Analysis and Visualization of Complex Networks
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Documentation for package ‘cograph’ version 2.1.1
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A B C D E F G H I K L M N O P R S T U V W
-- A --
| abbrev_label | Abbreviate Labels |
| aggregate_layers | Aggregate Layers |
| aggregate_weights | Aggregate Edge Weights |
| ai_coding | Human-AI Interaction Coding Sequences |
| ai_detailed | Human-AI Interaction Coding Sequences |
| assortativity | Degree Assortativity Coefficient |
| assortativity_attribute | Attribute Assortativity (Homophily) |
| as_cograph | Convert to Cograph Network |
| as_mcml | Convert to mcml |
| as_mcml.cluster_summary | Convert to mcml |
| as_mcml.default | Convert to mcml |
| as_mcml.group_tna | Convert to mcml |
| as_mcml.mcml | Convert to mcml |
| as_tna | Convert cluster_summary to tna Objects |
| as_tna.cluster_summary | Convert cluster_summary to tna Objects |
| as_tna.default | Convert cluster_summary to tna Objects |
| as_tna.mcml | Convert cluster_summary to tna Objects |
-- B --
| build_mcml | Build MCML from Raw Transition Data |
-- C --
| 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_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_hub | HITS Authority and Hub Scores |
| centrality_hubbell | Hubbell Centrality |
| centrality_incloseness | Closeness Centrality |
| centrality_indegree | Degree Centrality |
| centrality_ineccentricity | Eccentricity |
| centrality_information | Information Centrality (Stephenson-Zelen) |
| centrality_inharmonic | Harmonic Centrality |
| centrality_instrength | Strength Centrality (Weighted Degree) |
| 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_outcloseness | Closeness Centrality |
| centrality_outdegree | Degree Centrality |
| centrality_outeccentricity | Eccentricity |
| centrality_outharmonic | Harmonic Centrality |
| centrality_outstrength | Strength Centrality (Weighted Degree) |
| 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 |
| cluster_network | Summarize Network by Clusters |
| cluster_quality | Cluster Quality Metrics |
| cluster_significance | Test Significance of Community Structure |
| cluster_summary | Cluster Summary Statistics |
| cnet | Summarize Network by Clusters |
| coding | Human-AI Interaction Coding Sequences |
| coding_detailed | Human-AI Interaction Coding Sequences |
| cograph | Create a Network Visualization |
| CographLayout | CographLayout R6 Class |
| CographNetwork | CographNetwork R6 Class |
| 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 |
| com_consensus | Consensus Community Detection |
| com_eb | Edge Betweenness Community Detection |
| com_fg | Fast Greedy Community Detection |
| com_fl | Fluid Communities Detection |
| com_im | Infomap Community Detection |
| com_ld | Leiden Community Detection |
| com_le | Leading Eigenvector Community Detection |
| com_lp | Label Propagation Community Detection |
| com_lv | Louvain Community Detection |
| com_op | Optimal Community Detection |
| com_sg | Spinglass Community Detection |
| com_wt | Walktrap Community Detection |
| core_periphery | Detect Core-Periphery Structure |
| cqual | Cluster Quality Metrics |
| csig | Test Significance of Community Structure |
| csum | Cluster Summary Statistics |
-- D --
| degree_distribution | Degree Distribution Visualization |
| detect_communities | Detect Communities in a Network |
| disparity_filter | Disparity Filter |
| disparity_filter.cograph_network | Disparity Filter |
| disparity_filter.default | Disparity Filter |
| disparity_filter.igraph | Disparity Filter |
| disparity_filter.matrix | Disparity Filter |
| disparity_filter.tna | Disparity Filter |
| dispersion | Dispersion (Backstrom-Kleinberg 2014) |
-- E --
| edge_betweenness | Calculate Edge Centrality Measures |
| edge_centrality | Calculate Edge Centrality Measures |
