Man pages for cograph
Analysis and Visualization of Complex Networks
| abbrev_label | Abbreviate Labels |
| aes-edges | Edge Aesthetics |
| aes-nodes | Node Aesthetics |
| aes-scales | Aesthetic Scale Functions |
| aggregate_duplicate_edges | Aggregate Duplicate Edges |
| aggregate_layers | Aggregate Layers |
| aggregate_weights | Aggregate Edge Weights |
| arrow_base_midpoint | Calculate Arrow Base Midpoint |
| arrow_head_points | Calculate Arrow Head Points |
| arrow_points | Calculate Arrow Head Points |
| arrow_radius | Calculate Arrow Radius |
| as_cograph | Convert to Cograph Network |
| as_mcml | Convert to mcml |
| assortativity | Degree Assortativity Coefficient |
| assortativity_attribute | Attribute Assortativity (Homophily) |
| as_tna | Convert cluster_summary to tna Objects |
| atan2_usr | Aspect-Corrected atan2 |
| bezier_points | Calculate Bezier Curve Points |
| brain_vertices | Generate Brain Vertices |
| build_edge_labels_from_template | Build Edge Labels from Template |
| build_mcml | Build MCML from Raw Transition Data |
| centrality | Calculate Network Centrality Measures |
| centrality_alpha | Alpha (Katz) Centrality |
| centrality_authority | HITS Authority and Hub Scores |
| centrality_average_distance | Average Distance Centrality |
| centrality_barycenter | Barycenter Centrality |
| centrality_betweenness | Betweenness Centrality |
| centrality_bottleneck | Bottleneck Centrality |
| centrality_bridging | Bridging Centrality |
| centrality_brokerage_coordinator | Gould-Fernandez Brokerage — Coordinator Role |
| centrality_brokerage_gatekeeper | Gould-Fernandez Brokerage — Gatekeeper Role |
| centrality_brokerage_itinerant | Gould-Fernandez Brokerage — Itinerant (Consultant) Role |
| centrality_brokerage_liaison | Gould-Fernandez Brokerage — Liaison Role |
| centrality_brokerage_representative | Gould-Fernandez Brokerage — Representative Role |
| centrality_centroid | Centroid Value |
| centrality_closeness | Closeness Centrality |
| centrality_closeness_vitality | Closeness Vitality |
| centrality_clusterrank | ClusterRank Centrality |
| centrality_communicability | Communicability Centrality |
| centrality_communicability_betweenness | Communicability Betweenness Centrality |
| centrality_constraint | Burt's Constraint |
| centrality_coreness | K-Core Decomposition (Coreness) |
| centrality_cross_clique | Cross-Clique Connectivity |
| centrality_current_flow_betweenness | Current Flow Betweenness Centrality |
| centrality_current_flow_closeness | Current Flow Closeness Centrality |
| centrality_dangalchev | Dangalchev Closeness Centrality |
| centrality_decay | Decay Centrality |
| centrality_degree | Degree Centrality |
| centrality_diffusion | Diffusion Centrality |
| centrality_diversity | Diversity Centrality |
| centrality_dmnc | Density of Maximum Neighborhood Component (DMNC) |
| centrality_eccentricity | Eccentricity |
| centrality_effective_size | Effective Size (Burt's) |
| centrality_eigenvector | Eigenvector Centrality |
| centrality_entropy | Entropy Centrality |
| centrality_expected | Expected Centrality |
| centrality_expected_influence_1 | Expected Influence (one-step) |
| centrality_expected_influence_2 | Expected Influence (two-step) |
| centrality_flow_betweenness | Flow Betweenness Centrality |
| centrality_gateway | Gateway Coefficient |
| centrality_generalized_closeness | Generalized Closeness Centrality |
| centrality_gilschmidt | Gil-Schmidt Power Index |
| centrality_harary | Harary Centrality |
| centrality_harmonic | Harmonic Centrality |
| centrality_hubbell | Hubbell Centrality |
| centrality_information | Information Centrality (Stephenson-Zelen) |
| centrality_integration | Integration Centrality |
| centrality_katz | Katz Centrality |
| centrality_kreach | Geodesic K-Path Centrality |
