| Aggregate Partial Results from PBS Jobs | aggregate_partial_results |
| Align Cluster Labels to Ground Truth Using Hungarian Algorithm | align_clusters_to_truth |
| Align (Flip) Factor Signs in an MFA Model | align_factor_signs_mfa |
| Align (Flip) Factor Signs in a Mixture PCA Model | align_factor_signs_mpca |
| K-means-based cluster assignment | assign_by_kmeans |
| Bandpass Filter for EMG Signals | bandpass_filter |
| Bootstrap Confidence Intervals for Synergy Loadings | bootstrap_loading_ci |
| Compute SSE for a MixtureFA model | calc_reconstruction_error_mixtureFA |
| Compute SSE for a MixturePCA model | calc_reconstruction_error_mixturePCA |
| Compute Total Reconstruction SSE for Single FA | calc_reconstruction_error_singleFA |
| Compute Total Reconstruction SSE for Single PCA | calc_reconstruction_error_singlePCA |
| Compute the Total Sum of Squares (SST) for a List of Data Matrices | calc_total_SST |
| Compute Calibration from Model Fit | calibrate_model |
| Check if Future Packages are Available | check_future_available |
| Check PBS Job Status | check_pbs_job_status |
| Check SSE Diagnostics for Mixture Models | check_SSE_diagnostics |
| Compare Analysis Methods on v2 Dynamic Synergy Data | compare_baselines |
| Compare Analysis Methods on Dynamic Synergy Data (v2) | compare_static_vs_dynamic |
| Compute Adjusted Rand Index (ARI) | compute_ari |
| Compile ARI and VAF into a Single Table | compute_ari_vaf_table |
| Compute Bayesian Information Criterion (BIC) | compute_BIC |
| Compute BIC for an MFA model | compute_BIC_mfa |
| Compute BIC for a Mixture PCA Model | compute_BIC_mpca |
| Compute BIC for a Fitted Model | compute_bic_wrapper |
| Compute Calibration Statistics for Mixture Model | compute_calibration |
| Compute Cluster Sizes from a Fitted MFA (or Mixture PCA) Model | compute_cluster_sizes |
| Compute Cluster Sizes for Mixture PCA | compute_cluster_sizes_mpca |
| Compute Cluster-wise Subspace Recovery Score | compute_clusterwise_subspace_score |
| Compute Expected Calibration Error | compute_ece |
| Compute Classification Entropy from Responsibilities | compute_entropy |
| Compute Factor Scores for a Single MFA Cluster | compute_factor_scores |
| Compute Factor Scores for All Subjects in an MFA Model | compute_factor_scores_mfa |
| Compute PC Factor Scores for All Subjects in a Mixture PCA Model | compute_factor_scores_mpca |
| Compute Factor (PC) Scores for a Single Subject in a Mixture PCA Cluster | compute_factor_scores_mpca_single |
| Compute Factor Scores for a Single Subject in MFA | compute_factor_scores_optimized |
| Compute Global VAF (1 - SSE/SST) for an MFA Model | compute_global_vaf_mfa |
| Compute Global VAF (1 - SSE/SST) for Mixture PCA | compute_global_vaf_mpca |
| Compute ICL for a Mixture Model (Unified Interface) | compute_ICL |
| Compute ICL for a Mixture Factor Analysis Model | compute_ICL_mfa |
| Compute ICL for a Mixture PCA Model | compute_ICL_mpca |
| Compute Log-Likelihood for Mixture Models | compute_logLik |
| Compute the Mixture-Model Log-Likelihood for MFA | compute_logLik_mfa |
| Compute the Mixture-Model Log-Likelihood for Mixture PCA | compute_logLik_mpca |
| Compute MVC Reference Values | compute_mvc_reference |
| Compute Reconstruction Error | compute_reconstruction_error |
| Compute Smoothness Penalty for Factor Scores | compute_smoothness_penalty |
| Compute Subspace Similarity Between Two Basis Matrices | compute_subspace_similarity |
| Compute Global Variance Accounted For (VAF) | compute_VAF |
| Compute VAF for a Fitted MFA Model | compute_VAF_mfa |
| Compute VAF for a Mixture PCA (PPCA) Model | compute_VAF_mpca |
| Compute VAF (Variance Accounted For) for a Fitted Model | compute_vaf_wrapper |
| Compute VSS (Very Simple Structure) Criterion for Factor Loadings | compute_vss_criterion |
| Count Completed PBS Tasks | count_completed_tasks |
| EMG Preprocessing Preset Configurations | emg_preset_config |
| Evaluate Model Selection Results | evaluate_model_selection |
| Extract Cluster Labels from a Fitted Model | extract_cluster_labels |
