├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R ├── density.R ├── densityBernoulli.R ├── densityBeta.R ├── densityBinomial.R ├── densityCategorical.R ├── densityCauchy.R ├── densityDirichlet.R ├── densityExponential.R ├── densityGamma.R ├── densityGaussian.R ├── densityImproperUniform.R ├── densityInitialFixed.R ├── densityInitialSoftmax.R ├── densityInverseWishart.R ├── densityLKJCor.R ├── densityMVGaussian.R ├── densityMVGaussianCholeskyCor.R ├── densityMVStudent.R ├── densityMultinomial.R ├── densityNegativeBinomial.R ├── densityNegativeBinomialLocation.R ├── densityPoisson.R ├── densityRegBernoulliLogit.R ├── densityRegBinomialLogit.R ├── densityRegBinomialProbit.R ├── densityRegCategoricalSoftmax.R ├── densityRegGaussian.R ├── densityStudent.R ├── densityTransitionFixed.R ├── densityTransitionSoftmax.R ├── densityWishart.R ├── diagnose.R ├── extract.R ├── fit.R ├── optimization.R ├── optimizationList.R ├── parseInitial.R ├── parseObservation.R ├── parseTransition.R ├── plotFeatures.R ├── plotPredictive.R ├── plotSeries.R ├── plotUtils.R ├── print.R ├── printOptimizing.R ├── sortChain.R ├── specification.R ├── specificationHMM.R ├── specificationInternals.R ├── specificationMixture.R ├── stanfit.R ├── theme.R ├── utils.R ├── validate.R ├── write.R └── zzz.R ├── README.md ├── docs ├── LICENSE.html ├── articles │ ├── index.html │ ├── introduction.html │ ├── introduction2.html │ └── introduction_files │ │ └── figure-html │ │ └── unnamed-chunk-9-1.png ├── authors.html ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── BayesHMM-package.html │ ├── Bernoulli.html │ ├── Beta.html │ ├── Binomial.html │ ├── Categorical.html │ ├── Cauchy.html │ ├── CholeskyLKJCor.html │ ├── Density.html │ ├── Dirichlet.html │ ├── DiscreteDensity.html │ ├── Exponential.html │ ├── GammaDensity.html │ ├── Gaussian.html │ ├── ImproperUniform.html │ ├── InitialFixed.html │ ├── InitialSoftmax.html │ ├── InverseWishart.html │ ├── LinkDensity.html │ ├── MVGaussian.html │ ├── MVGaussianCholeskyCor.html │ ├── MVStudent.html │ ├── Multinomial.html │ ├── MultivariateDensity.html │ ├── MultivariateDiscreteDensity.html │ ├── NegativeBinomial.html │ ├── NegativeBinomialLocation.html │ ├── Poisson.html │ ├── PriorOnlyDensity.html │ ├── PriorOnlyMultivariateDensity.html │ ├── RegBernoulliLogit.html │ ├── RegBinomialLogit.html │ ├── RegBinomialProbit.html │ ├── RegCategoricalSoftmax.html │ ├── RegGaussian.html │ ├── Student.html │ ├── TransitionFixed.html │ ├── TransitionSoftmax.html │ ├── Wishart.html │ ├── block_data.Density.html │ ├── block_data.DiscreteDensity.html │ ├── block_data.RegBernoulliLogit.html │ ├── block_data.RegBinomialLogit.html │ ├── block_data.RegBinomialProbit.html │ ├── block_data.RegCategoricalSoftmax.html │ ├── block_data.RegGaussian.html │ ├── block_data.Specification.html │ ├── block_data.TransitionSoftmax.html │ ├── block_data.html │ ├── block_functions.Specification.html │ ├── block_functions.html │ ├── block_generated.Specification.html │ ├── block_generated.html │ ├── block_parameters.Specification.html │ ├── block_parameters.html │ ├── block_target.Specification.html │ ├── block_target.html │ ├── block_tdata.Specification.html │ ├── block_tdata.html │ ├── block_tparameters.Specification.html │ ├── block_tparameters.html │ ├── browse_model.Optimization.html │ ├── browse_model.Specification.html │ ├── browse_model.html │ ├── browse_model.stanfit.html │ ├── browse_model.stanmodel.html │ ├── classify_alpha.Optimization.html │ ├── classify_alpha.html │ ├── classify_alpha.stanfit.html │ ├── classify_gamma.Optimization.html │ ├── classify_gamma.html │ ├── classify_gamma.stanfit.html │ ├── classify_quantity.html │ ├── classify_zstar.Optimization.html │ ├── classify_zstar.html │ ├── classify_zstar.stanfit.html │ ├── compile.Specification.html │ ├── compile.html │ ├── constants.Binomial.html │ ├── constants.Categorical.html │ ├── constants.Density.html │ ├── constants.Multinomial.html │ ├── constants.RegBinomialLogit.html │ ├── constants.RegBinomialProbit.html │ ├── constants.RegCategoricalSoftmax.html │ ├── constants.html │ ├── draw_samples.Optimization.html │ ├── draw_samples.Specification.html │ ├── draw_samples.html │ ├── draw_samples.stanfit.html │ ├── draw_samples.stanmodel.html │ ├── explain.Specification.html │ ├── explain.html │ ├── explain_density.Density.html │ ├── explain_density.DensityList.html │ ├── explain_density.InitialFixed.html │ ├── explain_density.InitialSoftmax.html │ ├── explain_density.TransitionFixed.html │ ├── explain_density.TransitionSoftmax.html │ ├── explain_density.html │ ├── explain_initial.Specification.html │ ├── explain_initial.html │ ├── explain_observation.Specification.html │ ├── explain_observation.html │ ├── explain_transition.Specification.html │ ├── explain_transition.html │ ├── extract.html │ ├── extract_K.html │ ├── extract_R.html │ ├── extract_T.html │ ├── extract_alpha.html │ ├── extract_best.html │ ├── extract_data.html │ ├── extract_date.Optimization.html │ ├── extract_date.html │ ├── extract_date.stanfit.html │ ├── extract_diagnostics.html │ ├── extract_diagnostics.stanfit.html │ ├── extract_filename.html │ ├── extract_gamma.html │ ├── extract_grid.html │ ├── extract_model.html │ ├── extract_n_chains.html │ ├── extract_n_chains.stanfit.html │ ├── extract_n_iterations.html │ ├── extract_n_iterations.stanfit.html │ ├── extract_n_thin.html │ ├── extract_n_thin.stanfit.html │ ├── extract_n_warmup.html │ ├── extract_n_warmup.stanfit.html │ ├── extract_obs_parameters.html │ ├── extract_parameter_names.Optimization.html │ ├── extract_parameter_names.html │ ├── extract_parameter_names.stanfit.html │ ├── extract_parameters.html │ ├── extract_quantity.Optimization.html │ ├── extract_quantity.html │ ├── extract_quantity.stanfit.html │ ├── extract_sample_size.html │ ├── extract_sample_size.stanfit.html │ ├── extract_seed.Optimization.html │ ├── extract_seed.html │ ├── extract_seed.stanfit.html │ ├── extract_spec.html │ ├── extract_stanmodel.Optimization.html │ ├── extract_stanmodel.html │ ├── extract_stanmodel.stanfit.html │ ├── extract_stanmodel.stanmodel.html │ ├── extract_time.Optimization.html │ ├── extract_time.html │ ├── extract_time.stanfit.html │ ├── extract_y.html │ ├── extract_ypred.html │ ├── extract_ysim.html │ ├── extract_zpred.html │ ├── extract_zsim.html │ ├── extract_zstar.html │ ├── fit.Optimization.html │ ├── fit.Specification.html │ ├── fit.html │ ├── fit.stanfit.html │ ├── fit.stanmodel.html │ ├── fixedParameters.Bernoulli.html │ ├── fixedParameters.Beta.html │ ├── fixedParameters.Binomial.html │ ├── fixedParameters.Categorical.html │ ├── fixedParameters.Cauchy.html │ ├── fixedParameters.Dirichlet.html │ ├── fixedParameters.Exponential.html │ ├── fixedParameters.GammaDensity.html │ ├── fixedParameters.Gaussian.html │ ├── fixedParameters.InitialFixed.html │ ├── fixedParameters.InitialSoftmax.html │ ├── fixedParameters.MVGaussian.html │ ├── fixedParameters.MVGaussianCholeskyCor.html │ ├── fixedParameters.MVStudent.html │ ├── fixedParameters.Multinomial.html │ ├── fixedParameters.NegativeBinomial.html │ ├── fixedParameters.NegativeBinomialLocation.html │ ├── fixedParameters.Poisson.html │ ├── fixedParameters.PriorOnlyDensity.html │ ├── fixedParameters.RegBernoulliLogit.html │ ├── fixedParameters.RegBinomialLogit.html │ ├── fixedParameters.RegBinomialProbit.html │ ├── fixedParameters.RegCategoricalSoftmax.html │ ├── fixedParameters.RegGaussian.html │ ├── fixedParameters.Student.html │ ├── fixedParameters.TransitionFixed.html │ ├── fixedParameters.TransitionSoftmax.html │ ├── fixedParameters.html │ ├── freeParameters.Bernoulli.html │ ├── freeParameters.Beta.html │ ├── freeParameters.Binomial.html │ ├── freeParameters.Categorical.html │ ├── freeParameters.Cauchy.html │ ├── freeParameters.Dirichlet.html │ ├── freeParameters.Exponential.html │ ├── freeParameters.GammaDensity.html │ ├── freeParameters.Gaussian.html │ ├── freeParameters.InitialFixed.html │ ├── freeParameters.InitialSoftmax.html │ ├── freeParameters.MVGaussian.html │ ├── freeParameters.MVGaussianCholeskyCor.html │ ├── freeParameters.MVStudent.html │ ├── freeParameters.Multinomial.html │ ├── freeParameters.NegativeBinomial.html │ ├── freeParameters.NegativeBinomialLocation.html │ ├── freeParameters.Poisson.html │ ├── freeParameters.PriorOnlyDensity.html │ ├── freeParameters.RegBernoulliLogit.html │ ├── freeParameters.RegBinomialLogit.html │ ├── freeParameters.RegBinomialProbit.html │ ├── freeParameters.RegCategoricalSoftmax.html │ ├── freeParameters.RegGaussian.html │ ├── freeParameters.Student.html │ ├── freeParameters.TransitionFixed.html │ ├── freeParameters.TransitionSoftmax.html │ ├── freeParameters.html │ ├── generated.Bernoulli.html │ ├── generated.Beta.html │ ├── generated.Binomial.html │ ├── generated.Categorical.html │ ├── generated.Cauchy.html │ ├── generated.Dirichlet.html │ ├── generated.Exponential.html │ ├── generated.GammaDensity.html │ ├── generated.Gaussian.html │ ├── generated.MVGaussian.html │ ├── generated.MVGaussianCholeskyCor.html │ ├── generated.MVStudent.html │ ├── generated.Multinomial.html │ ├── generated.NegativeBinomial.html │ ├── generated.NegativeBinomialLocation.html │ ├── generated.Poisson.html │ ├── generated.PriorOnlyDensity.html │ ├── generated.RegBernoulliLogit.html │ ├── generated.RegBinomialLogit.html │ ├── generated.RegBinomialProbit.html │ ├── generated.RegCategoricalSoftmax.html │ ├── generated.RegGaussian.html │ ├── generated.Student.html │ ├── generated.html │ ├── getFixedParameters.Density.html │ ├── getFixedParameters.html │ ├── getFreeParameters.Density.html │ ├── getFreeParameters.PriorOnlyDensity.html │ ├── getFreeParameters.html │ ├── getParameterNames.Bernoulli.html │ ├── getParameterNames.Beta.html │ ├── getParameterNames.Binomial.html │ ├── getParameterNames.Categorical.html │ ├── getParameterNames.Cauchy.html │ ├── getParameterNames.Density.html │ ├── getParameterNames.Dirichlet.html │ ├── getParameterNames.Exponential.html │ ├── getParameterNames.GammaDensity.html │ ├── getParameterNames.Gaussian.html │ ├── getParameterNames.InitialFixed.html │ ├── getParameterNames.InitialSoftmax.html │ ├── getParameterNames.MVGaussian.html │ ├── getParameterNames.MVGaussianCholeskyCor.html │ ├── getParameterNames.MVStudent.html │ ├── getParameterNames.Multinomial.html │ ├── getParameterNames.NegativeBinomial.html │ ├── getParameterNames.NegativeBinomialLocation.html │ ├── getParameterNames.Poisson.html │ ├── getParameterNames.PriorOnlyDensity.html │ ├── getParameterNames.RegBernoulliLogit.html │ ├── getParameterNames.RegBinomialLogit.html │ ├── getParameterNames.RegBinomialProbit.html │ ├── getParameterNames.RegCategoricalSoftmax.html │ ├── getParameterNames.RegGaussian.html │ ├── getParameterNames.Student.html │ ├── getParameterNames.TransitionFixed.html │ ├── getParameterNames.TransitionSoftmax.html │ ├── getParameterNames.html │ ├── get_current_theme.html │ ├── get_default_theme.html │ ├── get_plot_theme.html │ ├── get_print_settings.html │ ├── hmm.html │ ├── index.html │ ├── is.Density.html │ ├── is.DensityList.html │ ├── is.FixedInitial.Density.html │ ├── is.FixedInitial.InitialFixed.html │ ├── is.FixedInitial.Specification.html │ ├── is.FixedInitial.html │ ├── is.FixedTransition.Density.html │ ├── is.FixedTransition.Specification.html │ ├── is.FixedTransition.TransitionFixed.html │ ├── is.FixedTransition.html │ ├── is.Specification.html │ ├── is.TVInitial.Density.html │ ├── is.TVInitial.InitialSoftmax.html │ ├── is.TVInitial.Specification.html │ ├── is.TVInitial.html │ ├── is.TVTransition.Density.html │ ├── is.TVTransition.Specification.html │ ├── is.TVTransition.TransitionSoftmax.html │ ├── is.TVTransition.html │ ├── is.discrete.Density.html │ ├── is.discrete.DensityList.html │ ├── is.discrete.DiscreteDensity.html │ ├── is.discrete.Specification.html │ ├── is.discrete.html │ ├── is.equal.Density.html │ ├── is.equal.html │ ├── is.link.Density.html │ ├── is.link.LinkDensity.html │ ├── is.link.html │ ├── is.multivariate.Density.html │ ├── is.multivariate.DensityList.html │ ├── is.multivariate.MultivariateDensity.html │ ├── is.multivariate.Specification.html │ ├── is.multivariate.html │ ├── is.ordered.Density.html │ ├── is.ordered.html │ ├── is.stanfit.html │ ├── is.stanoptim.html │ ├── link.Density.html │ ├── link.InitialFixed.html │ ├── link.InitialSoftmax.html │ ├── link.TransitionFixed.html │ ├── link.TransitionSoftmax.html │ ├── link.html │ ├── load_theme.html │ ├── logLike.Bernoulli.html │ ├── logLike.Beta.html │ ├── logLike.Binomial.html │ ├── logLike.Categorical.html │ ├── logLike.Cauchy.html │ ├── logLike.Dirichlet.html │ ├── logLike.Exponential.html │ ├── logLike.GammaDensity.html │ ├── logLike.Gaussian.html │ ├── logLike.MVGaussian.html │ ├── logLike.MVGaussianCholeskyCor.html │ ├── logLike.MVStudent.html │ ├── logLike.Multinomial.html │ ├── logLike.NegativeBinomial.html │ ├── logLike.NegativeBinomialLocation.html │ ├── logLike.Poisson.html │ ├── logLike.PriorOnlyDensity.html │ ├── logLike.RegBernoulliLogit.html │ ├── logLike.RegBinomialLogit.html │ ├── logLike.RegBinomialProbit.html │ ├── logLike.RegCategoricalSoftmax.html │ ├── logLike.RegGaussian.html │ ├── logLike.Student.html │ ├── logLike.html │ ├── make_text_header.html │ ├── make_text_line.html │ ├── make_text_subheader.html │ ├── match_parameter_names.html │ ├── mixture.html │ ├── modify_theme_entry.html │ ├── noLogLike.Density.html │ ├── noLogLike.html │ ├── optimizing.Optimization.html │ ├── optimizing.Specification.html │ ├── optimizing.html │ ├── optimizing.stanfit.html │ ├── optimizing.stanmodel.html │ ├── optimizing_all.html │ ├── optimizing_best.html │ ├── optimizing_run.html │ ├── parameters.html │ ├── plot_ppredictive.html │ ├── plot_ppredictive.stanfit.html │ ├── plot_series.html │ ├── plot_state_probability.html │ ├── plus-.Density.html │ ├── posterior_intervals.html │ ├── posterior_mode.html │ ├── print.Density.html │ ├── print.Optimization.html │ ├── print.Specification.html │ ├── print.stanfit.html │ ├── prior.Bernoulli.html │ ├── prior.Beta.html │ ├── prior.Binomial.html │ ├── prior.Categorical.html │ ├── prior.Cauchy.html │ ├── prior.CholeskyLKJCor.html │ ├── prior.Dirichlet.html │ ├── prior.Exponential.html │ ├── prior.GammaDensity.html │ ├── prior.Gaussian.html │ ├── prior.ImproperUniform.html │ ├── prior.InitialFixed.html │ ├── prior.InitialSoftmax.html │ ├── prior.InverseWishart.html │ ├── prior.MVGaussian.html │ ├── prior.MVGaussianCholeskyCor.html │ ├── prior.MVStudent.html │ ├── prior.Multinomial.html │ ├── prior.NegativeBinomial.html │ ├── prior.NegativeBinomialLocation.html │ ├── prior.Poisson.html │ ├── prior.RegBernoulliLogit.html │ ├── prior.RegBinomialLogit.html │ ├── prior.RegBinomialProbit.html │ ├── prior.RegCategoricalSoftmax.html │ ├── prior.RegGaussian.html │ ├── prior.Student.html │ ├── prior.TransitionFixed.html │ ├── prior.TransitionSoftmax.html │ ├── prior.Wishart.html │ ├── prior.html │ ├── run.Specification.html │ ├── run.html │ ├── select_all_parameters.html │ ├── select_initial_parameters.html │ ├── select_obs_parameters.html │ ├── select_parameters.html │ ├── select_transition_parameters.html │ ├── sim.Optimization.html │ ├── sim.Specification.html │ ├── sim.html │ ├── sim.stanfit.html │ ├── sim.stanmodel.html │ ├── specify.html │ ├── string_simplify.html │ ├── theme.html │ ├── validate_calibration.html │ ├── write_chunks.Specification.html │ ├── write_chunks.html │ ├── write_model.Specification.html │ └── write_model.html ├── inst ├── examples │ ├── compile-sampling.R │ ├── extract.R │ ├── hmm-fixed-initial.R │ ├── hmm-fixed-transition.R │ ├── hmm-multivariate-gaussian-correlation.R │ ├── hmm-multivariate-gaussian-covariance.R │ ├── hmm-multivariate-gaussian-priors.R │ ├── hmm-multivariate-gaussian.R │ ├── hmm-multivariate-priors-fixed.R │ ├── hmm-regression-bernoulli-logit.R │ ├── hmm-regression-binomial-logit.R │ ├── hmm-regression-binomial-probit.R │ ├── hmm-regression-gaussian.R │ ├── hmm-univariate-bernoulli.R │ ├── hmm-univariate-binomial.R │ ├── hmm-univariate-categorical.R │ ├── hmm-univariate-gaussian-equal-variance.R │ ├── hmm-univariate-gaussian-fixed-parameters.R │ ├── hmm-univariate-gaussian-ordered.R │ ├── hmm-univariate-gaussian.R │ ├── hmm-univariate-student.R │ ├── hmm-univariate.poisson.R │ ├── sampling-optimizing.R │ ├── simulate-multivariate.R │ ├── specifications.R │ ├── tvhmm-initial-softmax.R │ ├── tvhmm-univariate-gaussian.R │ └── visualizations.R ├── stan │ ├── chunks │ │ ├── hmm-forward.stan │ │ ├── hmm-forwardBackward.stan │ │ ├── hmm-mappath.stan │ │ ├── hmm-zpredictive.stan │ │ ├── mixture.stan │ │ ├── tvhmm-forward.stan │ │ ├── tvhmm-forwardBackward.stan │ │ ├── tvhmm-mappath.stan │ │ └── tvhmm-zpredictive.stan │ └── template.stan └── tests │ ├── compile.RDS │ ├── draw_samples.RDS │ ├── optimizing_all.RDS │ ├── optimizing_best.RDS │ ├── sim.RDS │ ├── testDensity.R │ ├── testFit.R │ ├── testSpecification.R │ ├── testWorkflow.R │ └── validate_calibration.RDS ├── man ├── BayesHMM-package.Rd ├── Bernoulli.Rd ├── Beta.Rd ├── Binomial.Rd ├── Categorical.Rd ├── Cauchy.Rd ├── CholeskyLKJCor.Rd ├── Density.Rd ├── Dirichlet.Rd ├── DiscreteDensity.Rd ├── Exponential.Rd ├── GammaDensity.Rd ├── Gaussian.Rd ├── ImproperUniform.Rd ├── InitialFixed.Rd ├── InitialSoftmax.Rd ├── InverseWishart.Rd ├── LinkDensity.Rd ├── MVGaussian.Rd ├── MVGaussianCholeskyCor.Rd ├── MVStudent.Rd ├── Multinomial.Rd ├── MultivariateDensity.Rd ├── MultivariateDiscreteDensity.Rd ├── NegativeBinomial.Rd ├── NegativeBinomialLocation.Rd ├── Poisson.Rd ├── PriorOnlyDensity.Rd ├── PriorOnlyMultivariateDensity.Rd ├── RegBernoulliLogit.Rd ├── RegBinomialLogit.Rd ├── RegBinomialProbit.Rd ├── RegCategoricalSoftmax.Rd ├── RegGaussian.Rd ├── Student.Rd ├── TransitionFixed.Rd ├── TransitionSoftmax.Rd ├── Wishart.Rd ├── block_data.Density.Rd ├── block_data.DiscreteDensity.Rd ├── block_data.Rd ├── block_data.RegBernoulliLogit.Rd ├── block_data.RegBinomialLogit.Rd ├── block_data.RegBinomialProbit.Rd ├── block_data.RegCategoricalSoftmax.Rd ├── block_data.RegGaussian.Rd ├── block_data.Specification.Rd ├── block_functions.Rd ├── block_functions.Specification.Rd ├── block_generated.Rd ├── block_generated.Specification.Rd ├── block_parameters.Rd ├── block_parameters.Specification.Rd ├── block_target.Rd ├── block_target.Specification.Rd ├── block_tdata.Rd ├── block_tdata.Specification.Rd ├── block_tparameters.Rd ├── block_tparameters.Specification.Rd ├── browse_model.Optimization.Rd ├── browse_model.Rd ├── browse_model.Specification.Rd ├── browse_model.stanfit.Rd ├── browse_model.stanmodel.Rd ├── classify_alpha.Optimization.Rd ├── classify_alpha.Rd ├── classify_alpha.stanfit.Rd ├── classify_gamma.Optimization.Rd ├── classify_gamma.Rd ├── classify_gamma.stanfit.Rd ├── classify_quantity.Rd ├── classify_zstar.Optimization.Rd ├── classify_zstar.Rd ├── classify_zstar.stanfit.Rd ├── compile.Rd ├── compile.Specification.Rd ├── constants.Binomial.Rd ├── constants.Categorical.Rd ├── constants.Density.Rd ├── constants.Multinomial.Rd ├── constants.Rd ├── constants.RegBinomialLogit.Rd ├── constants.RegBinomialProbit.Rd ├── constants.RegCategoricalSoftmax.Rd ├── draw_samples.Optimization.Rd ├── draw_samples.Rd ├── draw_samples.Specification.Rd ├── draw_samples.stanfit.Rd ├── draw_samples.stanmodel.Rd ├── explain.Rd ├── explain.Specification.Rd ├── explain_density.Density.Rd ├── explain_density.DensityList.Rd ├── explain_density.InitialFixed.Rd ├── explain_density.InitialSoftmax.Rd ├── explain_density.Rd ├── explain_density.TransitionFixed.Rd ├── explain_density.TransitionSoftmax.Rd ├── explain_initial.Rd ├── explain_initial.Specification.Rd ├── explain_observation.Rd ├── explain_observation.Specification.Rd ├── explain_transition.Rd ├── explain_transition.Specification.Rd ├── extract.Rd ├── extract_K.Rd ├── extract_R.Rd ├── extract_T.Rd ├── extract_alpha.Rd ├── extract_best.Rd ├── extract_data.Rd ├── extract_date.Optimization.Rd ├── extract_date.Rd ├── extract_date.stanfit.Rd ├── extract_diagnostics.Rd ├── extract_diagnostics.stanfit.Rd ├── extract_filename.Rd ├── extract_gamma.Rd ├── extract_grid.Rd ├── extract_model.Rd ├── extract_n_chains.Rd ├── extract_n_chains.stanfit.Rd ├── extract_n_iterations.Rd ├── extract_n_iterations.stanfit.Rd ├── extract_n_thin.Rd ├── extract_n_thin.stanfit.Rd ├── extract_n_warmup.Rd ├── extract_n_warmup.stanfit.Rd ├── extract_obs_parameters.Rd ├── extract_parameter_names.Optimization.Rd ├── extract_parameter_names.Rd ├── extract_parameter_names.stanfit.Rd ├── extract_parameters.Rd ├── extract_quantity.Optimization.Rd ├── extract_quantity.Rd ├── extract_quantity.stanfit.Rd ├── extract_sample_size.Rd ├── extract_sample_size.stanfit.Rd ├── extract_seed.Optimization.Rd ├── extract_seed.Rd ├── extract_seed.stanfit.Rd ├── extract_spec.Rd ├── extract_stanmodel.Optimization.Rd ├── extract_stanmodel.Rd ├── extract_stanmodel.stanfit.Rd ├── extract_stanmodel.stanmodel.Rd ├── extract_time.Optimization.Rd ├── extract_time.Rd ├── extract_time.stanfit.Rd ├── extract_y.Rd ├── extract_ypred.Rd ├── extract_ysim.Rd ├── extract_zpred.Rd ├── extract_zsim.Rd ├── extract_zstar.Rd ├── fit.Optimization.Rd ├── fit.Rd ├── fit.Specification.Rd ├── fit.stanfit.Rd ├── fit.stanmodel.Rd ├── fixedParameters.Bernoulli.Rd ├── fixedParameters.Beta.Rd ├── fixedParameters.Binomial.Rd ├── fixedParameters.Categorical.Rd ├── fixedParameters.Cauchy.Rd ├── fixedParameters.Dirichlet.Rd ├── fixedParameters.Exponential.Rd ├── fixedParameters.GammaDensity.Rd ├── fixedParameters.Gaussian.Rd ├── fixedParameters.InitialFixed.Rd ├── fixedParameters.InitialSoftmax.Rd ├── fixedParameters.MVGaussian.Rd ├── fixedParameters.MVGaussianCholeskyCor.Rd ├── fixedParameters.MVStudent.Rd ├── fixedParameters.Multinomial.Rd ├── fixedParameters.NegativeBinomial.Rd ├── fixedParameters.NegativeBinomialLocation.Rd ├── fixedParameters.Poisson.Rd ├── fixedParameters.PriorOnlyDensity.Rd ├── fixedParameters.Rd ├── fixedParameters.RegBernoulliLogit.Rd ├── fixedParameters.RegBinomialLogit.Rd ├── fixedParameters.RegBinomialProbit.Rd ├── fixedParameters.RegCategoricalSoftmax.Rd ├── fixedParameters.RegGaussian.Rd ├── fixedParameters.Student.Rd ├── fixedParameters.TransitionFixed.Rd ├── fixedParameters.TransitionSoftmax.Rd ├── freeParameters.Bernoulli.Rd ├── freeParameters.Beta.Rd ├── freeParameters.Binomial.Rd ├── freeParameters.Categorical.Rd ├── freeParameters.Cauchy.Rd ├── freeParameters.Dirichlet.Rd ├── freeParameters.Exponential.Rd ├── freeParameters.GammaDensity.Rd ├── freeParameters.Gaussian.Rd ├── freeParameters.InitialFixed.Rd ├── freeParameters.InitialSoftmax.Rd ├── freeParameters.MVGaussian.Rd ├── freeParameters.MVGaussianCholeskyCor.Rd ├── freeParameters.MVStudent.Rd ├── freeParameters.Multinomial.Rd ├── freeParameters.NegativeBinomial.Rd ├── freeParameters.NegativeBinomialLocation.Rd ├── freeParameters.Poisson.Rd ├── freeParameters.PriorOnlyDensity.Rd ├── freeParameters.Rd ├── freeParameters.RegBernoulliLogit.Rd ├── freeParameters.RegBinomialLogit.Rd ├── freeParameters.RegBinomialProbit.Rd ├── freeParameters.RegCategoricalSoftmax.Rd ├── freeParameters.RegGaussian.Rd ├── freeParameters.Student.Rd ├── freeParameters.TransitionFixed.Rd ├── freeParameters.TransitionSoftmax.Rd ├── generated.Bernoulli.Rd ├── generated.Beta.Rd ├── generated.Binomial.Rd ├── generated.Categorical.Rd ├── generated.Cauchy.Rd ├── generated.Dirichlet.Rd ├── generated.Exponential.Rd ├── generated.GammaDensity.Rd ├── generated.Gaussian.Rd ├── generated.MVGaussian.Rd ├── generated.MVGaussianCholeskyCor.Rd ├── generated.MVStudent.Rd ├── generated.Multinomial.Rd ├── generated.NegativeBinomial.Rd ├── generated.NegativeBinomialLocation.Rd ├── generated.Poisson.Rd ├── generated.PriorOnlyDensity.Rd ├── generated.Rd ├── generated.RegBernoulliLogit.Rd ├── generated.RegBinomialLogit.Rd ├── generated.RegBinomialProbit.Rd ├── generated.RegCategoricalSoftmax.Rd ├── generated.RegGaussian.Rd ├── generated.Student.Rd ├── getFixedParameters.Density.Rd ├── getFixedParameters.Rd ├── getFreeParameters.Density.Rd ├── getFreeParameters.PriorOnlyDensity.Rd ├── getFreeParameters.Rd ├── getParameterNames.Bernoulli.Rd ├── getParameterNames.Beta.Rd ├── getParameterNames.Binomial.Rd ├── getParameterNames.Categorical.Rd ├── getParameterNames.Cauchy.Rd ├── getParameterNames.Density.Rd ├── getParameterNames.Dirichlet.Rd ├── getParameterNames.Exponential.Rd ├── getParameterNames.GammaDensity.Rd ├── getParameterNames.Gaussian.Rd ├── getParameterNames.InitialFixed.Rd ├── getParameterNames.InitialSoftmax.Rd ├── getParameterNames.MVGaussian.Rd ├── getParameterNames.MVGaussianCholeskyCor.Rd ├── getParameterNames.MVStudent.Rd ├── getParameterNames.Multinomial.Rd ├── getParameterNames.NegativeBinomial.Rd ├── getParameterNames.NegativeBinomialLocation.Rd ├── getParameterNames.Poisson.Rd ├── getParameterNames.PriorOnlyDensity.Rd ├── getParameterNames.Rd ├── getParameterNames.RegBernoulliLogit.Rd ├── getParameterNames.RegBinomialLogit.Rd ├── getParameterNames.RegBinomialProbit.Rd ├── getParameterNames.RegCategoricalSoftmax.Rd ├── getParameterNames.RegGaussian.Rd ├── getParameterNames.Student.Rd ├── getParameterNames.TransitionFixed.Rd ├── getParameterNames.TransitionSoftmax.Rd ├── get_current_theme.Rd ├── get_default_theme.Rd ├── get_plot_theme.Rd ├── get_print_settings.Rd ├── hmm.Rd ├── is.Density.Rd ├── is.DensityList.Rd ├── is.FixedInitial.Density.Rd ├── is.FixedInitial.InitialFixed.Rd ├── is.FixedInitial.Rd ├── is.FixedInitial.Specification.Rd ├── is.FixedTransition.Density.Rd ├── is.FixedTransition.Rd ├── is.FixedTransition.Specification.Rd ├── is.FixedTransition.TransitionFixed.Rd ├── is.Specification.Rd ├── is.TVInitial.Density.Rd ├── is.TVInitial.InitialSoftmax.Rd ├── is.TVInitial.Rd ├── is.TVInitial.Specification.Rd ├── is.TVTransition.Density.Rd ├── is.TVTransition.Rd ├── is.TVTransition.Specification.Rd ├── is.TVTransition.TransitionSoftmax.Rd ├── is.discrete.Density.Rd ├── is.discrete.DensityList.Rd ├── is.discrete.DiscreteDensity.Rd ├── is.discrete.Rd ├── is.discrete.Specification.Rd ├── is.equal.Density.Rd ├── is.equal.Rd ├── is.link.Density.Rd ├── is.link.LinkDensity.Rd ├── is.link.Rd ├── is.multivariate.Density.Rd ├── is.multivariate.DensityList.Rd ├── is.multivariate.MultivariateDensity.Rd ├── is.multivariate.Rd ├── is.multivariate.Specification.Rd ├── is.ordered.Density.Rd ├── is.ordered.Rd ├── is.stanfit.Rd ├── is.stanoptim.Rd ├── link.Density.Rd ├── link.InitialFixed.Rd ├── link.InitialSoftmax.Rd ├── link.Rd ├── link.TransitionFixed.Rd ├── link.TransitionSoftmax.Rd ├── load_theme.Rd ├── logLike.Bernoulli.Rd ├── logLike.Beta.Rd ├── logLike.Binomial.Rd ├── logLike.Categorical.Rd ├── logLike.Cauchy.Rd ├── logLike.Dirichlet.Rd ├── logLike.Exponential.Rd ├── logLike.GammaDensity.Rd ├── logLike.Gaussian.Rd ├── logLike.MVGaussian.Rd ├── logLike.MVGaussianCholeskyCor.Rd ├── logLike.MVStudent.Rd ├── logLike.Multinomial.Rd ├── logLike.NegativeBinomial.Rd ├── logLike.NegativeBinomialLocation.Rd ├── logLike.Poisson.Rd ├── logLike.PriorOnlyDensity.Rd ├── logLike.Rd ├── logLike.RegBernoulliLogit.Rd ├── logLike.RegBinomialLogit.Rd ├── logLike.RegBinomialProbit.Rd ├── logLike.RegCategoricalSoftmax.Rd ├── logLike.RegGaussian.Rd ├── logLike.Student.Rd ├── make_text_header.Rd ├── make_text_line.Rd ├── make_text_subheader.Rd ├── match_parameter_names.Rd ├── mixture.Rd ├── modify_theme_entry.Rd ├── noLogLike.Density.Rd ├── noLogLike.Rd ├── optimizing.Optimization.Rd ├── optimizing.Rd ├── optimizing.Specification.Rd ├── optimizing.stanfit.Rd ├── optimizing.stanmodel.Rd ├── optimizing_all.Rd ├── optimizing_best.Rd ├── optimizing_run.Rd ├── parameters.Rd ├── plot_ppredictive.Rd ├── plot_ppredictive.stanfit.Rd ├── plot_series.Rd ├── plot_state_probability.Rd ├── plus-.Density.Rd ├── posterior_intervals.Rd ├── posterior_mode.Rd ├── print.Density.Rd ├── print.Optimization.Rd ├── print.Specification.Rd ├── print.stanfit.Rd ├── prior.Bernoulli.Rd ├── prior.Beta.Rd ├── prior.Binomial.Rd ├── prior.Categorical.Rd ├── prior.Cauchy.Rd ├── prior.CholeskyLKJCor.Rd ├── prior.Dirichlet.Rd ├── prior.Exponential.Rd ├── prior.GammaDensity.Rd ├── prior.Gaussian.Rd ├── prior.ImproperUniform.Rd ├── prior.InitialFixed.Rd ├── prior.InitialSoftmax.Rd ├── prior.InverseWishart.Rd ├── prior.MVGaussian.Rd ├── prior.MVGaussianCholeskyCor.Rd ├── prior.MVStudent.Rd ├── prior.Multinomial.Rd ├── prior.NegativeBinomial.Rd ├── prior.NegativeBinomialLocation.Rd ├── prior.Poisson.Rd ├── prior.Rd ├── prior.RegBernoulliLogit.Rd ├── prior.RegBinomialLogit.Rd ├── prior.RegBinomialProbit.Rd ├── prior.RegCategoricalSoftmax.Rd ├── prior.RegGaussian.Rd ├── prior.Student.Rd ├── prior.TransitionFixed.Rd ├── prior.TransitionSoftmax.Rd ├── prior.Wishart.Rd ├── run.Rd ├── run.Specification.Rd ├── select_all_parameters.Rd ├── select_initial_parameters.Rd ├── select_obs_parameters.Rd ├── select_parameters.Rd ├── select_transition_parameters.Rd ├── sim.Optimization.Rd ├── sim.Rd ├── sim.Specification.Rd ├── sim.stanfit.Rd ├── sim.stanmodel.Rd ├── specify.Rd ├── string_simplify.Rd ├── theme.Rd ├── validate_calibration.Rd ├── write_chunks.Rd ├── write_chunks.Specification.Rd ├── write_model.Rd └── write_model.Specification.Rd ├── tests ├── build.R ├── density.txt ├── run.R └── specification.txt └── vignettes ├── introduction.Rmd ├── introduction2.Rmd └── references.bib /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luisdamiano/BayesHMM/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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