| centrality_lac | Local Average Connectivity (LAC) |
| centrality_laplacian | Laplacian Centrality |
| centrality_leaderrank | LeaderRank Centrality |
| centrality_leverage | Leverage Centrality |
| centrality_lin | Lin Centrality |
| centrality_load | Load Centrality |
| centrality_lobby | Lobby Index (H-Index of Neighborhood) |
| centrality_local_bridging | Local Bridging Centrality |
| centrality_markov | Markov Centrality |
| centrality_mnc | Maximum Neighborhood Component (MNC) |
| centrality_pagerank | PageRank Centrality |
| centrality_pairwisedis | Pairwise Disconnectivity (Potapov et al. 2008) |
| centrality_participation | Participation Coefficient |
| centrality_percolation | Percolation Centrality |
| centrality_power | Bonacich Power Centrality |
| centrality_prestige_domain | Domain Prestige |
| centrality_prestige_domain_proximity | Domain Proximity Prestige |
| centrality_radiality | Radiality Centrality |
| centrality_random_walk | Random Walk Centrality |
| centrality_reaching_local | Local Reaching Centrality (Mones, Vicsek & Vicsek 2012) |
| centrality_residual_closeness | Residual Closeness Centrality |
| centrality_salsa | SALSA Authority Centrality |
| centrality_semilocal | Semi-Local Centrality |
| centrality_strength | Strength Centrality (Weighted Degree) |
| centrality_stress | Stress Centrality |
| centrality_subgraph | Subgraph Centrality |
| centrality_topological_coefficient | Topological Coefficient |
| centrality_transitivity | Local Transitivity (Clustering Coefficient) |
| centrality_voterank | VoteRank Centrality |
| centrality_wiener | Wiener Index Centrality |
| centrality_within_module_z | Within-Module Degree Z-Score |
| centralization | Centralization index |
| cent_to_edge | Calculate Point on Node Boundary |
| check_duplicate_edges | Check and Handle Duplicate Edges |
| circle_vertices | Generate Circle Vertices |
| cloud_vertices | Generate Cloud Vertices |
| cluster_quality | Cluster Quality Metrics |
| cluster_significance | Test Significance of Community Structure |
| cluster_summary | Cluster Summary Statistics |
| cograph | Create a Network Visualization |
| CographLayout | CographLayout R6 Class |
| cograph-main | Main Entry Point |
| CographNetwork | CographNetwork R6 Class |
| cograph-package | cograph: Modern Network Visualization for R |
| COGRAPH_SCALE | cograph Scaling Constants |
| COGRAPH_SCALE_LEGACY | Legacy Scaling Constants (Pre-v2.0 Behavior) |
| CographTheme | CographTheme R6 Class |
| color_communities | Color Nodes by Community |
| communities | Community Detection |
| community_consensus | Consensus Community Detection |
| community_edge_betweenness | Edge Betweenness Community Detection |
| community_fast_greedy | Fast Greedy Community Detection |
| community_fluid | Fluid Communities Detection |
| community_infomap | Infomap Community Detection |
| community_label_propagation | Label Propagation Community Detection |
| community_leading_eigenvector | Leading Eigenvector Community Detection |
| community_leiden | Leiden Community Detection |
| community_louvain | Louvain Community Detection |
| community_optimal | Optimal Community Detection |
| community_sizes | Get Community Sizes |
| community_spinglass | Spinglass Community Detection |
| community_walktrap | Walktrap Community Detection |
| compare_communities | Compare Community Structures |
| compute_adaptive_esize | Compute Adaptive Base Edge Size |
| compute_circular_layout | Compute Circular Layout |
| compute_connectivity_jitter_horizontal | Compute Connectivity-Based Jitter (Horizontal Layout) |
| compute_connectivity_jitter_vertical | Compute Connectivity-Based Jitter (Vertical Layout) |
| compute_edge_curvatures | Compute Edge Curvatures |
