is.stanfit.Rd man/is.stanoptim.Rd man/link.Density.Rd man/link.InitialFixed.Rd man/link.InitialSoftmax.Rd man/link.Rd man/link.TransitionFixed.Rd man/link.TransitionSoftmax.Rd man/load_theme.Rd man/logLike.Bernoulli.Rd man/logLike.Beta.Rd man/logLike.Binomial.Rd man/logLike.Categorical.Rd man/logLike.Cauchy.Rd man/logLike.Dirichlet.Rd man/logLike.Exponential.Rd man/logLike.GammaDensity.Rd man/logLike.Gaussian.Rd man/logLike.MVGaussian.Rd man/logLike.MVGaussianCholeskyCor.Rd man/logLike.MVStudent.Rd man/logLike.Multinomial.Rd 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man/select_transition_parameters.Rd man/sim.Optimization.Rd man/sim.Rd man/sim.Specification.Rd man/sim.stanfit.Rd man/sim.stanmodel.Rd man/specify.Rd man/string_simplify.Rd man/theme.Rd man/validate_calibration.Rd man/write_chunks.Rd man/write_chunks.Specification.Rd man/write_model.Rd man/write_model.Specification.Rd tests/build.R

tests/density.txt

tests/run.R

tests/specification.txt

vignettes/introduction.Rmd vignettes/introduction2.Rmd

vignettes/references.bib

luisdamiano/BayesHMM documentation built on May 20, 2019, 2:59 p.m.