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"topics": [ "CographLayout" ] }, { "page": "CographNetwork", "title": "CographNetwork R6 Class", "topics": [ "CographNetwork" ] }, { "page": "CographTheme", "title": "CographTheme R6 Class", "topics": [ "CographTheme" ] }, { "page": "color_communities", "title": "Color Nodes by Community", "topics": [ "color_communities" ] }, { "page": "communities", "title": "Community Detection", "topics": [ "communities" ] }, { "page": "community_consensus", "title": "Consensus Community Detection", "topics": [ "community_consensus", "com_consensus" ] }, { "page": "community_edge_betweenness", "title": "Edge Betweenness Community Detection", "topics": [ "community_edge_betweenness", "com_eb" ] }, { "page": "community_fast_greedy", "title": "Fast Greedy Community Detection", "topics": [ "community_fast_greedy", "com_fg" ] }, { "page": "community_fluid", "title": "Fluid Communities Detection", "topics": [ "community_fluid", "com_fl" ] }, { "page": "community_infomap", "title": "Infomap Community Detection", "topics": [ "community_infomap", "com_im" ] }, { "page": "community_label_propagation", "title": "Label Propagation Community Detection", "topics": [ "community_label_propagation", "com_lp" ] }, { "page": "community_leading_eigenvector", "title": "Leading Eigenvector Community Detection", "topics": [ "community_leading_eigenvector", "com_le" ] }, { "page": "community_leiden", "title": "Leiden Community Detection", "topics": [ "community_leiden", "com_ld" ] }, { "page": "community_louvain", "title": "Louvain Community Detection", "topics": [ "community_louvain", "com_lv" ] }, { "page": "community_optimal", "title": "Optimal Community Detection", "topics": [ "community_optimal", "com_op" ] }, { "page": "community_sizes", "title": "Get Community Sizes", "topics": [ "community_sizes" ] }, { "page": "community_spinglass", "title": "Spinglass Community Detection", "topics": [ "community_spinglass", "com_sg" ] }, { "page": "community_walktrap", "title": "Walktrap Community Detection", "topics": [ "community_walktrap", "com_wt" ] }, { "page": "compare_communities", "title": "Compare Community Structures", "topics": [ "compare_communities" ] }, { "page": "core_periphery", "title": "Detect Core-Periphery Structure", "topics": [ "core_periphery" ] }, { "page": "degree_distribution", "title": "Degree Distribution Visualization", "topics": [ "degree_distribution" ] }, { "page": "detect_communities", "title": "Detect Communities in a Network", "topics": [ "detect_communities" ] }, { "page": "disparity_filter", "title": "Disparity Filter", "topics": [ "disparity_filter", "disparity_filter.cograph_network", "disparity_filter.default", "disparity_filter.igraph", "disparity_filter.matrix", "disparity_filter.tna" ] }, { "page": "dispersion", "title": "Dispersion (Backstrom-Kleinberg 2014)", "topics": [ "dispersion" ] }, { "page": "edge_centrality", "title": "Calculate Edge Centrality Measures", "topics": [ "edge_betweenness", "edge_centrality" ] }, { "page": "edge_reciprocity", "title": "Edge Reciprocity", "topics": [ "edge_reciprocity" ] }, { "page": "estrada_index", "title": "Estrada Index", "topics": [ "estrada_index" ] }, { "page": "filter_edges", "title": "Filter Edges by Metadata", "topics": [ "filter_edges", "subset_edges" ] }, { "page": "filter_nodes", "title": "Filter Nodes by Metadata or Centrality", "topics": [ "filter_nodes", "subset_nodes" ] }, { "page": "fit_degree_distribution", "title": "Fit