| compute_layout_gephi_fr | Wrapper for Gephi FR Layout (for layout registry) |
| compute_plot_limits | Compute Plot Limits |
| compute_polygon_layout | Compute Polygon Layout |
| core_periphery | Detect Core-Periphery Structure |
| create_edges_df | Create Edge Data Frame |
| create_grid_grob | Create Grid Grob Tree |
| create_nodes_df | Create Node Data Frame |
| cross_vertices | Generate Cross/Plus Vertices |
| curve_control_point | Calculate Control Point for Curved Edge |
| degree_distribution | Degree Distribution Visualization |
| detect_communities | Detect Communities in a Network |
| detect_duplicate_edges | Detect Duplicate Edges in Undirected Network |
| diamond_vertices | Generate Diamond Vertices |
| disparity | Disparity Filter for Network Backbone Extraction |
| disparity_filter | Disparity Filter |
| dispersion | Dispersion (Backstrom-Kleinberg 2014) |
| dot-add_cluster_borders | Add Cluster Borders |
| dot-add_cluster_labels | Add Cluster Labels |
| dot-add_heatmap_values | Add Value Labels to Heatmap (with optional halo) |
| dot-as_mcml | Convert a cluster_summary to mcml (strip tna classes) |
| dot-auto_detect_clusters | Auto-detect clusters from cograph_network |
| dot-build_cluster_lookup | Build node-to-cluster lookup from cluster specification |
| dot-build_from_transitions | Build cluster_summary from transition vectors |
| dot-build_heatmap_base | Build Base Heatmap |
| dot-build_mcml_edgelist | Build MCML from edge list data.frame |
| dot-build_mcml_sequence | Build MCML from sequence data.frame |
| dot-build_ml_cells | Build cell polygon data |
| dot-build_ml_connections | Build inter-layer connection lines |
| dot-build_ml_labels | Build layer label positions |
| dot-build_ml_shells | Build layer shell outlines |
| dot-compute_modularity | Compute modularity |
| dot-create_cograph_network | Create Unified cograph_network Object |
| dot-decode_tna_data | Decode numeric tna_seq_data back to character labels |
| dot-detect_mcml_input | Detect input type for build_mcml |
| dot-disparity_filter_matrix | Disparity Filter Core Implementation |
| dot-draw_intra_arc | Draw a Smooth Bezier Arc for Intra-Group Edges |
| dot-draw_intra_group_edges | Draw Intra-Group Edges with Curvature |
| dot-edge_keys | Canonical edge keys for grouping/deduplication. Undirected:... |
| dot-extract_inits | Extract Initial Probabilities from Network Object |
| dot-extract_ml_layers | Extract layers from various input types |
| dot-extract_weights | Extract Weight Matrix from Network Object |
| dot-group_tna_to_mcml | Convert a group_tna to mcml |
| dot-heatmap_theme | Heatmap Theme |
| dot-matrix_to_long | Convert Matrix to Long Format |
| dot-normalize_clusters | Normalize cluster specification to list format |
| dot-plot_compare_all_pairs | Plot All Pairwise Comparisons |
| dot-plot_heatmap_clustered | Plot Clustered Heatmap |
| dot-plot_heatmap_group_tna | Plot Group TNA as Supra-Adjacency Heatmap |
| dot-plot_heatmap_single | Plot Single Network Heatmap |
| dot-process_weights | Process weights based on type |
| dot-psych_style_defaults | Psych Network Visual Style Defaults |
| dot-resolve_colors | Resolve Color Palette |
| dot-resolve_ml_colors | Resolve color palette |
| dot-resolve_weights | Resolve edge weights |
| dot-tna_style_defaults | TNA Visual Style Defaults |
| dot-transform_to_plane | Transform coordinates to perspective plane |
| dot-translate_qgraph_dots | Translate qgraph-style parameter names to cograph equivalents |
| dot-wrap_communities | Wrap igraph communities result |
| draw_arrow_base | Draw Arrow Head |
| draw_brain | Draw Brain Node |
| draw_chip | Draw Chip Node |
| draw_chip_node_base | Draw Chip Node (Base R) |
| draw_circle | Draw Circle Node |
| draw_circle_arrow_base | Draw Circle Arrow (Dot) |
| draw_cloud | Draw Cloud Node |
