pymcmcstat
v1.6.0
pymcmcstat package
pymcmcstat.MCMC module
pymcmcstat.ParallelMCMC module
Subpackages
pymcmcstat.chain package
pymcmcstat.chain.ChainProcessing module
pymcmcstat.chain.ChainStatistics module
pymcmcstat.plotting package
pymcmcstat.plotting.MCMCPlotting module
pymcmcstat.plotting.PredictionIntervals module
pymcmcstat.plotting.utilities module
pymcmcstat.procedures package
pymcmcstat.procedures.CovarianceProcedures module
pymcmcstat.procedures.ErrorVarianceEstimator module
pymcmcstat.procedures.PriorFunction module
pymcmcstat.procedures.SumOfSquares module
pymcmcstat.samplers package
pymcmcstat.samplers.Adaptation module
pymcmcstat.samplers.DelayedRejection module
pymcmcstat.samplers.Metropolis module
pymcmcstat.samplers.SamplingMethods module
pymcmcstat.samplers.utilities module
pymcmcstat.settings package
pymcmcstat.settings.DataStructure module
pymcmcstat.settings.ModelParameters module
pymcmcstat.settings.ModelSettings module
pymcmcstat.settings.SimulationOptions module
pymcmcstat.structures package
pymcmcstat.structures.ParameterSet module
pymcmcstat.structures.ResultsStructure module
pymcmcstat.utilities package
pymcmcstat.utilities.NumpyEncoder module
pymcmcstat.utilities.general module
pymcmcstat.utilities.progressbar module
pymcmcstat
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B
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C
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D
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E
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F
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G
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I
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L
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M
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N
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P
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R
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S
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U
A
acceptance_test() (in module pymcmcstat.samplers.utilities)
Adaptation (class in pymcmcstat.samplers.Adaptation)
add_basic() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
add_chain() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
add_data_set() (pymcmcstat.settings.DataStructure.DataStructure method)
add_dram() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
add_model() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
add_model_parameter() (pymcmcstat.settings.ModelParameters.ModelParameters method)
add_options() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
add_prior() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
add_random_number_sequence() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
add_s2chain() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
add_sschain() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
add_time_stats() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
add_updatesigma() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
adjust_cov_matrix() (in module pymcmcstat.samplers.Adaptation)
alphafun() (pymcmcstat.samplers.DelayedRejection.DelayedRejection method)
append_to_nrow_ncol_based_on_shape() (in module pymcmcstat.plotting.utilities)
assign_number_of_cores() (in module pymcmcstat.ParallelMCMC)
B
batch_mean_standard_deviation() (in module pymcmcstat.chain.ChainStatistics)
below_burnin_threshold() (in module pymcmcstat.samplers.Adaptation)
C
calculate_psrf() (in module pymcmcstat.chain.ChainStatistics)
chainstats() (in module pymcmcstat.chain.ChainStatistics)
check_directory() (in module pymcmcstat.ParallelMCMC)
