NAMESPACE

importFrom(Rcpp, evalCpp)

importClassesFrom(rstan,stanfit)

importFrom(grDevices, col2rgb, dev.off, n2mfrow, rgb)
importFrom(graphics, abline, axis, boxplot, hist, legend,
           lines, par, plot, points, polygon, rect,
           segments, title)
importFrom(methods, setMethod)
importFrom(stats, density, ks.test, median, quantile)
importFrom(utils, browseURL, capture.output, glob2rx, head, tail)

S3method(`+`, Density)
export(Bernoulli)
export(Beta)
export(Binomial)
S3method(block_data, Density)
S3method(block_data, DiscreteDensity)
S3method(block_data, HMMSpecification)
S3method(block_data, MixtureSpecification)
S3method(block_data, RegBernoulliLogit)
S3method(block_data, RegBinomialLogit)
S3method(block_data, RegBinomialProbit)
S3method(block_data, RegCategoricalSoftmax)
S3method(block_data, RegGaussian)
S3method(block_data, Specification)
S3method(block_functions, HMMSpecification)
S3method(block_functions, MixtureSpecification)
S3method(block_functions, Specification)
S3method(block_generated, HMMSpecification)
S3method(block_generated, MixtureSpecification)
S3method(block_generated, Specification)
S3method(block_parameters, HMMSpecification)
S3method(block_parameters, MixtureSpecification)
S3method(block_parameters, Specification)
S3method(block_target, Specification)
S3method(block_tdata, Specification)
S3method(block_tparameters, HMMSpecification)
S3method(block_tparameters, MixtureSpecification)
S3method(block_tparameters, Specification)
export(browse_model)
S3method(browse_model, stanmodel)
S3method(browse_model, stanfit)
S3method(browse_model, Optimization)
S3method(browse_model, Specification)
export(Categorical)
export(Cauchy)
export(CholeskyLKJCor)
S3method(chunk_calculate_target, HMMSpecification)
S3method(chunk_calculate_target, MixtureSpecification)
S3method(chunk_calculate_target, Specification)
S3method(chunk_increase_target, HMMSpecification)
S3method(chunk_increase_target, MixtureSpecification)
S3method(chunk_increase_target, Specification)
S3method(chunk_zpredictive, HMMSpecification)
S3method(chunk_zpredictive, MixtureSpecification)
S3method(chunk_zpredictive, Specification)
export(classify_alpha)
S3method(classify_alpha, Optimization)
S3method(classify_alpha, stanfit); # export(classify_alpha.Optimization)
export(classify_gamma)
S3method(classify_gamma, Optimization)
S3method(classify_gamma, stanfit); # export(classify_gamma.Optimization)
export(classify_zstar)
S3method(classify_zstar, Optimization)
S3method(classify_zstar, stanfit); # export(classify_zstar.Optimization)
export(compile)
S3method(compile, Specification)
S3method(constants, Binomial)
S3method(constants, Categorical)
S3method(constants, Density)
S3method(constants, Multinomial)
S3method(constants, RegBinomialLogit)
S3method(constants, RegBinomialProbit)
S3method(constants, RegCategoricalSoftmax)
export(ImproperUniform)
export(Dirichlet)
export(DiscreteDensity)
export(draw_samples)
S3method(draw_samples, stanmodel)
S3method(draw_samples, stanfit)
S3method(draw_samples, Optimization)
S3method(draw_samples, Specification)
export(explain)
S3method(explain_density, Density)
S3method(explain_density, DensityList)
S3method(explain_density, InitialFixed)
S3method(explain_density, InitialSoftmax)
S3method(explain_density, TransitionFixed)
S3method(explain_density, TransitionSoftmax)
S3method(explain_initial, Specification)