Statistical Distributions to Degree Sequence", "topics": [ "fit_degree_distribution" ] }, { "page": "from_qgraph", "title": "Convert a qgraph object to cograph parameters", "topics": [ "from_qgraph" ] }, { "page": "from_tna", "title": "Convert a tna object to cograph parameters", "topics": [ "from_tna" ] }, { "page": "get_data", "title": "Get Original Data from Cograph Network", "topics": [ "get_data" ] }, { "page": "get_edge_list", "title": "Extract Raw Edge List from TNA Model", "concept": [ "motifs" ], "topics": [ "get_edge_list" ] }, { "page": "get_edges", "title": "Get Edges from Cograph Network", "topics": [ "get_edges" ] }, { "page": "get_groups", "title": "Get Node Groups from Cograph Network", "topics": [ "get_groups" ] }, { "page": "get_labels", "title": "Get Labels from Cograph Network", "topics": [ "get_labels" ] }, { "page": "get_layout", "title": "Get a Registered Layout", "topics": [ "get_layout" ] }, { "page": "get_meta", "title": "Get Metadata from Cograph Network", "topics": [ "get_meta" ] }, { "page": "get_nodes", "title": "Get Nodes from Cograph Network", "topics": [ "get_nodes" ] }, { "page": "get_shape", "title": "Get a Registered Shape", "topics": [ "get_shape" ] }, { "page": "get_source", "title": "Get Source Type from Cograph Network", "topics": [ "get_source" ] }, { "page": "get_theme", "title": "Get a Registered Theme", "topics": [ "get_theme" ] }, { "page": "ggplot_robustness", "title": "Compare Network Robustness (ggplot2)", "topics": [ "ggplot_robustness" ] }, { "page": "group_centrality", "title": "Group Centrality (Everett-Borgatti 1999)", "topics": [ "group_centrality" ] }, { "page": "hai_datasets", "title": "Human-AI Interaction Coding Sequences", "topics": [ "ai_coding", "ai_detailed", "coding", "coding_detailed", "hai_datasets", "human_ai", "human_ai_detailed" ] }, { "page": "is_bipartite", "title": "Check if a Matrix Could Be Bipartite", "topics": [ "is_bipartite" ] }, { "page": "is_directed", "title": "Check if Network is Directed", "topics": [ "is_directed" ] }, { "page": "is_tna_network", "title": "Check if Network is TNA-based", "topics": [ "is_tna_network" ] }, { "page": "k_shortest_paths", "title": "Find K Shortest Loopless Paths (Yen's Algorithm)", "topics": [ "k_shortest_paths" ] }, { "page": "layer_degree_correlation", "title": "Degree Correlation Between Layers", "topics": [ "layer_degree_correlation", "ldegcor" ] }, { "page": "layer_similarity", "title": "Layer Similarity", "topics": [ "layer_similarity", "lsim" ] }, { "page": "layer_similarity_matrix", "title": "Pairwise Layer Similarities", "topics": [ "layer_similarity_matrix", "lsim_matrix" ] }, { "page": "layout_circle", "title": "Circular Layout", "topics": [ "layout_circle" ] }, { "page": "layout_groups", "title": "Group-based Layout", "topics": [ "layout_groups" ] }, { "page": "layout_oval", "title": "Oval Layout", "topics": [ "layout_oval" ] }, { "page": "layout_spring", "title": "Fruchterman-Reingold Spring Layout", "topics": [ "layout_spring" ] }, { "page": "list_layouts", "title": "List Available Layouts", "topics": [ "list_layouts" ] }, { "page": "list_palettes", "title": "List Available Color Palettes", "topics": [ "list_palettes" ] }, { "page": "list_shapes", "title": "List Available Shapes", "topics": [ "list_shapes" ] }, { "page": "list_svg_shapes", "title": "List Registered SVG Shapes", "topics": [ "list_svg_shapes" ] }, { "page": "list_themes", "title": "List Available Themes", "topics": [ "list_themes" ] }, { "page": "membership", "title": "Get