Index A | B | C | D | E | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W A apply_ica() (in module glhmm.preproc) apply_pca() (in module glhmm.preproc) approximate_Xi() (in module glhmm.auxiliary) B blue_colormap() (in module glhmm.graphics) build_data_autoregressive() (in module glhmm.preproc) build_data_partial_connectivity() (in module glhmm.preproc) build_data_tde() (in module glhmm.preproc) build_Fisherkernel() (in module glhmm.prediction) build_Fisherkernel_preall() (in module glhmm.prediction) C calculate_anova_f_test() (in module glhmm.statistics) calculate_baseline_difference() (in module glhmm.statistics) calculate_beta_session() (in module glhmm.statistics) calculate_combined_z_scores() (in module glhmm.statistics) calculate_correlation_and_tstats() (in module glhmm.statistics) calculate_manova_f_test() (in module glhmm.statistics) calculate_nan_correlation_matrix() (in module glhmm.statistics) calculate_nan_t_test() (in module glhmm.statistics) calculate_regression_f_stat_univariate() (in module glhmm.statistics) calculate_regression_statistics() (in module glhmm.statistics) calculate_statepair_difference() (in module glhmm.statistics) categorize_columns_by_statistical_method() (in module glhmm.statistics) classify_phenotype() (in module glhmm.prediction) compute_alpha_beta_parallel() (in module glhmm.auxiliary) compute_alpha_beta_serial() (in module glhmm.auxiliary) compute_cca_statistics() (in module glhmm.statistics) compute_correlation_tstats() (in module glhmm.statistics) compute_gradient() (in module glhmm.prediction) compute_gradient_preall() (in module glhmm.prediction) compute_max_permutations() (in module glhmm.statistics) compute_qstar_parallel() (in module glhmm.auxiliary) compute_qstar_serial() (in module glhmm.auxiliary) create_cmap_alpha() (in module glhmm.graphics) create_test_summary() (in module glhmm.statistics) custom_colormap() (in module glhmm.graphics) D dampen_peaks() (in module glhmm.preproc) decode() (glhmm.glhmm.glhmm method) deconfound() (in module glhmm.prediction) deconfound_values() (in module glhmm.statistics) define_predictor_outcome_names() (in module glhmm.statistics) detect_significant_intervals() (in module glhmm.statistics) dirichlet_kl() (in module glhmm.auxiliary) display_test_summary() (in module glhmm.statistics) download_file_with_progress_bar() (in module glhmm.io) dual_estimate() (glhmm.glhmm.glhmm method) E ensure_list() (in module glhmm.statistics) expand_variable_permute_beta() (in module glhmm.statistics) G Gamma_entropy() (in module glhmm.auxiliary) Gamma_indices_to_Xi_indices() (in module glhmm.auxiliary) gamma_kl() (in module glhmm.auxiliary) gauss1d_kl() (in module glhmm.auxiliary) gauss_kl() (in module glhmm.auxiliary) generate_vpath_1D() (in module glhmm.statistics) geometric_pvalue() (in module glhmm.statistics) get_active_K() (glhmm.glhmm.glhmm method) get_beta() (glhmm.glhmm.glhmm method) get_betas() (glhmm.glhmm.glhmm method) get_concatenate_data_memmap() (in module glhmm.statistics) get_concatenate_sessions() (in module glhmm.statistics) get_concatenate_subjects() (in module glhmm.statistics) get_covariance_matrices() (glhmm.glhmm.glhmm method) get_covariance_matrix() (glhmm.glhmm.glhmm method) get_event_epochs() (in module glhmm.statistics) get_f_t_stats() (in module glhmm.statistics) get_fe() (glhmm.glhmm.glhmm method) get_FO() (in module glhmm.utils) get_FO_entropy() (in module glhmm.utils) get_gamma_similarity() (in module glhmm.utils) get_groups() (in module glhmm.prediction) get_indices_array() (in module glhmm.statistics) get_indices_from_list() (in module glhmm.statistics) get_indices_range() (in module glhmm.statistics) get_indices_session() (in module glhmm.statistics) get_indices_timestamp() (in module glhmm.statistics) get_indices_update_nan() (in module glhmm.statistics) get_input_shape() (in module glhmm.statistics) get_inverse_covariance_matrices() (glhmm.glhmm.glhmm method) get_inverse_covariance_matrix() (glhmm.glhmm.glhmm method) get_life_times() (in module glhmm.utils) get_maxFO() (in module glhmm.utils) get_mean() (glhmm.glhmm.glhmm method) get_means() (glhmm.glhmm.glhmm method) get_P() (glhmm.glhmm.glhmm method) get_Pi() (glhmm.glhmm.glhmm method) get_pval() (in module glhmm.statistics) get_r2() (glhmm.glhmm.glhmm method) get_state_evoked_response() (in module glhmm.utils) get_state_evoked_response_entropy() (in module glhmm.utils) get_state_onsets() (in module glhmm.utils) get_summ_features() (in module glhmm.prediction) get_switching_rate() (in module glhmm.utils) get_T() (in module glhmm.auxiliary) get_visits() (in module glhmm.utils) glhmm (class in glhmm.glhmm) glhmm.auxiliary module glhmm.glhmm module glhmm.graphics module glhmm.io module glhmm.palm_functions module glhmm.prediction module glhmm.preproc module glhmm.statistics module glhmm.utils module H handle_nan_values() (in module glhmm.statistics) hcp2block() (in module glhmm.palm_functions) HMM hmm_kernel() (in module glhmm.prediction) I initialize() (glhmm.glhmm.glhmm method) initialize_arrays() (in module glhmm.statistics) initialize_permutation_matrices() (in