API for luisdamiano/BayesHMM
Full Bayesian Inference for Hidden Markov Models

Global functions
Bernoulli Source code
Beta Source code
Binomial Source code
Categorical Source code
Cauchy Source code
Default Source code
Density Source code
Dirichlet Source code
DiscreteDensity Source code
Gaussian Source code
InitialSoftmax Source code
LKJCor Source code
LinkDensity Source code
MVGaussian Source code
MVGaussianCor Source code
MVGaussianCov Source code
MVStudent Source code
Multinomial Source code
MultivariateDensity Source code
MultivariateDiscreteDensity Source code
NegativeBinomial Source code
NegativeBinomialLocation Source code
Poisson Source code
PriorOnlyDensity Source code
PriorOnlyMultivariateDensity Source code
RegBernoulliLogit Source code
RegBinomialLogit Source code
RegBinomialProbit Source code
RegCategoricalSoftmax Source code
RegGaussian Source code
Student Source code
TransitionFixed Source code
TransitionSoftmax Source code
Wishart Source code
add_colored_lines Source code
add_fan Source code
add_features Source code
add_legend_overlay Source code
add_shade Source code
add_title_overlay Source code
block_data Source code
block_data.Density Source code
block_data.DiscreteDensity Source code
block_data.HMMSpecification Source code
block_data.MixtureSpecification Source code
block_data.RegBernoulliLogit Source code
block_data.RegBinomialLogit Source code
block_data.RegBinomialProbit Source code
block_data.RegCategoricalSoftmax Source code
block_data.RegGaussian Source code
block_data.Specification Source code
block_data.TransitionFixed Source code
block_data.TransitionSoftmax Source code
block_functions Source code
block_functions.HMMSpecification Source code
block_functions.MixtureSpecification Source code
block_functions.Specification Source code
block_generated Source code
block_generated.HMMSpecification Source code
block_generated.MixtureSpecification Source code
block_generated.Specification Source code
block_parameters Source code
block_parameters.HMMSpecification Source code
block_parameters.MixtureSpecification Source code
block_parameters.Specification Source code
block_target Source code
block_target.Specification Source code
block_tdata Source code
block_tdata.Specification Source code
block_tparameters Source code
block_tparameters.HMMSpecification Source code
block_tparameters.MixtureSpecification Source code
block_tparameters.Specification Source code
browse_model Source code Source code
browse_model.Specification Source code
cast_to_matrix Source code
check Source code
check.Specification Source code
check_cholesky_factor Source code
check_cholesky_factor_cor Source code
check_cholesky_factor_cov Source code
check_cov_matrix Source code
check_list Source code
check_matrix Source code
check_natural Source code
check_psd Source code
check_scalar Source code
check_simplex Source code
check_transition_matrix Source code
check_vector Source code
check_whole Source code
chunk_calculate_target Source code
chunk_calculate_target.HMMSpecification Source code
chunk_calculate_target.MixtureSpecification Source code
chunk_calculate_target.Specification Source code
chunk_increase_target Source code
chunk_increase_target.HMMSpecification Source code
chunk_increase_target.MixtureSpecification Source code
chunk_increase_target.Specification Source code
chunk_zpredictive Source code
chunk_zpredictive.HMMSpecification Source code
chunk_zpredictive.MixtureSpecification Source code
chunk_zpredictive.Specification Source code
classify_alpha Source code
classify_alpha.Optimization Source code
classify_alpha.stanfit Source code
classify_gamma Source code
classify_gamma.Optimization Source code
classify_gamma.stanfit Source code
classify_zstar Source code
classify_zstar.Optimization Source code
classify_zstar.stanfit Source code
col2rgb_alpha Source code
collapse Source code
compile Source code
compile.Specification Source code
constants Source code
constants.Binomial Source code
constants.Categorical Source code
constants.Density Source code
constants.Multinomial Source code
