Modules

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