| draw_cross | Draw Cross/Plus Node |
| draw_curved_arrow_base | Draw Curved Arrow Head |
| draw_curved_edge | Draw Curved Edge |
| draw_curved_edge_base | Draw Curved Edge with xspline (qgraph-style) |
| draw_curve_with_start_segment | Draw Curve with Optional Start Segment |
| draw_database | Draw Database Node |
| draw_database_node_base | Draw Database Node (Base R) |
| draw_diamond | Draw Diamond Node |
| draw_donut | Draw Donut Node |
| draw_donut_node_base | Draw Donut Chart Node |
| draw_donut_pie | Draw Donut with Inner Pie Node |
| draw_donut_pie_node_base | Draw Donut with Inner Pie |
| draw_double_donut_pie | Draw Double Donut with Inner Pie Node |
| draw_double_donut_pie_node_base | Draw Double Donut with Inner Pie |
| draw_edge_label_base | Draw Edge Label |
| draw_ellipse | Draw Ellipse Node |
| draw_gear | Draw Gear Node |
| draw_heart | Draw Heart Node |
| draw_hexagon | Draw Hexagon Node |
| draw_network | Draw Network Node |
| draw_network_node_base | Draw Network Node (Base R) |
| draw_neural | Draw Neural Node |
| draw_neural_node_base | Draw Neural Node (Base R) |
| draw_node_base | Draw a Single Node |
| draw_node_label_base | Draw Node Label |
| draw_open_arrow_base | Draw Open Arrow Head |
| draw_pentagon | Draw Pentagon Node |
| draw_pie | Draw Pie Node |
| draw_pie_node_base | Draw Pie Chart Node |
| draw_polygon_donut | Draw Polygon Donut Node |
| draw_polygon_donut_node_base | Draw Polygon Donut Node (Base R) |
| draw_polygon_donut_pie_node_base | Draw Polygon Donut with Inner Pie |
| draw_robot | Draw Robot Node |
| draw_robot_node_base | Draw Robot Node (Base R) |
| draw_self_loop | Draw Self-Loop |
| draw_self_loop_base | Draw Self-Loop Edge (qgraph-style) |
| draw_square | Draw Square Node |
| draw_star | Draw Star Node |
| draw_straight_edge | Draw Straight Edge |
| draw_straight_edge_base | Draw Straight Edge |
| draw_svg_shape | Draw SVG Shape (Grid) |
| draw_svg_shape_base | Draw SVG Shape (Base R) |
| draw_triangle | Draw Triangle Node |
| edge_centrality | Calculate Edge Centrality Measures |
| edge_endpoint | Calculate Edge Endpoint on Node Border |
| edge_reciprocity | Edge Reciprocity |
| ellipse_vertices | Generate Ellipse Vertices |
| estrada_index | Estrada Index |
| expand_param | Expand Parameter to Length (Strict) |
| extract_motifs | Extract Motifs from Network Data |
| extract_triads | Extract Triads with Node Labels |
| filter_edges | Filter Edges by Metadata |
| filter_edges_by_weight | Filter Edges by Weight Threshold |
| filter_nodes | Filter Nodes by Metadata or Centrality |
| find_curve_split_index | Find Split Index for Curve Based on Arc Length Fraction |
| fit_degree_distribution | Fit Statistical Distributions to Degree Sequence |
| fontface_to_numeric | Convert Fontface String to Numeric |
| fontface_to_string | Convert Numeric Fontface to String |
| format_ci_range | Format CI Range |
| format_edge_label_template | Format Edge Label from Template |
| format_pvalue | Format P-value |
| from_qgraph | Convert a qgraph object to cograph parameters |
| from_tna | Convert a tna object to cograph parameters |
| gear_vertices | Generate Gear Vertices |
| get_data | Get Original Data from Cograph Network |
| get_donut_base_vertices | Get Polygon Vertices by Shape Name |
| get_edge_label_position | Get Label Position on Edge |
| get_edge_list | Extract Raw Edge List from TNA Model |
| get_edge_order | Get Edge Rendering Order |
| get_edges | Get Edges from Cograph Network |
| get_groups | Get Node Groups from Cograph Network |
| get_labels | Get Labels from Cograph Network |
| get_layout | Get a Registered Layout |
| get_meta | Get Metadata from Cograph Network |
| get_node_order | Get Node Rendering Order |
| get_nodes | Get Nodes from Cograph Network |