Community Membership", "topics": [ "membership" ] }, { "page": "motifs", "title": "Network Motif Analysis", "concept": [ "motifs" ], "topics": [ "motifs", "plot.cograph_motif_result", "print.cograph_motif_result" ] }, { "page": "n_communities", "title": "Get Number of Communities", "topics": [ "n_communities" ] }, { "page": "n_edges", "title": "Get Number of Edges", "topics": [ "n_edges" ] }, { "page": "n_nodes", "title": "Get Number of Nodes", "topics": [ "n_nodes" ] }, { "page": "neighborhood_overlap", "title": "Neighborhood Overlap (Jaccard) for Each Edge", "topics": [ "neighborhood_overlap" ] }, { "page": "network_bridges", "title": "Bridge Edges", "topics": [ "network_bridges" ] }, { "page": "network_clique_size", "title": "Largest Clique Size", "topics": [ "network_clique_size" ] }, { "page": "network_cut_vertices", "title": "Cut Vertices (Articulation Points)", "topics": [ "network_cut_vertices" ] }, { "page": "network_girth", "title": "Network Girth (Shortest Cycle Length)", "topics": [ "network_girth" ] }, { "page": "network_global_efficiency", "title": "Global Efficiency", "topics": [ "network_global_efficiency" ] }, { "page": "network_local_efficiency", "title": "Local Efficiency", "topics": [ "network_local_efficiency" ] }, { "page": "network_radius", "title": "Network Radius", "topics": [ "network_radius" ] }, { "page": "network_rich_club", "title": "Rich Club Coefficient", "topics": [ "network_rich_club" ] }, { "page": "network_small_world", "title": "Small-World Coefficient (Sigma)", "topics": [ "network_small_world" ] }, { "page": "network_summary", "title": "Network-Level Summary Statistics", "topics": [ "network_summary" ] }, { "page": "network_vertex_connectivity", "title": "Network Vertex Connectivity", "topics": [ "network_vertex_connectivity" ] }, { "page": "nodes", "title": "Get Nodes from Cograph Network (Deprecated)", "topics": [ "nodes" ] }, { "page": "overlay_communities", "title": "Overlay Community Blobs on a Network Plot", "topics": [ "overlay_communities" ] }, { "page": "palette_blues", "title": "Blues Palette", "topics": [ "palette_blues" ] }, { "page": "palette_colorblind", "title": "Colorblind-friendly Palette", "topics": [ "palette_colorblind" ] }, { "page": "palette_diverging", "title": "Diverging Palette", "topics": [ "palette_diverging" ] }, { "page": "palette_pastel", "title": "Pastel Palette", "topics": [ "palette_pastel" ] }, { "page": "palette_rainbow", "title": "Rainbow Palette", "topics": [ "palette_rainbow" ] }, { "page": "palette_reds", "title": "Reds Palette", "topics": [ "palette_reds" ] }, { "page": "palette_viridis", "title": "Viridis Palette", "topics": [ "palette_viridis" ] }, { "page": "palettes", "title": "Color Palettes", "topics": [ "palettes" ] }, { "page": "panel_layout", "title": "Configure a custom multi-panel layout", "topics": [ "panel_layout" ] }, { "page": "plot_alluvial", "title": "Plot Alluvial Diagram", "topics": [ "plot_alluvial" ] }, { "page": "plot_centrality", "title": "Plot Centrality", "topics": [ "plot_centrality" ] }, { "page": "plot_centrality_compare", "title": "Plot Centrality Comparison", "topics": [ "plot_centrality_compare" ] }, { "page": "plot_centrality_distribution", "title": "Plot Centrality Distribution", "topics": [ "plot_centrality_distribution" ] }, { "page": "plot_centrality_heatmap", "title": "Plot Centrality Heatmap", "topics": [ "plot_centrality_heatmap" ] }, { "page": "plot_chord", "title": "Chord Diagram", "topics": [ "plot_chord" ] }, { "page": "plot_compare", "title": "Plot Network Difference", "topics": [ "plot_compare" ] }, { "page": "plot_comparison_heatmap", "title": "Plot Comparison Heatmap", "topics": [ "plot_comparison_heatmap" ] }, { "page": "plot_degree_correlation", "title": "Plot Degree-Degree Correlation", "topics": [ "plot_degree_correlation" ] }, { "page": "plot_edge_diff_forest", "title": "Forest Plot for Bootstrap Edge Differences", "topics": [ "plot_edge_diff_forest", "plot_edge_diff_forest.boot_glasso" ] }, { "page": "plot_edge_weights", "title": "Plot Edge Weight Distribution", "topics": [ "plot_edge_weights" ] }, { "page": "plot_heatmap", "title": "Plot Network as Heatmap", "topics": [ "plot_heatmap" ] }, { "page": "plot_htna", "title": "Plot Heterogeneous TNA Network (Multi-Group Layout)", "topics": [ "htna", "plot_htna" ] }, { "page": "plot_mcml", "title": "Plot Multi-Cluster Multi-Layer Network", "topics": [ "plot_mcml" ] }, { "page": "plot_mixed_network", "title": "Plot Mixed Network", "topics": [ "plot_mixed_network" ] }, { "page": "plot_ml_heatmap", "title": "Multilayer Network Heatmap", "topics": [ "plot_ml_heatmap" ] }, { "page": "plot_mlna", "title": "Multilevel Network Visualization", "topics": [ "mlna", "plot_mlna" ] }, { "page": "plot_motifs", "title": "Plot a motif/subgraph result", "topics": [ "plot_motifs" ] }, { "page": "plot_mtna", "title": "Multi-Cluster TNA Network Plot", "topics": [ "mtna", "plot_mtna" ] }, { "page": "plot_net_bootstrap_group", "title": "Plot a Group Bootstrap Result", "topics": [ "plot.net_bootstrap_group", "plot_net_bootstrap_group" ] }, { "page": "plot_net_stability", "title": "Plot Centrality Stability Results", "topics": [ "plot.net_stability", "plot_net_stability" ] }, { "page": "plot_netobject_group", "title": "Plot a Group of Nestimate netobjects", "topics": [ "plot.netobject_group", "plot_netobject_group" ] }, { "page": "plot_netobject_ml", "title": "Plot a Multilevel Nestimate netobject", "topics": [ "plot.netobject_ml", "plot_netobject_ml" ] }, { "page": "plot_network_evolution", "title": "Plot Network Evolution (Small Multiples)", "topics": [ "plot_network_evolution" ] }, { "page": "plot_robustness", "title": "Plot Network Robustness", "topics": [ "plot_robustness" ] }, { "page": "plot_simplicial", "title": "Simplicial Complex Visualization", "topics": [ "plot_simplicial" ] }, { "page": "plot_temporal", "title": "Temporal Network Prism (3D Glass Box)", "topics": [ "plot_temporal" ] }, { "page": "plot_tna", "title": "TNA-Style Network Plot (qgraph Compatible)", "topics": [ "plot_tna", "tplot" ] }, { "page": "plot_trajectories", "title": "Plot Individual Trajectories", "topics": [ "plot_trajectories" ] }, { "page": "plot_transitions", "title": "Plot Transitions Between States", "topics": [ "plot_transitions" ] }, { "page": "plot.cograph_cluster_significance", "title": "Plot Cluster Significance", "topics": [ "plot.cograph_cluster_significance" ] }, { "page": "plot.cograph_communities", "title": "Plot Community Structure", "topics": [ "plot.cograph_communities" ] }, { "page": "plot.cograph_core_periphery", "title": "Plot Core-Periphery Structure", "topics": [ "plot.cograph_core_periphery" ] }, { "page": "plot.cograph_degree_fit", "title": "Plot method for cograph_degree_fit", "topics": [ "plot.cograph_degree_fit" ] }, { "page": "plot.cograph_motif_analysis", "title": "Plot Motif Analysis Results", "concept": [ "motifs" ], "topics": [ "plot.cograph_motif_analysis" ] }, { "page": "plot.cograph_motifs", "title": "Plot