S3method(explain_observation, Specification)
S3method(explain_transition, Specification)
S3method(explain, Specification)
export(Exponential)
export(extract_alpha)
export(extract_best)
S3method(extract_best, OptimizationList)
export(extract_data)
export(extract_date)
S3method(extract_date, Optimization)
S3method(extract_date, stanfit); # export(extract_date.Optimization)
export(extract_diagnostics)
S3method(extract_diagnostics, stanfit)
export(extract_filename)
export(extract_gamma)
export(extract_grid)
S3method(extract_grid, Optimization)
S3method(extract_grid, OptimizationList)
export(extract_K)
export(extract_n_chains)
S3method(extract_n_chains, stanfit)
export(extract_n_iterations)
S3method(extract_n_iterations, stanfit)
export(extract_n_thin)
S3method(extract_n_thin, stanfit)
export(extract_n_warmup)
S3method(extract_n_warmup, stanfit)
export(extract_model)
export(extract_obs_parameters)
export(extract_parameter_names)
S3method(extract_parameter_names, Optimization)
S3method(extract_parameter_names, stanfit) # export(extract_parameter_names.Optimization)
export(extract_parameters)
export(extract_quantity)
S3method(extract_quantity, Optimization)
S3method(extract_quantity, stanfit); # export(extract_quantity.Optimization)
export(extract_R)
export(extract_sample_size)
S3method(extract_sample_size, stanfit)
export(extract_seed)
S3method(extract_seed, Optimization)
S3method(extract_seed, stanfit); # export(extract_seed.Optimization)
export(extract_spec)
export(extract_T)
export(extract_time)
S3method(extract_time, Optimization)
S3method(extract_time, stanfit); # export(extract_time.Optimization)
export(extract_y)
export(extract_ypred)
export(extract_ysim)
export(extract_zpred)
export(extract_zsim)
export(extract_zstar)
export(fit)
S3method(fit, stanmodel)
S3method(fit, stanfit)
S3method(fit, Optimization)
S3method(fit, Specification)
S3method(fixedParameters, Bernoulli)
S3method(fixedParameters, Beta)
S3method(fixedParameters, Binomial)
S3method(fixedParameters, Categorical)
S3method(fixedParameters, Cauchy)
S3method(fixedParameters, Dirichlet)
S3method(fixedParameters, Exponential)
S3method(fixedParameters, GammaDensity)
S3method(fixedParameters, Gaussian)
S3method(fixedParameters, InitialFixed)
S3method(fixedParameters, InitialSoftmax)
S3method(fixedParameters, Multinomial)
S3method(fixedParameters, MVGaussian)
S3method(fixedParameters, MVGaussianCholeskyCor)
S3method(fixedParameters, MVStudent)
S3method(fixedParameters, NegativeBinomial)
S3method(fixedParameters, NegativeBinomialLocation)
S3method(fixedParameters, Poisson)
S3method(fixedParameters, PriorOnlyDensity)
S3method(fixedParameters, RegBernoulliLogit)
S3method(fixedParameters, RegBinomialLogit)
S3method(fixedParameters, RegBinomialProbit)
S3method(fixedParameters, RegCategoricalSoftmax)
S3method(fixedParameters, RegGaussian)
S3method(fixedParameters, Student)
S3method(fixedParameters, TransitionFixed)
S3method(fixedParameters, TransitionSoftmax)
S3method(freeParameters, Bernoulli)
S3method(freeParameters, Beta)
S3method(freeParameters, Binomial)
S3method(freeParameters, Categorical)
S3method(freeParameters, Cauchy)
S3method(freeParameters, Dirichlet)
S3method(freeParameters, Exponential)
S3method(freeParameters, GammaDensity)
S3method(freeParameters, Gaussian)
S3method(freeParameters, InitialFixed)
S3method(freeParameters, InitialSoftmax)