| get_scale_constants | Get Scaling Constants |
| get_shape | Get a Registered Shape |
| get_shape_vertices | Get Shape Vertices |
| get_significance_stars | Get Significance Stars from P-values |
| get_source | Get Source Type from Cograph Network |
| get_svg_shape | Get Registered SVG Shape |
| get_template_from_style | Get Template from Style Preset |
| get_theme | Get a Registered Theme |
| get_x_scale | Get X-axis Scale Factor (inches per user unit) |
| get_y_scale | Get Y-axis Scale Factor (inches per user unit) |
| ggplot_robustness | Compare Network Robustness (ggplot2) |
| globals | Global Registries for cograph |
| group_centrality | Group Centrality (Everett-Borgatti 1999) |
| hai_datasets | Human-AI Interaction Coding Sequences |
| handle_deprecated_param | Handle Deprecated Parameter |
| heart_vertices | Generate Heart Vertices |
| hexagon_vertices | Generate Hexagon Vertices |
| init_registries | Initialize Global Registries |
| input-edgelist | Edge List Input Parsing |
| input-igraph | igraph Input Parsing |
| input-matrix | Matrix Input Parsing |
| input-parse | Input Parsing Functions |
| input-qgraph | qgraph Input Parsing |
| input-statnet | Statnet Network Input Parsing |
| input-tna | tna Input Parsing |
| inset_polygon_vertices | Inset Polygon Vertices |
| in_to_usr_x | Convert Inches to User Coordinates (X-axis) |
| in_to_usr_y | Convert Inches to User Coordinates (Y-axis) |
| is_bipartite | Check if a Matrix Could Be Bipartite |
| is_cograph_network | Check if object is a CographNetwork |
| is_cograph_theme | Check if object is a CographTheme |
| is_directed | Check if Network is Directed |
| is_symmetric_matrix | Detect if Matrix is Symmetric |
| is_tna_network | Check if Network is TNA-based |
| k_shortest_paths | Find K Shortest Loopless Paths (Yen's Algorithm) |
| layer_degree_correlation | Degree Correlation Between Layers |
| layer_similarity | Layer Similarity |
| layer_similarity_matrix | Pairwise Layer Similarities |
| layout_circle | Circular Layout |
| layout-circle | Circular Layout |
| layout_gephi_fr | Gephi Fruchterman-Reingold Layout |
| layout_groups | Group-based Layout |
| layout-groups | Group-based Layout |
| layout_oval | Oval Layout |
| layout-oval | Oval/Ellipse Layout |
| layout-registry | Layout Registry Functions |
| layout_spring | Fruchterman-Reingold Spring Layout |
| layout-spring | Fruchterman-Reingold Spring Layout |
| list_layouts | List Available Layouts |
| list_palettes | List Available Color Palettes |
| list_shapes | List Available Shapes |
| list_svg_shapes | List Registered SVG Shapes |
| list_themes | List Available Themes |
| map_edge_colors | Map Edge Colors by Weight |
| map_node_colors | Map Node Colors by Group |
| map_qgraph_lty | Map qgraph lty codes to cograph edge style names |
| map_qgraph_shape | Map qgraph shape names to cograph equivalents |
| mcml | mcml - Deprecated alias for cluster_summary |
| membership | Get Community Membership |
| methods-plot | Plot Methods |
| methods-print | Print Methods |
| motif_census | Network Motif Analysis |
| motifs | Network Motif Analysis |
| n_communities | Get Number of Communities |
| n_edges | Get Number of Edges |
| neighborhood_overlap | Neighborhood Overlap (Jaccard) for Each Edge |
| network_bridges | Bridge Edges |
| network_clique_size | Largest Clique Size |
| network_cut_vertices | Cut Vertices (Articulation Points) |
| network_girth | Network Girth (Shortest Cycle Length) |
| network_global_efficiency | Global Efficiency |
| network_local_efficiency | Local Efficiency |
| network_radius | Network Radius |
| network_rich_club | Rich Club Coefficient |
| network_small_world | Small-World Coefficient (Sigma) |
| network_summary | Network-Level Summary Statistics |
| network_vertex_connectivity | Network Vertex Connectivity |