check_for_restart_file() (in module pymcmcstat.ParallelMCMC)
check_for_singular_cov_matrix() (in module pymcmcstat.samplers.Adaptation)
check_initial_values() (in module pymcmcstat.ParallelMCMC)
check_noadaptind() (in module pymcmcstat.settings.ModelParameters)
check_options_output() (in module pymcmcstat.ParallelMCMC)
check_settings() (in module pymcmcstat.plotting.utilities)
check_shape_of_users_initial_values() (in module pymcmcstat.ParallelMCMC)
check_symmetric() (in module pymcmcstat.plotting.utilities)
check_users_initial_values_wrt_limits() (in module pymcmcstat.ParallelMCMC)
check_verbosity() (in module pymcmcstat.settings.ModelParameters)
cholupdate() (in module pymcmcstat.samplers.Adaptation)
convert_flag_to_boolean() (in module pymcmcstat.plotting.utilities)
CovarianceProcedures (class in pymcmcstat.procedures.CovarianceProcedures)
D
DataStructure (class in pymcmcstat.settings.DataStructure)
default() (pymcmcstat.utilities.NumpyEncoder.NumpyEncoder method)
default_priorfun() (pymcmcstat.procedures.PriorFunction.PriorFunction class method)
define_model_settings() (pymcmcstat.settings.ModelSettings.ModelSettings method)
define_simulation_options() (pymcmcstat.settings.SimulationOptions.SimulationOptions method)
DelayedRejection (class in pymcmcstat.samplers.DelayedRejection)
determine_filename() (pymcmcstat.structures.ResultsStructure.ResultsStructure class method)
display_covariance_settings() (pymcmcstat.procedures.CovarianceProcedures.CovarianceProcedures method)
display_current_mcmc_settings() (pymcmcstat.MCMC.MCMC method)
display_gelman_rubin() (in module pymcmcstat.chain.ChainStatistics)
display_individual_chain_statistics() (pymcmcstat.ParallelMCMC.ParallelMCMC method)
display_model_settings() (pymcmcstat.settings.ModelSettings.ModelSettings method)
display_parameter_settings() (pymcmcstat.settings.ModelParameters.ModelParameters method)
display_simulation_options() (pymcmcstat.settings.SimulationOptions.SimulationOptions method)
E
empirical_quantiles() (in module pymcmcstat.plotting.utilities)
ErrorVarianceEstimator (class in pymcmcstat.procedures.ErrorVarianceEstimator)
evaluate_likelihood_function() (pymcmcstat.samplers.Metropolis.Metropolis class method)
evaluate_prior() (pymcmcstat.procedures.PriorFunction.PriorFunction method)
evaluate_sos_function() (pymcmcstat.procedures.SumOfSquares.SumOfSquares method)
export_simulation_results_to_json_file() (pymcmcstat.structures.ResultsStructure.ResultsStructure method)
extend_names_to_match_nparam() (in module pymcmcstat.plotting.utilities)
extract_state_elements() (in module pymcmcstat.samplers.DelayedRejection)
F
format_number_to_str() (in module pymcmcstat.settings.ModelParameters)
G
gammar() (pymcmcstat.procedures.ErrorVarianceEstimator.ErrorVarianceEstimator method)
gammar_mt() (pymcmcstat.procedures.ErrorVarianceEstimator.ErrorVarianceEstimator method)
gaussian_density_function() (in module pymcmcstat.plotting.utilities)
gelman_rubin() (in module pymcmcstat.chain.ChainStatistics)
generate_chain_list() (in module pymcmcstat.chain.ChainProcessing)
generate_combined_chain_with_index() (in module pymcmcstat.chain.ChainProcessing)
generate_default_name() (in module pymcmcstat.settings.ModelParameters)
generate_default_names() (in module pymcmcstat.plotting.utilities)
generate_ellipse() (in module pymcmcstat.plotting.utilities)
generate_initial_values() (in module pymcmcstat.ParallelMCMC)
generate_names() (in module pymcmcstat.plotting.utilities)
generate_prediction_intervals() (pymcmcstat.plotting.PredictionIntervals.PredictionIntervals method)
generate_subplot_grid() (in module pymcmcstat.plotting.utilities)
get_number_of_batches() (pymcmcstat.settings.DataStructure.DataStructure method)