S3method(freeParameters, Multinomial)
S3method(freeParameters, MVGaussian)
S3method(freeParameters, MVGaussianCholeskyCor)
S3method(freeParameters, MVStudent)
S3method(freeParameters, NegativeBinomial)
S3method(freeParameters, NegativeBinomialLocation)
S3method(freeParameters, Poisson)
S3method(freeParameters, PriorOnlyDensity)
S3method(freeParameters, RegBernoulliLogit)
S3method(freeParameters, RegBinomialLogit)
S3method(freeParameters, RegBinomialProbit)
S3method(freeParameters, RegCategoricalSoftmax)
S3method(freeParameters, RegGaussian)
S3method(freeParameters, Student)
S3method(freeParameters, TransitionFixed)
S3method(freeParameters, TransitionSoftmax)
export(GammaDensity)
export(Gaussian)
S3method(generated, Bernoulli)
S3method(generated, Beta)
S3method(generated, Binomial)
S3method(generated, Categorical)
S3method(generated, Cauchy)
S3method(generated, Dirichlet)
S3method(generated, Exponential)
S3method(generated, GammaDensity)
S3method(generated, Gaussian)
S3method(generated, Multinomial)
S3method(generated, MVGaussian)
S3method(generated, MVGaussianCholeskyCor)
S3method(generated, MVStudent)
S3method(generated, NegativeBinomial)
S3method(generated, NegativeBinomialLocation)
S3method(generated, Poisson)
S3method(generated, PriorOnlyDensity)
S3method(generated, RegBernoulliLogit)
S3method(generated, RegBinomialLogit)
S3method(generated, RegBinomialProbit)
S3method(generated, RegCategoricalSoftmax)
S3method(generated, RegGaussian)
S3method(generated, Student)
export(get_current_theme)
export(get_default_theme)
S3method(getFixedParameters, Density)
S3method(getFreeParameters, Density)
S3method(getFreeParameters, PriorOnlyDensity)
S3method(getParameterNames, Bernoulli)
S3method(getParameterNames, Beta)
S3method(getParameterNames, Binomial)
S3method(getParameterNames, Categorical)
S3method(getParameterNames, Cauchy)
S3method(getParameterNames, Density)
S3method(getParameterNames, Dirichlet)
S3method(getParameterNames, Exponential)
S3method(getParameterNames, GammaDensity)
S3method(getParameterNames, Gaussian)
S3method(getParameterNames, InitialFixed)
S3method(getParameterNames, InitialSoftmax)
S3method(getParameterNames, Multinomial)
S3method(getParameterNames, MVGaussian)
S3method(getParameterNames, MVGaussianCholeskyCor)
S3method(getParameterNames, MVStudent)
S3method(getParameterNames, NegativeBinomial)
S3method(getParameterNames, NegativeBinomialLocation)
S3method(getParameterNames, Poisson)
S3method(getParameterNames, PriorOnlyDensity)
S3method(getParameterNames, RegBernoulliLogit)
S3method(getParameterNames, RegBinomialLogit)
S3method(getParameterNames, RegBinomialProbit)
S3method(getParameterNames, RegCategoricalSoftmax)
S3method(getParameterNames, RegGaussian)
S3method(getParameterNames, Student)
S3method(getParameterNames, TransitionFixed)
S3method(getParameterNames, TransitionSoftmax)
export(hmm)
export(InitialFixed)
export(InitialSoftmax)
export(InverseWishart)
S3method(is.discrete, Density)
S3method(is.discrete, DensityList)
S3method(is.discrete, DiscreteDensity)
S3method(is.discrete, Specification)
S3method(is.FixedInitial, Density)
S3method(is.FixedInitial, InitialFixed)
S3method(is.FixedTransition, Density)
S3method(is.FixedTransition, TransitionFixed)
S3method(is.link, Density)
S3method(is.link, LinkDensity)
S3method(is.multivariate, Density)
S3method(is.multivariate, DensityList)