| n_nodes | Get Number of Nodes |
| nodes | Get Nodes from Cograph Network (Deprecated) |
| offset_point | Offset Point from Center |
| output-save | Output and Saving |
| overlay_communities | Overlay Community Blobs on a Network Plot |
| palette_blues | Blues Palette |
| palette_colorblind | Colorblind-friendly Palette |
| palette_diverging | Diverging Palette |
| palette_pastel | Pastel Palette |
| palette_rainbow | Rainbow Palette |
| palette_reds | Reds Palette |
| palettes | Color Palettes |
| palette_viridis | Viridis Palette |
| panel_layout | Configure a custom multi-panel layout |
| parse_input | Parse Network Input |
| parse_svg | Parse SVG Content |
| pentagon_vertices | Generate Pentagon Vertices |
| perp_mid | Calculate Perpendicular Midpoint for Curved Edges |
| plot_alluvial | Plot Alluvial Diagram |
| plot-bootstrap | Bootstrap Plotting Methods |
| plot_bootstrap_forest | Forest Plot for Bootstrap Network Results |
| plot_centrality | Plot Centrality |
| plot_centrality_compare | Plot Centrality Comparison |
| plot_centrality_distribution | Plot Centrality Distribution |
| plot_centrality_heatmap | Plot Centrality Heatmap |
| plot_chord | Chord Diagram |
| plot.cograph_cluster_significance | Plot Cluster Significance |
| plot.cograph_communities | Plot Community Structure |
| plot.cograph_core_periphery | Plot Core-Periphery Structure |
| plot.cograph_degree_fit | Plot method for cograph_degree_fit |
| plot.cograph_motif_analysis | Plot Motif Analysis Results |
| plot.cograph_motifs | Plot Network Motifs |
| plot.cograph_network | Plot cograph_network Object |
| plot.cograph_rich_club | Plot Rich Club Results |
| plot.cograph_vulnerability | Plot Node Vulnerability |
| plot_compare | Plot Network Difference |
| plot-compare | Network Comparison Plots |
| plot_comparison_heatmap | Plot Comparison Heatmap |
| plot_degree_correlation | Plot Degree-Degree Correlation |
| plot_edge_diff_forest | Forest Plot for Bootstrap Edge Differences |
| plot_edge_weights | Plot Edge Weight Distribution |
| plot_group_permutation | Plot Group Permutation Test Results |
| plot_heatmap | Plot Network as Heatmap |
| plot-heatmap | Network Heatmap Plots |
| plot_htna | Plot Heterogeneous TNA Network (Multi-Group Layout) |
| plot_mcml | Plot Multi-Cluster Multi-Layer Network |
| plot_mixed_network | Plot Mixed Network |
| plot_ml_heatmap | Multilayer Network Heatmap |
| plot_mlna | Multilevel Network Visualization |
| plot-mlvar | Plot Nestimate mlVAR Networks |
| plot_motifs | Plot a motif/subgraph result |
| plot_mtna | Multi-Cluster TNA Network Plot |
| plot-nestimate | Nestimate Plotting Methods |
| plot_net_bootstrap_group | Plot a Group Bootstrap Result |
| plot_netobject_group | Plot a Group of Nestimate netobjects |
| plot_netobject_ml | Plot a Multilevel Nestimate netobject |
| plot_net_stability | Plot Centrality Stability Results |
| plot_network_evolution | Plot Network Evolution (Small Multiples) |
| plot_permutation | Plot Permutation Test Results |
| plot-permutation | Permutation Test Plotting |
| plot_robustness | Plot Network Robustness |
| plot_simplicial | Simplicial Complex Visualization |
| plot_temporal | Temporal Network Prism (3D Glass Box) |
| plot_tna | TNA-Style Network Plot (qgraph Compatible) |
| plot.tna_disparity | Plot Disparity Filter Result |
| plot_trajectories | Plot Individual Trajectories |
| plot_transitions | Plot Transitions Between States |
| plot-transitions | Transition Flow Visualization |
| point_angle | Calculate Angle Between Two Points |
| point_distance | Calculate Distance Between Two Points |
| point_on_circle | Calculate Point on Circle |
| print.cograph_communities | Print Community Structure |
| print.cograph_degree_fit | Print method for cograph_degree_fit |
