Index

A

ActiveInformationStorage (class in idtxl.active_information_storage) add_edge() (idtxl.results.AdjacencyMatrix method) add_edge_list() (idtxl.results.AdjacencyMatrix method) AdjacencyMatrix (class in idtxl.results) ais_fdr() (in module idtxl.stats) AlgorithmExhaustedError alpha_ML() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method) analyse_auto_MI() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) analyse_network() (idtxl.active_information_storage.ActiveInformationStorage method) (idtxl.bivariate_mi.BivariateMI method) (idtxl.bivariate_pid.BivariatePID method) (idtxl.bivariate_te.BivariateTE method) (idtxl.multivariate_mi.MultivariateMI method) (idtxl.multivariate_pid.MultivariatePID method) (idtxl.multivariate_te.MultivariateTE method)

analyse_single_process() (idtxl.active_information_storage.ActiveInformationStorage method) analyse_single_target() (idtxl.bivariate_mi.BivariateMI method) (idtxl.bivariate_pid.BivariatePID method) (idtxl.bivariate_te.BivariateTE method) (idtxl.multivariate_mi.MultivariateMI method) (idtxl.multivariate_pid.MultivariatePID method) (idtxl.multivariate_te.MultivariateTE method) argsort_descending() (in module idtxl.idtxl_utils) autocorrelation() (in module idtxl.idtxl_utils)

B

bayesian_bias_criterion() (idtxl.estimators_Rudelt.RudeltBBCEstimator method) BivariateMI (class in idtxl.bivariate_mi)

BivariatePID (class in idtxl.bivariate_pid) BivariateTE (class in idtxl.bivariate_te) BROJA_2PID_Exception

C

calculate_link_te() (idtxl.network_comparison.NetworkComparison method) calculate_mi() (in module idtxl.idtxl_utils) check_inputs() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) check_n_perm() (in module idtxl.stats) combine_discrete_dimensions() (in module idtxl.idtxl_utils) combine_results() (idtxl.results.Results method)

common_estimate_surrogates_analytic() (in module idtxl.estimators_jidt) compare_between() (idtxl.network_comparison.NetworkComparison method) compare_links_within() (idtxl.network_comparison.NetworkComparison method) compare_within() (idtxl.network_comparison.NetworkComparison method) compute_CIs() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) conflicting_entries() (in module idtxl.idtxl_utils) current_value (idtxl.network_analysis.NetworkAnalysis property)

D

d2_log_rho() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method) d2_log_rho_xi() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method) d2_xi() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method) d3_xi() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method) d_log_rho() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method) d_log_rho_xi() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method)

d_xi() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method) Data (class in idtxl.data) data (idtxl.data.Data property) discretise() (in module idtxl.idtxl_utils) discretise_max_ent() (in module idtxl.idtxl_utils) DotDict (class in idtxl.results)

E

equal_dicts() (in module idtxl.idtxl_utils) estimate() (idtxl.estimators_jidt.JidtDiscreteAIS method) (idtxl.estimators_jidt.JidtDiscreteCMI method) (idtxl.estimators_jidt.JidtDiscreteMI method) (idtxl.estimators_jidt.JidtDiscreteTE method) (idtxl.estimators_jidt.JidtGaussianAIS method) (idtxl.estimators_jidt.JidtGaussianCMI method) (idtxl.estimators_jidt.JidtGaussianMI method) (idtxl.estimators_jidt.JidtGaussianTE method) (idtxl.estimators_jidt.JidtKraskovAIS method) (idtxl.estimators_jidt.JidtKraskovCMI method) (idtxl.estimators_jidt.JidtKraskovMI method) (idtxl.estimators_jidt.JidtKraskovTE method) (idtxl.estimators_mpi.MPIEstimator method) (idtxl.estimators_multivariate_pid.SxPID method) (idtxl.estimators_opencl.OpenCLKraskovCMI method) (idtxl.estimators_opencl.OpenCLKraskovMI method) (idtxl.estimators_pid.SydneyPID method) (idtxl.estimators_pid.TartuPID method) (idtxl.estimators_python.PythonKraskovCMI method) (idtxl.estimators_Rudelt.RudeltBBCEstimator method) (idtxl.estimators_Rudelt.RudeltNSBEstimatorSymbolsMI method) (idtxl.estimators_Rudelt.RudeltPluginEstimatorSymbolsMI method) (idtxl.estimators_Rudelt.RudeltShufflingEstimator method)

estimate_surrogates_analytic() (idtxl.estimators_jidt.JidtDiscrete method) (idtxl.estimators_jidt.JidtGaussian method) (idtxl.estimators_mpi.MPIEstimator method) export_brain_net_viewer() (in module idtxl.idtxl_io) export_networkx_graph() (in module idtxl.idtxl_io) export_networkx_source_graph() (in module idtxl.idtxl_io)