S3method(is.multivariate, MultivariateDensity)
S3method(is.multivariate, Specification)
S3method(is.ordered, Density)
S3method(is.TVInitial, Density)
S3method(is.TVInitial, InitialSoftmax)
S3method(is.TVInitial, Specification)
S3method(is.TVTransition, Density)
S3method(is.TVTransition, Specification)
S3method(is.TVTransition, TransitionSoftmax)
S3method(link, Density)
S3method(link, InitialFixed)
S3method(link, InitialSoftmax)
S3method(link, TransitionFixed)
S3method(link, TransitionSoftmax)
export(LinkDensity)
S3method(logLike, Bernoulli)
S3method(logLike, Beta)
S3method(logLike, Binomial)
S3method(logLike, Categorical)
S3method(logLike, Cauchy)
S3method(logLike, Dirichlet)
S3method(logLike, Exponential)
S3method(logLike, GammaDensity)
S3method(logLike, Gaussian)
S3method(logLike, Multinomial)
S3method(logLike, MVGaussian)
S3method(logLike, MVGaussianCholeskyCor)
S3method(logLike, MVStudent)
S3method(logLike, NegativeBinomial)
S3method(logLike, NegativeBinomialLocation)
S3method(logLike, Poisson)
S3method(logLike, PriorOnlyDensity)
S3method(logLike, RegBernoulliLogit)
S3method(logLike, RegBinomialLogit)
S3method(logLike, RegBinomialProbit)
S3method(logLike, RegCategoricalSoftmax)
S3method(logLike, RegGaussian)
S3method(logLike, Student)
S3method(make_data, Specification)
export(match_parameter_names)
export(modify_theme_entry)
# export(mixture)
export(Multinomial)
export(MVGaussian)
export(MVGaussianCholeskyCor)
export(MVStudent)
export(NegativeBinomial)
export(NegativeBinomialLocation)
S3method(noLogLike, Density)
export(optimizing)
S3method(optimizing, stanmodel)
S3method(optimizing, stanfit)
S3method(optimizing, Optimization)
S3method(optimizing, Specification)
export(plot_ppredictive)
S3method(plot_ppredictive, stanfit)
export(plot_series)
export(plot_state_probability)
export(Poisson)
export(posterior_intervals)
export(posterior_mode)
S3method(print, Density)
S3method(print, Optimization)
S3method(print, Specification)
S3method(print, stanfit)
S3method(prior, Bernoulli)
S3method(prior, Beta)
S3method(prior, Binomial)
S3method(prior, Categorical)
S3method(prior, Cauchy)
S3method(prior, CholeskyLKJCor)
S3method(prior, Dirichlet)
S3method(prior, Exponential)
S3method(prior, GammaDensity)
S3method(prior, Gaussian)
S3method(prior, InitialFixed)
S3method(prior, InitialSoftmax)
S3method(prior, InverseWishart)
S3method(prior, ImproperUniform)
S3method(prior, Multinomial)
S3method(prior, MVGaussian)
S3method(prior, MVGaussianCholeskyCor)
S3method(prior, MVStudent)
S3method(prior, NegativeBinomial)
S3method(prior, NegativeBinomialLocation)
S3method(prior, Poisson)
S3method(prior, RegBernoulliLogit)
S3method(prior, RegBinomialLogit)
S3method(prior, RegBinomialProbit)
S3method(prior, RegCategoricalSoftmax)
S3method(prior, RegGaussian)
S3method(prior, Student)
S3method(prior, TransitionFixed)
S3method(prior, TransitionSoftmax)
S3method(prior, Wishart)
export(RegBernoulliLogit)
export(RegBinomialLogit)
export(RegBinomialProbit)
export(RegCategoricalSoftmax)
export(RegGaussian)
S3method(run, Specification)
export(sim)
S3method(sim, stanmodel)
S3method(sim, stanfit)
S3method(sim, Optimization)
S3method(sim, Specification)
export(specify)
export(Student)
export(TransitionFixed)
export(TransitionSoftmax)
# export(validate)
export(validate_calibration)
export(Wishart)
S3method(write_chunks, Specification)
S3method(write_model, Specification)