pymcmcstat
stable
pymcmcstat package
pymcmcstat.MCMC module
pymcmcstat.ParallelMCMC module
pymcmcstat.propagation 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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O
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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_intervals() (in module pymcmcstat.propagation)
calculate_log_posterior_ratio() (in module pymcmcstat.samplers.utilities)
calculate_posterior_ratio() (pymcmcstat.samplers.Metropolis.Metropolis class method)
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_lightly_save() (in module pymcmcstat.settings.SimulationOptions)
check_noadaptind() (in module pymcmcstat.settings.ModelParameters)
check_options_output() (in module pymcmcstat.ParallelMCMC)
check_parallel_directory_contents() (in module pymcmcstat.chain.ChainProcessing)
check_s2chain() (in module pymcmcstat.propagation)
check_settings() (in module pymcmcstat.plotting.utilities)
(in module pymcmcstat.utilities.general)
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_sample_points() (in module pymcmcstat.propagation)
define_simulation_options() (pymcmcstat.settings.SimulationOptions.SimulationOptions method)
DelayedRejection (class in pymcmcstat.samplers.DelayedRejection)
deprecation() (in module pymcmcstat.plotting.MCMCPlotting)
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_prior() (pymcmcstat.procedures.PriorFunction.PriorFunction method)
evaluate_sos_function() (pymcmcstat.procedures.SumOfSquares.SumOfSquares method)
export_lightly() (pymcmcstat.structures.ResultsStructure.ResultsStructure 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.utilities.general)
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_quantiles() (in module pymcmcstat.propagation)
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)
lighten_results() (in module pymcmcstat.structures.ResultsStructure)
load_json_object() (in module pymcmcstat.chain.ChainProcessing)
(pymcmcstat.structures.ResultsStructure.ResultsStructure class method)
load_parallel_simulation_results() (in module pymcmcstat.chain.ChainProcessing)
(in module pymcmcstat.ParallelMCMC)
load_serial_simulation_results() (in module pymcmcstat.chain.ChainProcessing)
log_posterior_ratio() (in module pymcmcstat.samplers.DelayedRejection)
log_posterior_ratio_acceptance_test() (in module pymcmcstat.samplers.utilities)
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)
module
pymcmcstat.chain.ChainProcessing
pymcmcstat.chain.ChainStatistics
pymcmcstat.MCMC
pymcmcstat.ParallelMCMC
pymcmcstat.plotting.MCMCPlotting
pymcmcstat.plotting.PredictionIntervals
pymcmcstat.plotting.utilities
pymcmcstat.procedures.CovarianceProcedures
pymcmcstat.procedures.ErrorVarianceEstimator
pymcmcstat.procedures.PriorFunction
pymcmcstat.procedures.SumOfSquares
pymcmcstat.propagation
pymcmcstat.samplers.Adaptation
pymcmcstat.samplers.DelayedRejection
pymcmcstat.samplers.Metropolis
pymcmcstat.samplers.SamplingMethods
pymcmcstat.samplers.utilities
pymcmcstat.settings.DataStructure
pymcmcstat.settings.ModelParameters
pymcmcstat.settings.ModelSettings
pymcmcstat.settings.SimulationOptions
pymcmcstat.structures.ParameterSet
pymcmcstat.structures.ResultsStructure
pymcmcstat.utilities.general
pymcmcstat.utilities.NumpyEncoder
pymcmcstat.utilities.progressbar
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)
O
observation_sample() (in module pymcmcstat.propagation)
P
ParallelMCMC (class in pymcmcstat.ParallelMCMC)
ParameterSet (class in pymcmcstat.structures.ParameterSet)
Plot (class in pymcmcstat.plotting.MCMCPlotting)
plot_3d_intervals() (in module pymcmcstat.propagation)
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_intervals() (in module pymcmcstat.propagation)
plot_pairwise_correlation_panel() (in module pymcmcstat.plotting.MCMCPlotting)
plot_prediction_intervals() (pymcmcstat.plotting.PredictionIntervals.PredictionIntervals method)
posterior_ratio_acceptance_test() (in module pymcmcstat.samplers.utilities)
power_spectral_density_using_hanning_window() (in module pymcmcstat.chain.ChainStatistics)
PredictionIntervals (class in pymcmcstat.plotting.PredictionIntervals)
print_chain_acceptance_info() (in module pymcmcstat.chain.ChainStatistics)
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.propagation
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_display_settings() (in module pymcmcstat.propagation)
setup_interval_colors() (in module pymcmcstat.propagation)
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_subsample() (in module pymcmcstat.plotting.utilities)
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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