G

generate_logistic_maps_data() (idtxl.data.Data method) generate_mute_data() (idtxl.data.Data method) generate_var_data() (idtxl.data.Data method) get_adjacency_matrix() (idtxl.results.ResultsNetworkComparison method) (idtxl.results.ResultsNetworkInference method) get_analytic_distribution() (idtxl.estimators_jidt.JidtDiscrete method) (idtxl.estimators_jidt.JidtDiscreteAIS method) (idtxl.estimators_jidt.JidtDiscreteCMI method) (idtxl.estimators_jidt.JidtDiscreteMI method) (idtxl.estimators_jidt.JidtDiscreteTE method) (idtxl.estimators_jidt.JidtGaussian method) (idtxl.estimators_jidt.JidtGaussianCMI method) get_auto_MI() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) get_bbc_term() (idtxl.estimators_Rudelt.RudeltBBCEstimator method) get_beta_MAP() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method) get_bootstrap_history_dependence() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) get_edge_list() (idtxl.results.AdjacencyMatrix method) get_embeddings() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) get_embeddings_that_maximise_R() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) get_H0_X_past_cond_X() (idtxl.estimators_Rudelt.RudeltShufflingEstimator method) get_H0_X_past_cond_X_eq_x() (idtxl.estimators_Rudelt.RudeltShufflingEstimator method) get_H_X_past_cond_X() (idtxl.estimators_Rudelt.RudeltShufflingEstimator method) get_H_X_past_uncond() (idtxl.estimators_Rudelt.RudeltShufflingEstimator method) get_history_dependence() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) get_information_timescale_tau_R() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) get_integration_bounds() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method) get_marginal_frequencies_of_spikes_in_bins() (idtxl.estimators_Rudelt.RudeltShufflingEstimator method) get_median_number_of_spikes_per_bin() (idtxl.estimators_Rudelt.RudeltAbstractEstimator method)

get_multiplicities() (idtxl.estimators_Rudelt.RudeltAbstractEstimator method) get_P_X_past_cond_X() (idtxl.estimators_Rudelt.RudeltShufflingEstimator method) get_P_X_past_uncond() (idtxl.estimators_Rudelt.RudeltShufflingEstimator method) get_P_X_uncond() (idtxl.estimators_Rudelt.RudeltShufflingEstimator method) get_past_range() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) (idtxl.estimators_Rudelt.RudeltAbstractEstimator method) get_R_tot() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) get_raw_symbols() (idtxl.estimators_Rudelt.RudeltAbstractEstimator method) get_realisations() (idtxl.data.Data method) get_seed() (idtxl.data.Data method) get_set_of_scalings() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) get_shuffled_symbol_counts() (idtxl.estimators_Rudelt.RudeltShufflingEstimator method) get_significant_processes() (idtxl.results.ResultsSingleProcessAnalysis method) get_single_process() (idtxl.results.ResultsSingleProcessAnalysis method) (idtxl.results.ResultsSingleProcessRudelt method) get_single_target() (idtxl.results.ResultsMultivariatePID method) (idtxl.results.ResultsNetworkAnalysis method) (idtxl.results.ResultsNetworkComparison method) (idtxl.results.ResultsPID method) get_source_variables() (idtxl.results.ResultsNetworkInference method) get_state() (idtxl.data.Data method) get_symbol_counts() (idtxl.estimators_Rudelt.RudeltAbstractEstimator method) get_target_delays() (idtxl.results.ResultsNetworkInference method) get_target_sources() (idtxl.results.ResultsNetworkAnalysis method) (idtxl.results.ResultsNetworkComparison method) get_temporal_depth_T_D() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) get_window_delimiters() (idtxl.estimators_Rudelt.RudeltAbstractEstimator method) getit() (idtxl.multivariate_te.MultivariateTE method)

H

H1() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method)