get_number_of_data_sets() (pymcmcstat.settings.DataStructure.DataStructure method)
get_number_of_observations() (pymcmcstat.settings.DataStructure.DataStructure method)
get_parameter_features() (in module pymcmcstat.ParallelMCMC)
get_parameter_names() (in module pymcmcstat.chain.ChainStatistics)
geweke() (in module pymcmcstat.chain.ChainStatistics)
I
initialize_covariance_mean_sum() (in module pymcmcstat.samplers.Adaptation)
initialize_next_metropolis_step() (pymcmcstat.samplers.DelayedRejection.DelayedRejection class method)
integrated_autocorrelation_time() (in module pymcmcstat.chain.ChainStatistics)
iqrange() (in module pymcmcstat.plotting.utilities)
is_sample_outside_bounds() (in module pymcmcstat.samplers.utilities)
is_semi_pos_def_chol() (in module pymcmcstat.plotting.utilities)
(in module pymcmcstat.samplers.Adaptation)
L
less_than_or_equal_to_zero() (in module pymcmcstat.settings.ModelParameters)
load_json_object() (in module pymcmcstat.chain.ChainProcessing)
(pymcmcstat.structures.ResultsStructure.ResultsStructure class method)
load_parallel_simulation_results() (in module pymcmcstat.ParallelMCMC)
log_posterior_ratio() (in module pymcmcstat.samplers.DelayedRejection)
M
make_x_grid() (in module pymcmcstat.plotting.utilities)
MCMC (class in pymcmcstat.MCMC)
mcmc_sos_function() (pymcmcstat.procedures.SumOfSquares.SumOfSquares class method)
message() (in module pymcmcstat.utilities.general)
Metropolis (class in pymcmcstat.samplers.Metropolis)
ModelParameters (class in pymcmcstat.settings.ModelParameters)
ModelSettings (class in pymcmcstat.settings.ModelSettings)
N
noadapt_display_setting() (in module pymcmcstat.settings.ModelParameters)
nth_stage_log_proposal_ratio() (in module pymcmcstat.samplers.DelayedRejection)
NumpyEncoder (class in pymcmcstat.utilities.NumpyEncoder)
P
ParallelMCMC (class in pymcmcstat.ParallelMCMC)
ParameterSet (class in pymcmcstat.structures.ParameterSet)
Plot (class in pymcmcstat.plotting.MCMCPlotting)
plot_chain_metrics() (in module pymcmcstat.plotting.MCMCPlotting)
plot_chain_panel() (in module pymcmcstat.plotting.MCMCPlotting)
plot_density_panel() (in module pymcmcstat.plotting.MCMCPlotting)
plot_histogram_panel() (in module pymcmcstat.plotting.MCMCPlotting)
plot_pairwise_correlation_panel() (in module pymcmcstat.plotting.MCMCPlotting)
plot_prediction_intervals() (pymcmcstat.plotting.PredictionIntervals.PredictionIntervals method)
power_spectral_density_using_hanning_window() (in module pymcmcstat.chain.ChainStatistics)
PredictionIntervals (class in pymcmcstat.plotting.PredictionIntervals)
print_chain_statistics() (in module pymcmcstat.chain.ChainStatistics)
print_log_files() (in module pymcmcstat.chain.ChainProcessing)
print_rejection_statistics() (in module pymcmcstat.MCMC)
prior_display_setting() (in module pymcmcstat.settings.ModelParameters)
PriorFunction (class in pymcmcstat.procedures.PriorFunction)
progress_bar() (in module pymcmcstat.utilities.progressbar)
pymcmcstat.chain.ChainProcessing (module)
pymcmcstat.chain.ChainStatistics (module)
pymcmcstat.MCMC (module)
pymcmcstat.ParallelMCMC (module)
pymcmcstat.plotting.MCMCPlotting (module)
pymcmcstat.plotting.PredictionIntervals (module)
pymcmcstat.plotting.utilities (module)
pymcmcstat.procedures.CovarianceProcedures (module)
pymcmcstat.procedures.ErrorVarianceEstimator (module)
pymcmcstat.procedures.PriorFunction (module)
pymcmcstat.procedures.SumOfSquares (module)
pymcmcstat.samplers.Adaptation (module)
pymcmcstat.samplers.DelayedRejection (module)
pymcmcstat.samplers.Metropolis (module)
pymcmcstat.samplers.SamplingMethods (module)
pymcmcstat.samplers.utilities (module)
pymcmcstat.settings.DataStructure (module)