| Extract Envelope from EMG Signal | extract_envelope |
| Extract Selection Summary as Data Frame | extract_selection_summary |
| Extract subject-level features by single PCA | extract_subject_features_by_singlePCA |
| Apply Consistent Faceting for Cluster and Factor Visualizations | facet_mixsynergy |
| Fit a Single Factor Analysis (Ignoring Clusters) | fit_single_factor_analysis |
| Fit a Single PCA (Ignoring Clusters) | fit_single_pca |
| Two-step Baseline Algorithm for PCA/FA | fit_two_step_baseline |
| Generate PBS Job Script | generate_pbs_script |
| Generate v2 Dynamic Synergy Data for Model Selection Experiments | generate_synergy_data |
| Retrieve a Specific Model by (K, r) from a Grid Search | get_model_by_K_r |
| Retrieve a Mixture PCA Model by (K, r) | get_model_by_K_r_mpca |
| Create a Static Table of Simulation Conditions (Table 1) | make_table1 |
| Summarize Results for a Subset (Table 2) | make_table2 |
| Fit a Mixture Factor Analysis Model (with optional multi-initialization) | mfa_em_fit |
| Single-Run Mixture Factor Analysis with a Preset Initial Assignment | mfa_em_fit_cpp_singleInit |
| Fit a Mixture PCA Model (Using mpcaTimeseriesCpp) with optional multi-initialization | mixture_pca_em_fit |
| Single-Run Mixture PCA with a Preset Initial Assignment | mixture_pca_em_fit_cpp_singleInit |
| Normalize EMG Signal | normalize_emg |
| Notch Filter for Power Line Noise Removal | notch_filter |
| Plot Activation Patterns | plot_activation_patterns |
| Plot Aligned Basis Heatmaps | plot_aligned_basis_heatmaps |
| Plot All Factor Scores (Z) for MFA, Faceted by Cluster and Factor | plot_all_factor_scores_mfa |
| Plot All Factor Scores (Z) for MPCA, Faceted by Cluster and Factor | plot_all_factor_scores_mpca |
| Plot Reconstructed Waveforms for All Clusters and Channels (MFA) | plot_all_reconstructed_waveforms_mfa |
| Plot Reconstructed Waveforms for All Clusters and Channels (MPCA) | plot_all_reconstructed_waveforms_mpca |
| Plot Basis UMAP Embedding | plot_basis_umap |
| Plot BIC Comparison for Parameter Sweep | plot_bic_comparison |
| Line Plot of BIC vs. K or r | plot_bic_line |
| Plot Calibration Curve | plot_calibration |
| Plot Cluster Embedding | plot_cluster_embedding |
| Plot Cluster-Specific Synergy Coefficients (Factor Loadings) for MFA | plot_cluster_synergy_loadings_mfa |
| Plot Cluster-Specific Synergy Coefficients (Factor Loadings) for MPCA | plot_cluster_synergy_loadings_mpca |
| Plot Confusion Matrix for Cluster Assignments | plot_confusion_matrix |
| Plot ARI vs. Separation/Noise (Figure 1) | plot_fig1_ARI |
| Plot Baseline Comparison (ARI and VAF) | plot_fig1_baseline_comparison |
| Plot BIC Heatmap for a Subset (Figure 2) | plot_fig2_BIC_heatmap |
| Plot Boxplot of ARI for Multiple Initial Seeds (Figure 3) | plot_fig3_init_boxplot |
| Plot Reconstruction Error and VAF (Figures 4-6) | plot_fig4to6_reconstruction_vaf |
| Plot Metric vs Axis for Parameter Sweep | plot_metric_vs_axis |
| Plot Neural Command Trajectories | plot_neural_command |
| Plot Noise Profiles | plot_noise_profiles |
| Plot Reconstructed EMG Signals | plot_reconstructed_emg |
| Plot SSE Heatmap Across Methods and Subjects | plot_sse_heatmap |
| Plot Summary Comparison for Parameter Sweep | plot_sweep_summary |
| Plot Synergy Bases (Lambda Matrices) | plot_synergy_bases |
| Plot Synergy Correlation Comparison | plot_synergy_correlation_comparison |
| Plot Synergy Summary | plot_synergy_summary |
| Plot Original vs. Reconstructed Waveform for an MFA Model | plot_waveform_comparison_mfa |
| Plot Original vs. Reconstructed Waveform for an MPCA Model | plot_waveform_comparison_mpca |
| Plot Win Rate Heatmap for Parameter Sweep | plot_winrate_heatmap |
| Plot Method for mixture_r_selection Objects | plot.mixture_r_selection |
| Post-hoc Evaluation of MFA Grid Search | posthoc_mfa_evaluation |
| Post-hoc Evaluation of Mixture PCA Grid Search | posthoc_mpca_evaluation |
| EMG Preprocessing Pipeline | preprocess_emg |
| Print Summary of Bootstrap CI Results | print.bootstrap_ci |
| Print Summary of Calibration Results | print.calibration_result |