Network Motifs", "concept": [ "motifs" ], "topics": [ "plot.cograph_motifs" ] }, { "page": "plot.cograph_network", "title": "Plot cograph_network Object", "topics": [ "plot.cograph_network" ] }, { "page": "plot.cograph_rich_club", "title": "Plot Rich Club Results", "topics": [ "plot.cograph_rich_club" ] }, { "page": "plot.cograph_vulnerability", "title": "Plot Node Vulnerability", "topics": [ "plot.cograph_vulnerability" ] }, { "page": "splot.tna_bootstrap", "title": "Plot Bootstrap Results", "topics": [ "plot.tna_bootstrap", "splot.tna_bootstrap" ] }, { "page": "plot.tna_disparity", "title": "Plot Disparity Filter Result", "topics": [ "plot.tna_disparity" ] }, { "page": "print.cograph_communities", "title": "Print Community Structure", "topics": [ "print.cograph_communities" ] }, { "page": "print.cograph_degree_fit", "title": "Print method for cograph_degree_fit", "topics": [ "print.cograph_degree_fit" ] }, { "page": "print.cograph_network", "title": "Print cograph_network Object", "topics": [ "print.cograph_network" ] }, { "page": "project_bipartite", "title": "Project Bipartite Network to One-Mode", "topics": [ "project_bipartite" ] }, { "page": "reaching_global", "title": "Global Reaching Centrality (Mones, Vicsek & Vicsek 2012)", "topics": [ "reaching_global" ] }, { "page": "register_layout", "title": "Register a Custom Layout", "topics": [ "register_layout" ] }, { "page": "register_shape", "title": "Register a Custom Shape", "topics": [ "register_shape" ] }, { "page": "register_svg_shape", "title": "Register Custom SVG Shape", "topics": [ "register_svg_shape" ] }, { "page": "register_theme", "title": "Register a Custom Theme", "topics": [ "register_theme" ] }, { "page": "render-ggplot", "title": "ggplot2 Conversion", "topics": [ "render-ggplot" ] }, { "page": "render-grid", "title": "Grid Rendering", "topics": [ "render-grid" ] }, { "page": "rich_club", "title": "Rich Club Coefficient", "topics": [ "rich_club" ] }, { "page": "rich_club_local", "title": "Local Rich Club Score", "topics": [ "rich_club_local" ] }, { "page": "robustness", "title": "Network Robustness Analysis", "topics": [ "robustness" ] }, { "page": "robustness_auc", "title": "Calculate Area Under Robustness Curve (AUC)", "topics": [ "robustness_auc" ] }, { "page": "robustness_summary", "title": "Summary of Robustness Analysis", "topics": [ "robustness_summary" ] }, { "page": "select_bridges", "title": "Select Bridge Edges", "topics": [ "select_bridges" ] }, { "page": "select_component", "title": "Select Connected Component", "topics": [ "select_component" ] }, { "page": "select_edges", "title": "Select Edges with Lazy Computation", "topics": [ "select_edges" ] }, { "page": "select_edges_between", "title": "Select Edges Between Node Sets", "topics": [ "select_edges_between" ] }, { "page": "select_edges_involving", "title": "Select Edges Involving Nodes", "topics": [ "select_edges_involving" ] }, { "page": "select_neighbors", "title": "Select Node Neighbors (Ego Network)", "topics": [ "select_neighbors" ] }, { "page": "select_nodes", "title": "Select Nodes with Lazy Centrality Computation", "topics": [ "select_nodes" ] }, { "page": "select_top", "title": "Select Top N Nodes by Centrality", "topics": [ "select_top" ] }, { "page": "select_top_edges", "title": "Select Top N Edges", "topics": [ "select_top_edges" ] }, { "page": "set_edges", "title": "Set Edges in Cograph Network", "topics": [ "set_edges" ] }, { "page": "set_groups", "title": "Set