constants.RegBinomialLogit Source code
constants.RegBinomialProbit Source code
constants.RegCategoricalSoftmax Source code
densityApply Source code
densityCollect Source code
explain Source code Source code
explain.Density Source code
explain.DensityList Source code
explain.Specification Source code
explain.TransitionSoftmax Source code
explain_initial Source code
explain_initial.Specification Source code
explain_observation Source code
explain_observation.Specification Source code
explain_transition Source code
explain_transition.Specification Source code
extract_K Source code
extract_R Source code
extract_T Source code
extract_alpha Source code
extract_best Source code
extract_best.OptimizationList Source code
extract_data Source code
extract_filename Source code
extract_gamma Source code
extract_grid Source code
extract_grid.Optimization Source code
extract_grid.OptimizationList Source code
extract_obs_parameters Source code
extract_parameter_names Source code
extract_parameter_names.Optimization Source code
extract_parameter_names.stanfit Source code
extract_parameters Source code
extract_quantity Source code
extract_quantity.Optimization Source code
extract_quantity.stanfit Source code
extract_seed Source code
extract_seed.Optimization Source code
extract_seed.stanfit Source code
extract_spec Source code
extract_time Source code
extract_time.Optimization Source code
extract_time.stanfit Source code
extract_y Source code
extract_ypred Source code
extract_ysim Source code
extract_zpred Source code
extract_zstar Source code
fit Source code
fit.Specification Source code
fixedParameters Source code
fixedParameters.Bernoulli Source code
fixedParameters.Beta Source code
fixedParameters.Binomial Source code
fixedParameters.Categorical Source code
fixedParameters.Cauchy Source code
fixedParameters.Dirichlet Source code
fixedParameters.Gaussian Source code
fixedParameters.InitialSoftmax Source code
fixedParameters.MVGaussian Source code
fixedParameters.MVGaussianCor Source code
fixedParameters.MVGaussianCov Source code
fixedParameters.MVStudent Source code
fixedParameters.Multinomial Source code
fixedParameters.NegativeBinomial Source code
fixedParameters.NegativeBinomialLocation Source code
fixedParameters.Poisson Source code
fixedParameters.PriorOnlyDensity Source code
fixedParameters.RegBernoulliLogit Source code
fixedParameters.RegBinomialLogit Source code
fixedParameters.RegBinomialProbit Source code
fixedParameters.RegCategoricalSoftmax Source code
fixedParameters.RegGaussian Source code
fixedParameters.Student Source code
fixedParameters.TransitionFixed Source code
fixedParameters.TransitionSoftmax Source code
format_fixed_parameters Source code
freeParameters Source code
freeParameters.Bernoulli Source code
freeParameters.Beta Source code
freeParameters.Binomial Source code
freeParameters.Categorical Source code
freeParameters.Cauchy Source code
freeParameters.Dirichlet Source code
freeParameters.Gaussian Source code
freeParameters.InitialSoftmax Source code
freeParameters.MVGaussian Source code
freeParameters.MVGaussianCor Source code
freeParameters.MVGaussianCov Source code
freeParameters.MVStudent Source code
freeParameters.Multinomial Source code
freeParameters.NegativeBinomial Source code
freeParameters.NegativeBinomialLocation Source code
freeParameters.Poisson Source code
freeParameters.PriorOnlyDensity Source code
freeParameters.RegBernoulliLogit Source code
freeParameters.RegBinomialLogit Source code
freeParameters.RegBinomialProbit Source code
freeParameters.RegCategoricalSoftmax Source code
freeParameters.RegGaussian Source code
freeParameters.Student Source code
freeParameters.TransitionFixed Source code
freeParameters.TransitionSoftmax Source code
funinvarName Source code
generated Source code
generated.Bernoulli Source code
generated.Beta Source code
generated.Binomial Source code
generated.Categorical Source code
generated.Cauchy Source code
generated.Dirichlet Source code
generated.Gaussian Source code
generated.InitialSoftmax Source code