pymcmcstat.settings.ModelParameters (module)
pymcmcstat.settings.ModelSettings (module)
pymcmcstat.settings.SimulationOptions (module)
pymcmcstat.structures.ParameterSet (module)
pymcmcstat.structures.ResultsStructure (module)
pymcmcstat.utilities.general (module)
pymcmcstat.utilities.NumpyEncoder (module)
pymcmcstat.utilities.progressbar (module)
R
read_in_bin_file() (in module pymcmcstat.chain.ChainProcessing)
read_in_parallel_json_results_files() (in module pymcmcstat.chain.ChainProcessing)
read_in_parallel_savedir_files() (in module pymcmcstat.chain.ChainProcessing)
read_in_savedir_files() (in module pymcmcstat.chain.ChainProcessing)
read_in_txt_file() (in module pymcmcstat.chain.ChainProcessing)
removekey() (in module pymcmcstat.utilities.general)
replace_list_elements() (in module pymcmcstat.settings.ModelParameters)
ResultsStructure (class in pymcmcstat.structures.ResultsStructure)
run_adaptation() (pymcmcstat.samplers.Adaptation.Adaptation method)
run_delayed_rejection() (pymcmcstat.samplers.DelayedRejection.DelayedRejection method)
run_metropolis_step() (pymcmcstat.samplers.Metropolis.Metropolis method)
run_parallel_simulation() (pymcmcstat.ParallelMCMC.ParallelMCMC method)
run_serial_simulation() (in module pymcmcstat.ParallelMCMC)
run_simulation() (pymcmcstat.MCMC.MCMC method)
S
sample_candidate_from_gaussian_proposal() (in module pymcmcstat.samplers.utilities)
SamplingMethods (class in pymcmcstat.samplers.SamplingMethods)
save_json_object() (pymcmcstat.structures.ResultsStructure.ResultsStructure class method)
scale_bandwidth() (in module pymcmcstat.plotting.utilities)
scale_cholesky_decomposition() (in module pymcmcstat.samplers.Adaptation)
scan_for_local_variables() (pymcmcstat.settings.ModelParameters.ModelParameters class method)
set_local_parameters() (in module pymcmcstat.plotting.utilities)
set_outside_bounds() (in module pymcmcstat.samplers.utilities)
setup_adaptation_indices() (pymcmcstat.settings.ModelParameters.ModelParameters class method)
setup_adapting() (pymcmcstat.settings.ModelParameters.ModelParameters class method)
setup_cholupdate() (in module pymcmcstat.samplers.Adaptation)
setup_covariance_matrix() (pymcmcstat.procedures.CovarianceProcedures.CovarianceProcedures method)
setup_parallel_simulation() (pymcmcstat.ParallelMCMC.ParallelMCMC method)
setup_plot_features() (in module pymcmcstat.plotting.utilities)
setup_prediction_interval_calculation() (pymcmcstat.plotting.PredictionIntervals.PredictionIntervals method)
setup_prior_mu() (pymcmcstat.settings.ModelParameters.ModelParameters class method)
setup_prior_sigma() (pymcmcstat.settings.ModelParameters.ModelParameters class method)
setup_w_R() (in module pymcmcstat.samplers.Adaptation)
SimulationOptions (class in pymcmcstat.settings.SimulationOptions)
spectral_estimate_for_variance() (in module pymcmcstat.chain.ChainStatistics)
SumOfSquares (class in pymcmcstat.procedures.SumOfSquares)
U
unpack_covariance_settings() (in module pymcmcstat.samplers.Adaptation)
unpack_mcmc_set() (in module pymcmcstat.ParallelMCMC)
unpack_set() (pymcmcstat.samplers.Metropolis.Metropolis class method)
unpack_simulation_options() (in module pymcmcstat.samplers.Adaptation)
update_cov_from_covchain() (in module pymcmcstat.samplers.Adaptation)
update_cov_via_ram() (in module pymcmcstat.samplers.Adaptation)
update_covariance_mean_sum() (in module pymcmcstat.samplers.Adaptation)
update_delayed_rejection() (in module pymcmcstat.samplers.Adaptation)
update_error_variance() (pymcmcstat.procedures.ErrorVarianceEstimator.ErrorVarianceEstimator method)
update_set_based_on_acceptance() (in module pymcmcstat.samplers.DelayedRejection)
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