Node Groups", "topics": [ "set_groups" ] }, { "page": "set_layout", "title": "Set Layout in Cograph Network", "topics": [ "set_layout" ] }, { "page": "set_nodes", "title": "Set Nodes in Cograph Network", "topics": [ "set_nodes" ] }, { "page": "shortest_paths", "title": "Compute Shortest Path Distances", "topics": [ "shortest_paths" ] }, { "page": "simmelian_strength", "title": "Simmelian Strength (Triangle Count per Edge)", "topics": [ "simmelian_strength" ] }, { "page": "simplify", "title": "Simplify a Network", "topics": [ "simplify", "simplify.cograph_network", "simplify.default", "simplify.igraph", "simplify.matrix", "simplify.tna" ] }, { "page": "sn_edges", "title": "Set Edge Aesthetics", "topics": [ "sn_edges" ] }, { "page": "sn_ggplot", "title": "Convert Network to ggplot2", "topics": [ "sn_ggplot" ] }, { "page": "sn_layout", "title": "Apply Layout to Network", "topics": [ "sn_layout" ] }, { "page": "sn_nodes", "title": "Set Node Aesthetics", "topics": [ "sn_nodes" ] }, { "page": "sn_palette", "title": "Apply Color Palette to Network", "topics": [ "sn_palette" ] }, { "page": "sn_save", "title": "Save Network Visualization", "topics": [ "sn_save" ] }, { "page": "sn_save_ggplot", "title": "Save as ggplot2", "topics": [ "sn_save_ggplot" ] }, { "page": "sn_theme", "title": "Apply Theme to Network", "topics": [ "sn_theme" ] }, { "page": "soplot", "title": "Plot Cograph Network", "topics": [ "sn_render", "soplot" ] }, { "page": "plot_group_permutation", "title": "Plot Group Permutation Test Results", "topics": [ "plot_group_permutation", "splot.group_tna_permutation" ] }, { "page": "splot", "title": "Plot Nestimate Bootstrap Results", "topics": [ "splot", "splot.boot_glasso", "splot.cograph_communities", "splot.netobject", "splot.net_bootstrap", "splot.net_mlvar", "splot.net_permutation", "splot.tna_communities", "splot.wtna_mixed" ] }, { "page": "splot.tna_disparity", "title": "Plot Disparity Results with splot", "topics": [ "splot.tna_disparity" ] }, { "page": "plot_permutation", "title": "Plot Permutation Test Results", "topics": [ "plot_permutation", "splot.tna_permutation" ] }, { "page": "student_interactions", "title": "Student Interaction Edge List", "topics": [ "student_interactions" ] }, { "page": "subgraphs", "title": "Extract Specific Motif Instances (Subgraphs)", "concept": [ "motifs" ], "topics": [ "subgraphs" ] }, { "page": "summarize_network", "title": "Summarize Network by Clusters", "topics": [ "cnet", "summarize_network" ] }, { "page": "summary.cograph_network", "title": "Summary of cograph_network Object", "topics": [ "summary.cograph_network" ] }, { "page": "supra_adjacency", "title": "Supra-Adjacency Matrix", "topics": [ "supra", "supra_adjacency" ] }, { "page": "supra_interlayer", "title": "Extract Inter-Layer Block", "topics": [ "extract_interlayer", "supra_interlayer" ] }, { "page": "supra_layer", "title": "Extract Layer from Supra-Adjacency Matrix", "topics": [ "extract_layer", "supra_layer" ] }, { "page": "theme_cograph_classic", "title": "Classic Theme", "topics": [ "theme_cograph_classic" ] }, { "page": "theme_cograph_colorblind", "title": "Colorblind-friendly Theme", "topics": [ "theme_cograph_colorblind" ] }, { "page": "theme_cograph_dark", "title": "Dark Theme", "topics": [ "theme_cograph_dark" ] }, { "page": "theme_cograph_gray", "title": "Grayscale Theme", "topics": [ "theme_cograph_gray" ] }, { "page": "theme_cograph_minimal", "title": 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