I

idtxl module idtxl.active_information_storage module idtxl.bivariate_mi module idtxl.bivariate_pid module idtxl.bivariate_te module idtxl.data module idtxl.embedding_optimization_ais_Rudelt module idtxl.estimators_jidt module idtxl.estimators_mpi module idtxl.estimators_multivariate_pid module idtxl.estimators_opencl module idtxl.estimators_pid module idtxl.estimators_python module idtxl.estimators_Rudelt module idtxl.idtxl_exceptions module idtxl.idtxl_io module idtxl.idtxl_utils module idtxl.multivariate_mi module idtxl.multivariate_pid module

idtxl.multivariate_te module idtxl.network_analysis module idtxl.network_comparison module idtxl.network_inference module idtxl.results module idtxl.single_process_analysis module idtxl.stats module idtxl.visualise_graph module import_fieldtrip() (in module idtxl.idtxl_io) import_matarray() (in module idtxl.idtxl_io) is_analytic_null_estimator() (idtxl.estimators_jidt.JidtDiscrete method) (idtxl.estimators_jidt.JidtGaussian method) (idtxl.estimators_jidt.JidtKraskov method) (idtxl.estimators_mpi.MPIEstimator method) (idtxl.estimators_multivariate_pid.SxPID method) (idtxl.estimators_opencl.OpenCLKraskov method) (idtxl.estimators_pid.SydneyPID method) (idtxl.estimators_pid.TartuPID method) (idtxl.estimators_python.PythonKraskovCMI method) (idtxl.estimators_Rudelt.RudeltAbstractEstimator method) is_parallel() (idtxl.estimators_jidt.JidtEstimator method) (idtxl.estimators_mpi.MPIEstimator method) (idtxl.estimators_multivariate_pid.SxPID method) (idtxl.estimators_opencl.OpenCLKraskov method) (idtxl.estimators_pid.SydneyPID method) (idtxl.estimators_pid.TartuPID method) (idtxl.estimators_python.PythonKraskovCMI method) (idtxl.estimators_Rudelt.RudeltAbstractEstimator method)

J

JidtDiscrete (class in idtxl.estimators_jidt) JidtDiscreteAIS (class in idtxl.estimators_jidt) JidtDiscreteCMI (class in idtxl.estimators_jidt) JidtDiscreteMI (class in idtxl.estimators_jidt) JidtDiscreteTE (class in idtxl.estimators_jidt) JidtEstimator (class in idtxl.estimators_jidt) JidtGaussian (class in idtxl.estimators_jidt) JidtGaussianAIS (class in idtxl.estimators_jidt)

JidtGaussianCMI (class in idtxl.estimators_jidt) JidtGaussianMI (class in idtxl.estimators_jidt) JidtGaussianTE (class in idtxl.estimators_jidt) JidtKraskov (class in idtxl.estimators_jidt) JidtKraskovAIS (class in idtxl.estimators_jidt) JidtKraskovCMI (class in idtxl.estimators_jidt) JidtKraskovMI (class in idtxl.estimators_jidt) JidtKraskovTE (class in idtxl.estimators_jidt) JidtOutOfMemoryError

L

load_json() (in module idtxl.idtxl_io)

load_pickle() (in module idtxl.idtxl_io) log_likelihood_DP_alpha() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method)

M

max_statistic() (in module idtxl.stats) max_statistic_sequential() (in module idtxl.stats) max_statistic_sequential_bivariate() (in module idtxl.stats) mi_against_surrogates() (in module idtxl.stats) min_statistic() (in module idtxl.stats) module idtxl idtxl.active_information_storage idtxl.bivariate_mi idtxl.bivariate_pid idtxl.bivariate_te idtxl.data idtxl.embedding_optimization_ais_Rudelt idtxl.estimators_jidt idtxl.estimators_mpi idtxl.estimators_multivariate_pid idtxl.estimators_opencl idtxl.estimators_pid idtxl.estimators_python idtxl.estimators_Rudelt idtxl.idtxl_exceptions idtxl.idtxl_io idtxl.idtxl_utils idtxl.multivariate_mi idtxl.multivariate_pid idtxl.multivariate_te idtxl.network_analysis idtxl.network_comparison idtxl.network_inference idtxl.results idtxl.single_process_analysis idtxl.stats idtxl.visualise_graph

MPIEstimator (class in idtxl.estimators_mpi) MultivariateMI (class in idtxl.multivariate_mi) MultivariatePID (class in idtxl.multivariate_pid) MultivariateTE (class in idtxl.multivariate_te)

N

n_edges() (idtxl.results.AdjacencyMatrix method) n_nodes() (idtxl.results.AdjacencyMatrix method) n_realisations() (idtxl.data.Data method) n_realisations_repl() (idtxl.data.Data method) n_realisations_samples() (idtxl.data.Data method) network_fdr() (in module idtxl.stats) NetworkAnalysis (class in idtxl.network_analysis)