| print.cograph_network | Print cograph_network Object |
| project_bipartite | Project Bipartite Network to One-Mode |
| qgraph_arrow_size | qgraph-style Arrow Size Calculation |
| qgraph_cent2edge | qgraph Cent2Edge (EXACT - critical formula) |
| qgraph_cent_to_edge_simple | qgraph Point on Node Boundary |
| qgraph_default_esize | qgraph Default Edge Size |
| qgraph_default_vsize | qgraph Default Node Size |
| qgraph_norm_curve | qgraph Curve Normalization Factor |
| qgraph_plot_info | Get Plot Dimension Info |
| QGRAPH_SCALE | qgraph Scaling Constants (Exact Values) |
| qgraph_scale_edge_widths | qgraph Edge Width Scaling (EXACT) |
| qgraph_vsize_to_user | qgraph Node Size to User Coordinates |
| reaching_global | Global Reaching Centrality (Mones, Vicsek & Vicsek 2012) |
| rectangle_vertices | Generate Rectangle Vertices |
| recycle_to_length | Recycle Value to Length |
| register_builtin_layouts | Register Built-in Layouts |
| register_builtin_palettes | Register Built-in Palettes |
| register_builtin_shapes | Register Built-in Shapes |
| register_builtin_themes | Register Built-in Themes |
| register_layout | Register a Custom Layout |
| register_shape | Register a Custom Shape |
| register_svg_shape | Register Custom SVG Shape |
| register_theme | Register a Custom Theme |
| regular_polygon_vertices | Generate Regular Polygon Vertices |
| render_edge_labels_grid | Render Edge Labels |
| render-edges | Edge Rendering |
| render_edges_base | Render All Edges |
| render_edges_grid | Render All Edges |
| render_edges_splot | Render Edges for splot |
| render-ggplot | ggplot2 Conversion |
| render-grid | Grid Rendering |
| render_legend_grid | Render Legend |
| render-legend-shared | Shared Legend Renderer |
| render_legend_splot | Render Legend for splot |
| render_node_labels_grid | Render Node Labels |
| render-nodes | Node Rendering |
| render_nodes_base | Render All Nodes |
| render_nodes_grid | Render All Nodes |
| render_nodes_splot | Render Nodes for splot |
| rescale_layout | Rescale Layout to -1 to 1 Range |
| resolve_aesthetic | Resolve Aesthetic Value |
| resolve_centrality_sizes | Resolve Centrality-Based Node Sizes |
| resolve_donut_params | Resolve Donut Parameters |
| resolve_edge_colors | Resolve Edge Colors |
| resolve_edge_labels | Resolve Edge Labels |
| resolve_edge_styles | Resolve Edge Styles |
| resolve_edge_widths | Resolve Edge Widths |
| resolve_labels | Resolve Labels |
| resolve_label_sizes | Resolve Label Sizes |
| resolve_loop_rotation | Resolve Loop Rotation |
| resolve_node_colors | Resolve Node Colors |
| resolve_node_sizes | Resolve Node Sizes |
| resolve_shapes | Resolve Shape Parameter |
| resolve_stars | Resolve Stars from Various Inputs |
| rich_club | Rich Club Coefficient |
| rich_club_local | Local Rich Club Score |
| robustness | Network Robustness Analysis |
| robustness_auc | Calculate Area Under Robustness Curve (AUC) |
| robustness_edge_attack | Edge Attack Analysis |
| robustness_summary | Summary of Robustness Analysis |
| robustness_vertex_attack | Vertex Attack Analysis |
| scale_alpha | Create an Alpha Scale |
| scale_color | Create a Color Scale |
| scale_color_discrete | Create a Categorical Color Scale |
| scale-constants | Scaling Constants |
| scale_edge_widths | Scale Edge Widths Based on Weights |
| scale_edge_widths_simple | Scale Edge Widths (Simple Version) |
| scale_node_sizes | Scale Node Sizes |
| scale_size | Create a Size Scale |
| scale_width | Create a Width Scale |
| select_bridges | Select Bridge Edges |
| select_component | Select Connected Component |
| select_edges | Select Edges with Lazy Computation |
| select_edges_between | Select Edges Between Node Sets |
| select_edges_involving | Select Edges Involving Nodes |
| select_neighbors | Select Node Neighbors (Ego Network) |