module glhmm.statistics) interpolate_colormap() (in module glhmm.graphics) inverse_fisher_z() (in module glhmm.statistics) is_single_value() (in module glhmm.palm_functions) J jls_extract_def() (in module glhmm.auxiliary) L lmaxflipnode() (in module glhmm.palm_functions) lmaxpermnode() (in module glhmm.palm_functions) load_files() (in module glhmm.io) (in module glhmm.preproc) load_hmm() (in module glhmm.io) load_statistics() (in module glhmm.io) loglikelihood() (glhmm.glhmm.glhmm method) lseq2np() (in module glhmm.palm_functions) M make_indices_from_T() (in module glhmm.auxiliary) maketree() (in module glhmm.palm_functions) maxflipnode() (in module glhmm.palm_functions) maxpermnode() (in module glhmm.palm_functions) module glhmm.auxiliary glhmm.glhmm glhmm.graphics glhmm.io glhmm.palm_functions glhmm.prediction glhmm.preproc glhmm.statistics glhmm.utils N n_parcels n_samples n_sessions n_states O ols_regression_sessions() (in module glhmm.statistics) ols_regression_stats() (in module glhmm.statistics) P pad_vpath() (in module glhmm.statistics) padGamma() (in module glhmm.auxiliary) palm_factorial() (in module glhmm.palm_functions) palm_maxshuf() (in module glhmm.palm_functions) palm_permtree() (in module glhmm.palm_functions) palm_quickperms() (in module glhmm.palm_functions) palm_reindex() (in module glhmm.palm_functions) palm_shuftree() (in module glhmm.palm_functions) palm_tree() (in module glhmm.palm_functions) permutation_matrix_across_subjects() (in module glhmm.statistics) permutation_matrix_across_trials_within_session() (in module glhmm.statistics) permutation_matrix_within_and_between_groups() (in module glhmm.statistics) permutation_matrix_within_subject_across_sessions() (in module glhmm.statistics) permute_subject_trial_idx() (in module glhmm.statistics) pickperm() (in module glhmm.palm_functions) plot_average_probability() (in module glhmm.graphics) plot_condition_difference() (in module glhmm.graphics) plot_correlation_matrix() (in module glhmm.graphics) plot_data_grid() (in module glhmm.graphics) plot_FO() (in module glhmm.graphics) plot_p_value_matrix() (in module glhmm.graphics) plot_p_values_bar() (in module glhmm.graphics) plot_p_values_over_time() (in module glhmm.graphics) plot_permutation_distribution() (in module glhmm.graphics) plot_scatter_with_labels() (in module glhmm.graphics) plot_state_lifetimes() (in module glhmm.graphics) plot_state_prob_and_covariance() (in module glhmm.graphics) plot_switching_rates() (in module glhmm.graphics) plot_vpath() (in module glhmm.graphics) predict_phenotype() (in module glhmm.prediction) prepare_data_directory() (in module glhmm.io) preprocess_data() (in module glhmm.preproc) preprocess_response() (in module glhmm.statistics) process_family_structure() (in module glhmm.statistics) pval_cluster_based_correction() (in module glhmm.statistics) pval_correction() (in module glhmm.statistics) pval_FWER_correction() (in module glhmm.statistics) R randomperm() (in module glhmm.palm_functions) read_flattened_hmm_mat() (in module glhmm.io) reconfound() (in module glhmm.prediction) reconstruct_concatenated_to_3D() (in module glhmm.statistics) red_colormap() (in module glhmm.graphics) remove_nan_values() (in module glhmm.statistics) renumber() (in module glhmm.palm_functions) roll_by_vector() (in module glhmm.auxiliary) S sample() (glhmm.glhmm.glhmm method) sample_Gamma() (glhmm.glhmm.glhmm method) save_hmm() (in module glhmm.io) save_statistics() (in module glhmm.io) seq2np() (in module glhmm.palm_functions) set_beta() (glhmm.glhmm.glhmm method) set_covariance_matrix() (glhmm.glhmm.glhmm method) set_mean() (glhmm.glhmm.glhmm method) set_P() (glhmm.glhmm.glhmm method) set_Pi() (glhmm.glhmm.glhmm method) show_beta() (in module glhmm.graphics) show_Gamma() (in module glhmm.graphics) show_temporal_statistic() (in module glhmm.graphics) show_trans_prob_mat() (in module glhmm.graphics) slice_matrix() (in module glhmm.auxiliary) squeeze_first_dim() (in module glhmm.statistics) state mixing surrogate_state_time() (in module glhmm.statistics) surrogate_state_time_matrix() (in module glhmm.statistics) surrogate_viterbi_path() (in module glhmm.statistics) T test_across_sessions_within_subject() (in module glhmm.statistics) test_across_state_visits() (in module glhmm.statistics) test_across_subjects() (in module glhmm.statistics) test_across_trials() (in module glhmm.statistics) test_classif() (in module glhmm.prediction) test_pred() (in module glhmm.prediction) test_statistics_calculations() (in module glhmm.statistics) train() (glhmm.glhmm.glhmm method) train_classif() (in module glhmm.prediction) train_pred() (in module glhmm.prediction) train_test_indices() (in module glhmm.statistics) train_test_update_indices() (in module glhmm.statistics) U update_indices() (in module glhmm.statistics) update_permutation_matrix() (in module glhmm.statistics) V validate_condition() (in module glhmm.statistics) viterbi_path_to_stc() (in module glhmm.statistics) vpath_check_2D() (in module glhmm.statistics) W wishart_kl() (in module glhmm.auxiliary)