generated.MVGaussian Source code
generated.MVGaussianCor Source code
generated.MVGaussianCov Source code
generated.MVStudent Source code
generated.Multinomial Source code
generated.NegativeBinomial Source code
generated.NegativeBinomialLocation Source code
generated.Poisson Source code
generated.PriorOnlyDensity Source code
generated.RegBernoulliLogit Source code
generated.RegBinomialLogit Source code
generated.RegBinomialProbit Source code
generated.RegCategoricalSoftmax Source code
generated.RegGaussian Source code
generated.Student Source code
generated.TransitionFixed Source code
generated.TransitionSoftmax Source code
getFixedParameters Source code
getFixedParameters.Density Source code
getFreeParameters Source code
getFreeParameters.Density Source code
getFreeParameters.PriorOnlyDensity Source code
getParameterNames Source code
getParameterNames.Bernoulli Source code
getParameterNames.Beta Source code
getParameterNames.Binomial Source code
getParameterNames.Categorical Source code
getParameterNames.Cauchy Source code
getParameterNames.Density Source code
getParameterNames.Dirichlet Source code
getParameterNames.Gaussian Source code
getParameterNames.InitialSoftmax Source code
getParameterNames.MVGaussian Source code
getParameterNames.MVGaussianCor Source code
getParameterNames.MVGaussianCov Source code
getParameterNames.MVStudent Source code
getParameterNames.Multinomial Source code
getParameterNames.NegativeBinomial Source code
getParameterNames.NegativeBinomialLocation Source code
getParameterNames.Poisson Source code
getParameterNames.RegBernoulliLogit Source code
getParameterNames.RegBinomialLogit Source code
getParameterNames.RegBinomialProbit Source code
getParameterNames.RegCategoricalSoftmax Source code
getParameterNames.RegGaussian Source code
getParameterNames.Student Source code
getParameterNames.TransitionFixed Source code
getParameterNames.TransitionSoftmax Source code
get_diagnose_chain_convergence Source code
get_diagnose_parameters Source code
get_diagnose_ppredictive Source code
get_dim Source code
get_package_info Source code
get_print_settings Source code
get_rstan_info Source code
get_theme Source code
get_ybottom Source code
get_ytop Source code
hmm Source code
is.Density Source code
is.DensityList Source code
is.TVInitial Source code
is.TVInitial.Density Source code
is.TVInitial.Specification Source code
is.TVTransition Source code
is.TVTransition.Density Source code
is.TVTransition.Specification Source code
is.discrete Source code
is.discrete.Density Source code
is.discrete.DiscreteDensity Source code
is.discrete.Specification Source code
is.empty Source code
is.link Source code
is.link.Density Source code
is.link.LinkDensity Source code
is.multivariate Source code
is.multivariate.Density Source code
is.multivariate.DensityList Source code
is.multivariate.MultivariateDensity Source code
is.multivariate.Specification Source code
is.stanfit Source code
is.stanoptim Source code
link Source code
link.Density Source code
link.InitialSoftmax Source code
link.TransitionFixed Source code
link.TransitionSoftmax Source code
logLike Source code
logLike.Bernoulli Source code
logLike.Beta Source code
logLike.Binomial Source code
logLike.Categorical Source code
logLike.Cauchy Source code
logLike.Dirichlet Source code
logLike.Gaussian Source code
logLike.InitialSoftmax Source code
logLike.MVGaussian Source code
logLike.MVGaussianCor Source code
logLike.MVGaussianCov Source code
logLike.MVStudent Source code
logLike.Multinomial Source code
logLike.NegativeBinomial Source code
logLike.NegativeBinomialLocation Source code
logLike.Poisson Source code
logLike.PriorOnlyDensity Source code
logLike.RegBernoulliLogit Source code
logLike.RegBinomialLogit Source code
logLike.RegBinomialProbit Source code
logLike.RegCategoricalSoftmax Source code
logLike.RegGaussian Source code
logLike.Student Source code
logLike.TransitionFixed Source code
logLike.TransitionSoftmax Source code
make_bounds Source code
make_data Source code
make_data.Specification Source code