NetworkComparison (class in idtxl.network_comparison) NetworkInference (class in idtxl.network_inference) NetworkInferenceBivariate (class in idtxl.network_inference) NetworkInferenceMI (class in idtxl.network_inference) NetworkInferenceMultivariate (class in idtxl.network_inference) NetworkInferenceTE (class in idtxl.network_inference) nsb_entropy() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method) nsb_estimator() (idtxl.estimators_Rudelt.RudeltNSBEstimatorSymbolsMI method)

O

omnibus_test() (in module idtxl.stats) OpenCLKraskov (class in idtxl.estimators_opencl) OpenCLKraskovCMI (class in idtxl.estimators_opencl)

OpenCLKraskovMI (class in idtxl.estimators_opencl) OptimizationRudelt (class in idtxl.embedding_optimization_ais_Rudelt) optimize() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) optimize_single_run() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method)

P

package_missing() (in module idtxl.idtxl_exceptions) permute_replications() (idtxl.data.Data method) permute_samples() (idtxl.data.Data method) plot_mute_graph() (in module idtxl.visualise_graph) plot_network() (in module idtxl.visualise_graph) plot_network_comparison() (in module idtxl.visualise_graph) plot_selected_vars() (in module idtxl.visualise_graph) plugin_entropy() (idtxl.estimators_Rudelt.RudeltPluginEstimatorSymbolsMI method)

plugin_estimator() (idtxl.estimators_Rudelt.RudeltPluginEstimatorSymbolsMI method) print_dict() (in module idtxl.idtxl_utils) print_edge_list() (idtxl.results.ResultsNetworkComparison method) (idtxl.results.ResultsNetworkInference method) print_matrix() (idtxl.results.AdjacencyMatrix method) processes_analysed (idtxl.results.ResultsSingleProcessAnalysis property) (idtxl.results.ResultsSingleProcessRudelt property) PythonKraskovCMI (class in idtxl.estimators_python)

R

remove_column() (in module idtxl.idtxl_utils) remove_row() (in module idtxl.idtxl_utils) remove_subresults_single_process() (idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt method) Results (class in idtxl.results) ResultsMultivariatePID (class in idtxl.results) ResultsNetworkAnalysis (class in idtxl.results) ResultsNetworkComparison (class in idtxl.results) ResultsNetworkInference (class in idtxl.results) ResultsPID (class in idtxl.results)

ResultsSingleProcessAnalysis (class in idtxl.results) ResultsSingleProcessRudelt (class in idtxl.results) resume_checkpoint() (idtxl.network_analysis.NetworkAnalysis method) rho() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method) RudeltAbstractEstimator (class in idtxl.estimators_Rudelt) RudeltAbstractNSBEstimator (class in idtxl.estimators_Rudelt) RudeltBBCEstimator (class in idtxl.estimators_Rudelt) RudeltNSBEstimatorSymbolsMI (class in idtxl.estimators_Rudelt) RudeltPluginEstimatorSymbolsMI (class in idtxl.estimators_Rudelt) RudeltShufflingEstimator (class in idtxl.estimators_Rudelt)

S

save_json() (in module idtxl.idtxl_io) save_pickle() (in module idtxl.idtxl_io) selected_vars_full (idtxl.network_analysis.NetworkAnalysis property) selected_vars_sources (idtxl.network_analysis.NetworkAnalysis property) selected_vars_target (idtxl.network_analysis.NetworkAnalysis property) separate_arrays() (in module idtxl.idtxl_utils) set_data() (idtxl.data.Data method) shuffling_MI() (idtxl.estimators_Rudelt.RudeltShufflingEstimator method) SingleProcessAnalysis (class in idtxl.single_process_analysis)

slice_permute_replications() (idtxl.data.Data method) slice_permute_samples() (idtxl.data.Data method) sort_descending() (in module idtxl.idtxl_utils) standardise() (in module idtxl.idtxl_utils) swap_chars() (in module idtxl.idtxl_utils) SxPID (class in idtxl.estimators_multivariate_pid) SydneyPID (class in idtxl.estimators_pid) symbol_array_to_binary() (idtxl.estimators_Rudelt.RudeltAbstractEstimator method) symbol_binary_to_array() (idtxl.estimators_Rudelt.RudeltAbstractEstimator method) syn_shd_against_surrogates() (in module idtxl.stats)

T

targets_analysed (idtxl.results.ResultsNetworkAnalysis property) TartuPID (class in idtxl.estimators_pid)

timeout (class in idtxl.idtxl_utils) timeout_handler() (idtxl.idtxl_utils.timeout method)

U

unnormalized_posterior() (idtxl.estimators_Rudelt.RudeltAbstractNSBEstimator method)

unq_against_surrogates() (in module idtxl.stats)