| edge_reciprocity | Edge Reciprocity |
| estrada_index | Estrada Index |
| extract_interlayer | Extract Inter-Layer Block |
| extract_layer | Extract Layer from Supra-Adjacency Matrix |
-- F --
| filter_edges | Filter Edges by Metadata |
| filter_nodes | Filter Nodes by Metadata or Centrality |
| fit_degree_distribution | Fit Statistical Distributions to Degree Sequence |
| from_qgraph | Convert a qgraph object to cograph parameters |
| from_tna | Convert a tna object to cograph parameters |
-- G --
| get_data | Get Original Data from Cograph Network |
| get_edges | Get Edges from Cograph Network |
| get_edge_list | Extract Raw Edge List from TNA Model |
| 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_nodes | Get Nodes from Cograph Network |
| get_shape | Get a Registered Shape |
| get_source | Get Source Type from Cograph Network |
| get_theme | Get a Registered Theme |
| ggplot_robustness | Compare Network Robustness (ggplot2) |
| group_centrality | Group Centrality (Everett-Borgatti 1999) |
-- H --
| hai_datasets | Human-AI Interaction Coding Sequences |
| homophily | Attribute Assortativity (Homophily) |
| htna | Plot Heterogeneous TNA Network (Multi-Group Layout) |
| human_ai | Human-AI Interaction Coding Sequences |
| human_ai_detailed | Human-AI Interaction Coding Sequences |
-- I --
| is_bipartite | Check if a Matrix Could Be Bipartite |
| is_directed | Check if Network is Directed |
| is_tna_network | Check if Network is TNA-based |
-- K --
| k_shortest_paths | Find K Shortest Loopless Paths (Yen's Algorithm) |
-- L --
| label_abbrev | Abbreviate Labels |
| lagg | Aggregate Layers |
| layer_degree_correlation | Degree Correlation Between Layers |
| layer_similarity | Layer Similarity |
| layer_similarity_matrix | Pairwise Layer Similarities |
| layout_circle | Circular Layout |
| layout_groups | Group-based Layout |
| layout_oval | Oval Layout |
| layout_spring | Fruchterman-Reingold Spring Layout |
| ldegcor | Degree Correlation Between Layers |
| 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 |
| lsim | Layer Similarity |
| lsim_matrix | Pairwise Layer Similarities |
-- M --
| membership | Get Community Membership |
| mlna | Multilevel Network Visualization |
| motifs | Network Motif Analysis |
| mtna | Multi-Cluster TNA Network Plot |
-- N --
| 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 |
| nodes | Get Nodes from Cograph Network (Deprecated) |
| n_communities | Get Number of Communities |
| n_edges | Get Number of Edges |
| n_nodes | Get Number of Nodes |
-- O --
| overlay_communities | Overlay Community Blobs on a Network Plot |
-- P --
| palettes | Color Palettes |
| 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 |
| palette_viridis | Viridis Palette |
| 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_motifs | Plot Network Motifs |
| plot.cograph_motif_analysis | Plot Motif Analysis Results |
| plot.cograph_motif_result | Network Motif Analysis |
| plot.cograph_network | Plot cograph_network Object |
| plot.cograph_rich_club | Plot Rich Club Results |
| plot.cograph_vulnerability | Plot Node Vulnerability |
| plot.netobject_group | Plot a Group of Nestimate netobjects |
| plot.netobject_ml | Plot a Multilevel Nestimate netobject |
| plot.net_bootstrap_group | Plot a Group Bootstrap Result |
| plot.net_stability | Plot Centrality Stability Results |
| plot.tna_bootstrap | Plot Bootstrap Results |
| plot.tna_disparity | Plot Disparity Filter Result |
| plot_alluvial | Plot Alluvial Diagram |
| plot_centrality_distribution | Plot Centrality Distribution |
| plot_chord | Chord Diagram |
| plot_compare | Plot Network Difference |
| 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_diff_forest.boot_glasso | 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_htna | Plot Heterogeneous TNA Network (Multi-Group Layout) |
| plot_mcml | Plot Multi-Cluster Multi-Layer Network |