| select_nodes | Select Nodes with Lazy Centrality Computation |
| select_top | Select Top N Nodes by Centrality |
| select_top_edges | Select Top N Edges |
| set_edges | Set Edges in Cograph Network |
| set_groups | Set Node Groups |
| set_layout | Set Layout in Cograph Network |
| set_nodes | Set Nodes in Cograph Network |
| shapes-basic | Basic Node Shapes |
| shapes-registry | Shape Registry Functions |
| shapes-special | Special Node Shapes |
| shapes-svg | Custom SVG Node Shapes |
| shorten_edge_for_arrow | Calculate Shortened Edge Endpoint |
| shortest_paths | Compute Shortest Path Distances |
| simmelian_strength | Simmelian Strength (Triangle Count per Edge) |
| simplify | Simplify a Network |
| sn_edges | Set Edge Aesthetics |
| sn_ggplot | Convert Network to ggplot2 |
| sn_layout | Apply Layout to Network |
| sn_nodes | Set Node Aesthetics |
| sn_palette | Apply Color Palette to Network |
| sn_save | Save Network Visualization |
| sn_save_ggplot | Save as ggplot2 |
| sn_theme | Apply Theme to Network |
| sonplot-qgraph-geometry | qgraph-Compatible Geometry Utilities |
| soplot | Plot Cograph Network |
| splot | Plot Nestimate Bootstrap Results |
| splot_angle | Calculate Angle Between Two Points |
| splot-arrows | Base R Arrow Drawing |
| splot-edges | Base R Edge Rendering |
| splot-geometry | Base R Graphics Geometry Utilities |
| splot-labels | Edge Label Template Formatting |
| splot-nodes | Base R Node Rendering |
| splot-params | splot Parameter Vectorization Helpers |
| splot-polygons | Base R Polygon Shape Definitions |
| splot.tna_bootstrap | Plot Bootstrap Results |
| splot.tna_disparity | Plot Disparity Results with splot |
| square_vertices | Generate Square Vertices |
| star_vertices | Generate Star Vertices |
| student_interactions | Student Interaction Edge List |
| subdivide_polygon | Subdivide Polygon Edges |
| subgraphs | Extract Specific Motif Instances (Subgraphs) |
| summarize_network | Summarize Network by Clusters |
| summary.cograph_network | Summary of cograph_network Object |
| supra_adjacency | Supra-Adjacency Matrix |
| supra_interlayer | Extract Inter-Layer Block |
| supra_layer | Extract Layer from Supra-Adjacency Matrix |
| theme_cograph_classic | Classic Theme |
| theme_cograph_colorblind | Colorblind-friendly Theme |
| theme_cograph_dark | Dark Theme |
| theme_cograph_gray | Grayscale Theme |
| theme_cograph_minimal | Minimal Theme |
| theme_cograph_nature | Nature Theme |
| theme_cograph_viridis | Viridis Theme |
| themes-builtin | Built-in Themes |
| themes-registry | Theme Registry Functions |
| tna_color_palette | Generate TNA-style Color Palette for Nodes |
| to_data_frame | Export Network as Edge List Data Frame |
| to_igraph | Convert Network to igraph Object |
| to_matrix | Convert Network to Adjacency Matrix |
| to_network | Convert Network to statnet network Object |
| triad_census | Triad Census |
| triangle_vertices | Generate Triangle Vertices |
| trophic_incoherence | Trophic Incoherence Parameter |
| unregister_svg_shape | Unregister SVG Shape |
| usr_to_in_x | Convert User Coordinates to Inches (X-axis) |
| usr_to_in_y | Convert User Coordinates to Inches (Y-axis) |
| utils-colors | Color Utilities |
| utils-deprecation | Deprecation Utilities |
| utils-geometry | Geometry Utilities |
| utils-globals | Global Variable Declarations |
| utils-validation | Input Validation Utilities |
| validate_choice | Validate Choice |
| validate_color | Validate Color |
| validate_length | Validate Length Match |
| validate_network | Validate Network Object |
| validate_range | Validate Numeric Range |
| verify_with_igraph | Verify Against igraph |
| visual-scale | Visual Scale Helper |
| vulnerability | Node Vulnerability |
| zzz | Package Load and Unload Functions |