| Print Method for mixture_r_selection Objects | print.mixture_r_selection |
| Print Method for preprocessed_emg Objects | print.preprocessed_emg |
| Read All Results from .rds Files | read_all_results |
| Read All Results and Produce Tables/Figures | read_and_visualize_all |
| Reconstruct a single subject's data from a Mixture PCA model | reconstruct_singleMPCA |
| Rectify EMG Signal | rectify |
| Remove DC Offset from EMG Signal | remove_dc_offset |
| Post-hoc Rotation for an MFA Model | rotate_mfa_model |
| Post-hoc Rotation for a Mixture PCA Model | rotate_mpca_model |
| Run K Selection Method Comparison (v3) | run_k_selection_comparison |
| Run Parameter Sweep Experiment | run_param_sweep |
| Run Parameter Sweep for Baseline Method Comparisons (v2) | run_param_sweep_baselines |
| Run Parameter Sweep with Model Selection | run_param_sweep_modelsel |
| Run a Single Task from Parameter Grid | run_single_task |
| Run Parameter Sweep Using Future | run_sweep_future |
| Get Unified Color Scale for Discrete Categories | scale_color_mixsynergy |
| Get Unified Viridis Color Scale for Continuous Values | scale_fill_mixsynergy |
| Get Unified Fill Scale for Discrete Categories | scale_fill_mixsynergy_discrete |
| Get Unified Viridis Color Scale for Diverging Values | scale_fill_mixsynergy_diverging |
| Select K Using Bootstrap Stability Selection | select_K_bootstrap_stability |
| Select K Using Cross-Validation | select_K_crossvalidation |
| Unified Model Selection for K and r | select_K_r |
| Search for the Best (K, r) for MFA via Grid Search (Using mfa_em_fit) | select_optimal_K_r_mfa |
| Two-Stage Model Selection for MFA: Select K First, Then r | select_optimal_K_r_mfa_twostage |
| Search for the Best (K, r) for Mixture PCA via Grid Search | select_optimal_K_r_mpca |
| Two-Stage Model Selection for MPCA: Select K First, Then r | select_optimal_K_r_mpca_twostage |
| Select Optimal r by Smoothness Penalty for MFA | select_r_by_smoothness_mfa |
| Select Optimal r by Smoothness Penalty for MPCA | select_r_by_smoothness_mpca |
| Select Minimum r Based on VAF Threshold for MFA | select_r_by_vaf_mfa |
| Select Minimum r Based on VAF Threshold for MPCA | select_r_by_vaf_mpca |
| Select Optimal r by VSS Criterion for MFA | select_r_by_vss_mfa |
| Select Optimal r by VSS Criterion for MPCA | select_r_by_vss_mpca |
| Select Optimal r Using Cluster-wise Evaluation for MFA | select_r_clusterwise_mfa |
| Select Optimal r Using Cluster-wise Evaluation for MPCA | select_r_clusterwise_mpca |
| Select Optimal r Using Global Model (FA or PPCA) with Cross-Validation | select_r_global_mfa |
| Select Optimal r Using Global Model (PPCA) with Cross-Validation for MPCA | select_r_global_mpca |
| Unified r Selection for Mixture Models (MFA/MPCA) | select_r_mixture |
| Select Optimal r Using Multi-Criteria Approach for MFA | select_r_multicriteria_mfa |
| Select Optimal r Using Multi-Criteria Approach for MPCA | select_r_multicriteria_mpca |
| Setup Future Backend for HPC | setup_future_backend |
| Print Summary of Available Parallelization Options | show_parallel_options |
| Simulate Dynamic Synergy Data with Three Orthogonal Control Axes | simulate_dynamic_synergy_data |
| Simulation Comparison Functions | simulation_comparison |
| Simulation Visualization Functions | simulation_visualization |
| Strip All Attributes Except Essential Ones | strip_attributes |
| Submit Parameter Sweep to HPC (Simple Interface) | submit_hpc_sweep |
| Submit PBS Parameter Sweep | submit_pbs_sweep |
| Summarize VAF and SSE for an MFA Model | summarize_vaf_sse_mfa |
| Summary Method for mixture_r_selection Objects | summary.mixture_r_selection |
| Summary Method for preprocessed_emg Objects | summary.preprocessed_emg |
| Unified Theme and Style Definitions for synergyMixR Visualizations | theme_mixsynergy |
| Get Unified Heatmap Theme for synergyMixR | theme_mixsynergy_heatmap |
| Theme for Parameter Sweep Plots | theme_sweep |
| Visualization Functions for Two-Step Algorithm Diagnostics | visualize_twostep_diagnostics |
| Wait for PBS Job Completion | wait_for_pbs_job |