| plot_mixed_network | Plot Mixed Network |
| plot_mlna | Multilevel Network Visualization |
| plot_ml_heatmap | Multilayer Network Heatmap |
| plot_mtna | Multi-Cluster TNA Network Plot |
| plot_netobject_group | Plot a Group of Nestimate netobjects |
| plot_netobject_ml | Plot a Multilevel Nestimate netobject |
| plot_network_evolution | Plot Network Evolution (Small Multiples) |
| plot_net_bootstrap_group | Plot a Group Bootstrap Result |
| plot_net_stability | Plot Centrality Stability Results |
| plot_permutation | Plot Permutation Test Results |
| 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_trajectories | Plot Individual Trajectories |
| plot_transitions | Plot Transitions Between States |
| print.cograph_communities | Print Community Structure |
| print.cograph_degree_fit | Print method for cograph_degree_fit |
| print.cograph_motif_result | Network Motif Analysis |
| print.cograph_network | Print cograph_network Object |
| project_bipartite | Project Bipartite Network to One-Mode |
-- R --
| reaching_global | Global Reaching Centrality (Mones, Vicsek & Vicsek 2012) |
| 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 |
| render-ggplot | ggplot2 Conversion |
| render-grid | Grid Rendering |
| 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_summary | Summary of Robustness Analysis |
-- S --
| 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 |
| shortest_paths | Compute Shortest Path Distances |
| simmelian_strength | Simmelian Strength (Triangle Count per Edge) |
| simplify | Simplify a Network |
| simplify.cograph_network | Simplify a Network |
| simplify.default | Simplify a Network |
| simplify.igraph | Simplify a Network |
| simplify.matrix | Simplify a Network |
| simplify.tna | 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_render | Plot Cograph Network |
| sn_save | Save Network Visualization |
| sn_save_ggplot | Save as ggplot2 |
| sn_theme | Apply Theme to Network |
| soplot | Plot Cograph Network |
| splot | Plot Nestimate Bootstrap Results |
| splot.boot_glasso | Plot Nestimate Bootstrap Results |
| splot.cograph_communities | Plot Nestimate Bootstrap Results |
| splot.group_tna_permutation | Plot Group Permutation Test Results |
| splot.netobject | Plot Nestimate Bootstrap Results |
| splot.net_bootstrap | Plot Nestimate Bootstrap Results |
| splot.net_mlvar | Plot Nestimate Bootstrap Results |
| splot.net_permutation | Plot Nestimate Bootstrap Results |
| splot.tna_bootstrap | Plot Bootstrap Results |
| splot.tna_communities | Plot Nestimate Bootstrap Results |
| splot.tna_disparity | Plot Disparity Results with splot |
| splot.tna_permutation | Plot Permutation Test Results |
| splot.wtna_mixed | Plot Nestimate Bootstrap Results |
| student_interactions | Student Interaction Edge List |
| subgraphs | Extract Specific Motif Instances (Subgraphs) |
| subset_edges | Filter Edges by Metadata |
| subset_nodes | Filter Nodes by Metadata or Centrality |
| summarize_network | Summarize Network by Clusters |
| summary.cograph_network | Summary of cograph_network Object |
| supra | Supra-Adjacency Matrix |
| supra_adjacency | Supra-Adjacency Matrix |
| supra_interlayer | Extract Inter-Layer Block |
| supra_layer | Extract Layer from Supra-Adjacency Matrix |
-- T --
| themes-builtin | Built-in Themes |
| 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 |
| to_cograph | Convert to Cograph Network |
| to_data_frame | Export Network as Edge List Data Frame |
| to_df | 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 |
| tplot | TNA-Style Network Plot (qgraph Compatible) |
| trophic_incoherence | Trophic Incoherence Parameter |
-- U --
| unregister_svg_shape | Unregister SVG Shape |
-- V --
| verify_igraph | Verify Against igraph |
| verify_with_igraph | Verify Against igraph |
| vulnerability | Node Vulnerability |
-- W --
| wagg | Aggregate Edge Weights |