make_fixed_parameters Source code
make_free_parameters Source code
make_limit Source code
make_names Source code
make_parameters Source code
make_rsubindex Source code
make_text Source code
make_text_header Source code
make_text_line Source code
make_text_subheader Source code
make_trunc Source code
matrix_to_stan Source code
mixture Source code
monitor Source code
monitor_initial Source code
monitor_observation Source code
monitor_transition Source code
noLogLike Source code
noLogLike.Density Source code
onAttach Source code
onLoad Source code
optimizing Source code
optimizing.Specification Source code
optimizing_all Source code
optimizing_best Source code
optimizing_run Source code
order_block Source code
par_edit Source code
par_reset Source code
parameters Source code
parse_initial Source code
parse_initial_build_K Source code
parse_initial_build_none_multivariate Source code
parse_initial_build_none_univariate Source code
parse_observation Source code
parse_observation_build_K Source code
parse_observation_build_KxR Source code
parse_observation_build_R Source code
parse_observation_build_none Source code
parse_observation_build_priors Source code
parse_transition Source code
parse_transition_build_K Source code
parse_transition_build_KxK Source code
parse_transition_build_none_multivariate Source code
parse_transition_build_none_univariate Source code
permutations Source code
plot.Optimization Source code
plot_obs Source code
plot_params Source code
plot_ppredictive.stanfit Source code
plot_ppredictive_boxplot Source code
plot_ppredictive_cumulative Source code
plot_ppredictive_density Source code
plot_ppredictive_hist Source code
plot_ppredictive_ks Source code
plot_ppredictive_scatter Source code
plot_series Source code
plot_state_probability Source code
posterior_intervals Source code
posterior_mode Source code
prank Source code
print.Optimization Source code
print_all Source code
print_fit Source code
print_initial Source code
print_monitor Source code
print_obs Source code
print_observation Source code
print_transition Source code
prior Source code
prior.Bernoulli Source code
prior.Beta Source code
prior.Binomial Source code
prior.Categorical Source code
prior.Cauchy Source code
prior.Default Source code
prior.Dirichlet Source code
prior.Gaussian Source code
prior.InitialSoftmax Source code
prior.LKJCor Source code
prior.MVGaussian Source code
prior.MVGaussianCor Source code
prior.MVGaussianCov Source code
prior.MVStudent Source code
prior.Multinomial Source code
prior.NegativeBinomial Source code
prior.NegativeBinomialLocation Source code
prior.Poisson Source code
prior.RegBernoulliLogit Source code
prior.RegBinomialLogit Source code
prior.RegBinomialProbit Source code
prior.RegCategoricalSoftmax Source code
prior.RegGaussian Source code
prior.Student Source code
prior.TransitionFixed Source code
prior.TransitionSoftmax Source code
prior.Wishart Source code
run Source code
run.Specification Source code
sampling Source code
sampling.Specification Source code
select_all_parameters Source code
select_initial_parameters Source code
select_obs_parameters Source code
select_parameters Source code
select_transition_parameters Source code
sim Source code
sim.Specification Source code
sort_block Source code
sort_chain Source code
spec Source code
stan_sort_chain Source code
summary Source code
toproper Source code
validate Source code
validate_calibration Source code
vector_to_stan Source code
write_chunks Source code
write_chunks.Specification Source code
write_constants Source code
write_data Source code
write_functions Source code
write_generated Source code
write_link Source code
write_logLikelihood Source code
write_model Source code
write_model.Specification Source code
write_parameters Source code
write_priors Source code
write_stanfile Source code
write_target Source code
write_tdata Source code
write_tparameters Source code
write_ypredictive Source code
write_zpredictive Source code
luisdamiano/BayesHMM documentation built on Sept. 1, 2018, 3:05 p.m.