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"title": "Plot Cluster-Specific Synergy Coefficients (Factor Loadings) for MPCA", "topics": [ "plot_cluster_synergy_loadings_mpca" ] }, { "page": "plot_confusion_matrix", "title": "Plot Confusion Matrix for Cluster Assignments", "topics": [ "plot_confusion_matrix" ] }, { "page": "plot_fig1_ARI", "title": "Plot ARI vs. Separation/Noise (Figure 1)", "topics": [ "plot_fig1_ARI" ] }, { "page": "plot_fig1_baseline_comparison", "title": "Plot Baseline Comparison (ARI and VAF)", "topics": [ "plot_fig1_baseline_comparison" ] }, { "page": "plot_fig2_BIC_heatmap", "title": "Plot BIC Heatmap for a Subset (Figure 2)", "topics": [ "plot_fig2_BIC_heatmap" ] }, { "page": "plot_fig3_init_boxplot", "title": "Plot Boxplot of ARI for Multiple Initial Seeds (Figure 3)", "topics": [ "plot_fig3_init_boxplot" ] }, { "page": "plot_fig4to6_reconstruction_vaf", "title": "Plot Reconstruction Error and VAF (Figures 4-6)", "topics": [ "plot_fig4to6_reconstruction_vaf" ] }, { "page": "plot_metric_vs_axis", "title": "Plot Metric vs Axis for Parameter Sweep", "topics": [ "plot_metric_vs_axis" ] }, { "page": "plot_neural_command", "title": "Plot Neural Command Trajectories", "topics": [ "plot_neural_command" ] }, { "page": "plot_noise_profiles", "title": "Plot Noise Profiles", "topics": [ "plot_noise_profiles" ] }, { "page": "plot_reconstructed_emg", "title": "Plot Reconstructed EMG Signals", "topics": [ "plot_reconstructed_emg" ] }, { "page": "plot_sse_heatmap", "title": "Plot SSE Heatmap Across Methods and Subjects", "topics": [ "plot_sse_heatmap" ] }, { "page": "plot_sweep_summary", "title": "Plot Summary Comparison for Parameter Sweep", "topics": [ "plot_sweep_summary" ] }, { "page": "plot_synergy_bases", "title": "Plot Synergy Bases (Lambda Matrices)", "topics": [ "plot_synergy_bases" ] }, { "page": "plot_synergy_correlation_comparison", "title": "Plot Synergy Correlation Comparison", "topics": [ "plot_synergy_correlation_comparison" ] }, { "page": "plot_synergy_summary", "title": "Plot Synergy Summary", "topics": [ "plot_synergy_summary" ] }, { "page": "plot_waveform_comparison_mfa", "title": "Plot Original vs. Reconstructed Waveform for an MFA Model", "topics": [ "plot_waveform_comparison_mfa" ] }, { "page": "plot_waveform_comparison_mpca", "title": "Plot Original vs. Reconstructed Waveform for an MPCA Model", "topics": [ "plot_waveform_comparison_mpca" ] }, { "page": "plot_winrate_heatmap", "title": "Plot Win Rate Heatmap for Parameter Sweep", "topics": [ "plot_winrate_heatmap" ] }, { "page": "plot.mixture_r_selection", "title": "Plot Method for mixture_r_selection Objects", "topics": [ "plot.mixture_r_selection" ] }, { "page": "posthoc_mfa_evaluation", "title": "Post-hoc Evaluation of MFA Grid Search", "topics": [ "posthoc_mfa_evaluation" ] }, { "page": "posthoc_mpca_evaluation", "title": "Post-hoc Evaluation of Mixture PCA Grid Search", "topics": [ "posthoc_mpca_evaluation" ] }, { "page": "preprocess_emg", "title": "EMG Preprocessing Pipeline", "topics": [ "preprocess_emg" ] }, { "page": "print.bootstrap_ci", "title": "Print Summary of Bootstrap CI Results", "topics": [ "print.bootstrap_ci" ] }, { "page": "print.calibration_result", "title": "Print Summary of Calibration Results", "topics": [ "print.calibration_result" ] }, { "page": "print.mixture_r_selection", "title": "Print Method for mixture_r_selection Objects", "topics": [ "print.mixture_r_selection" ] }, { "page": "print.preprocessed_emg", "title": "Print Method for preprocessed_emg Objects", "topics": [ "print.preprocessed_emg" ] }, { "page": "read_all_results", "title": "Read All Results from .rds Files", "topics": [ "read_all_results" ] }, { "page": "read_and_visualize_all", "title": "Read All Results and Produce Tables/Figures", "topics": [ "read_and_visualize_all" ] }, { "page": "reconstruct_singleMPCA", "title": "Reconstruct a single subject's data from a Mixture PCA model", "topics": [ "reconstruct_singleMPCA" ] }, { "page": "rectify", "title": "Rectify EMG Signal", "topics": [ "rectify" ] }, { "page": "remove_dc_offset", "title": "Remove DC Offset from EMG Signal", "topics": [ "remove_dc_offset" ] }, { "page": "rotate_mfa_model", "title": "Post-hoc Rotation for an MFA Model", "topics": [ "rotate_mfa_model" ] }, { "page": "rotate_mpca_model", "title": "Post-hoc Rotation for a Mixture PCA Model", "topics": [ "rotate_mpca_model" ] }, { "page": "run_k_selection_comparison", "title": "Run K Selection Method Comparison (v3)", "topics": [ "run_k_selection_comparison" ] }, { "page": "run_param_sweep", "title": "Run Parameter Sweep Experiment", "topics": [ "run_param_sweep" ] }, { "page": "run_param_sweep_baselines", "title": "Run Parameter Sweep for Baseline Method Comparisons (v2)", "topics": [ "run_param_sweep_baselines" ] }, { "page": "run_param_sweep_modelsel", "title": "Run Parameter Sweep with Model Selection", "topics": [ "run_param_sweep_modelsel" ] }, { "page": "run_single_task", "title": "Run a Single Task from Parameter Grid", "topics": [ "run_single_task" ] }, { "page": "run_sweep_future", "title": "Run Parameter Sweep Using Future", "topics": [ "run_sweep_future" ] }, { "page": "scale_color_mixsynergy", "title": "Get Unified Color Scale for Discrete Categories", "topics": [ "scale_color_mixsynergy" ] }, { "page": "scale_fill_mixsynergy", "title": "Get Unified Viridis Color Scale for Continuous Values", "topics": [ "scale_fill_mixsynergy" ] }, { "page": "scale_fill_mixsynergy_discrete", "title": "Get Unified Fill Scale for Discrete Categories", "topics": [ "scale_fill_mixsynergy_discrete" ] }, { "page": "scale_fill_mixsynergy_diverging", "title": "Get Unified Viridis Color Scale for Diverging Values", "topics": [ "scale_fill_mixsynergy_diverging" ] }, { "page": "select_K_bootstrap_stability", "title": "Select K Using Bootstrap Stability Selection", "topics": [ "select_K_bootstrap_stability" ] }, { "page": "select_K_crossvalidation", "title": "Select K Using Cross-Validation", "topics": [ "select_K_crossvalidation" ] }, { "page": "select_K_r", "title": "Unified Model Selection for K and r", "topics": [ "select_K_r" ] }, { "page": "select_optimal_K_r_mfa", "title": "Search for the Best (K, r) for MFA via Grid Search (Using mfa_em_fit)", "topics": [ "select_optimal_K_r_mfa" ] }, { "page": "select_optimal_K_r_mfa_twostage", "title": "Two-Stage Model Selection for MFA: Select K First, Then r", "topics": [ "select_optimal_K_r_mfa_twostage" ] }, { "page": "select_optimal_K_r_mpca", "title": "Search for the Best (K, r) for Mixture PCA via Grid Search", "topics": [ "select_optimal_K_r_mpca" ] }, { "page": "select_optimal_K_r_mpca_twostage", "title": "Two-Stage Model Selection for MPCA: Select K First, Then r", "topics": [ "select_optimal_K_r_mpca_twostage" ] }, { "page": "select_r_by_smoothness_mfa", "title": "Select Optimal r by Smoothness Penalty for MFA", "topics": [ "select_r_by_smoothness_mfa" ] }, { "page": "select_r_by_smoothness_mpca", "title": "Select Optimal r by Smoothness Penalty for MPCA", "topics": [ "select_r_by_smoothness_mpca" ] }, { "page": "select_r_by_vaf_mfa", "title": "Select Minimum r Based on VAF Threshold for MFA", "topics": [ "select_r_by_vaf_mfa" ] }, { "page": "select_r_by_vaf_mpca", "title": "Select Minimum r Based on VAF Threshold for MPCA", "topics": [ "select_r_by_vaf_mpca" ] }, { "page": "select_r_by_vss_mfa", "title": "Select Optimal r by VSS Criterion for MFA", "topics": [ "select_r_by_vss_mfa" ] }, { "page": "select_r_by_vss_mpca", "title": "Select Optimal r by VSS Criterion for MPCA", "topics": [ "select_r_by_vss_mpca" ] }, { "page": "select_r_clusterwise_mfa", "title": "Select Optimal r Using Cluster-wise Evaluation for MFA", "topics": [ "select_r_clusterwise_mfa" ] }, { "page": "select_r_clusterwise_mpca", "title": "Select Optimal r Using Cluster-wise Evaluation for MPCA", "topics": [ "select_r_clusterwise_mpca" ] }, { "page": "select_r_global_mfa", "title": "Select Optimal r Using Global Model (FA or PPCA) with Cross-Validation", "topics": [ 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