Analysis and Visualization of Complex Networks
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Documentation for package ‘cograph’ version 2.7.2
Help Pages
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 |
| add_edges | Add Edges to a Network |
| add_nodes | Add Nodes to a Network |
| aggregate_layers | Aggregate Layers |
| aggregate_weights | Aggregate Edge Weights |
| ai_coding | Human-AI Interaction Coding Sequences |
| ai_detailed | Human-AI Interaction Coding Sequences |
| as.data.frame.cograph_motif_result | Motif Results as a Data Frame |
| as.data.frame.cograph_network | Cograph Network as a Data Frame |
| 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 --
| binarize | Binarize Edge Weights |
| bind_networks | Combine Two Networks |
-- C --
| centrality | Calculate Network Centrality Measures |
| centrality_access_information | Access and Hide Information |
| centrality_adaptive_leaderrank | Adaptive LeaderRank centrality |
| centrality_alpha | Alpha (Katz) Centrality |
| centrality_authority | HITS Authority and Hub Scores |
| centrality_average_distance | Average Distance Centrality |
| centrality_barycenter | Barycenter Centrality |
| centrality_beta_measure | BG-index or beta power measure |
| centrality_betweenness | Betweenness Centrality |
| centrality_bottleneck | Bottleneck Centrality |
| centrality_bridging | Bridging Centrality |
| centrality_bridging_capital | Bridging capital from lost information walks |
| centrality_bridging_coefficient | Truss, mixed-degree decomposition and local social-capital measures |
| 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_cda | Clustering degree algorithm centrality |
| centrality_centroid | Centroid Value |
| centrality_closeness | Closeness Centrality |
| centrality_closeness_vitality | Closeness Vitality |
| centrality_clusterrank | ClusterRank Centrality |
| centrality_coleman_theil | Coleman-Theil hierarchy index |
| centrality_communicability | Communicability Centrality |
| centrality_communicability_betweenness | Communicability Betweenness Centrality |
| centrality_community_based | Community-Based Centrality, Comm Centrality and Community-Based Mediator |
| centrality_community_hub_bridge | Community Hub-Bridge Centrality |
| centrality_community_mediator | Community-Based Centrality, Comm Centrality and Community-Based Mediator |
| centrality_comm_centrality | Community-Based Centrality, Comm Centrality and Community-Based Mediator |
| centrality_constraint | Burt's Constraint |
| centrality_controlrank | ControlRank centrality |
| 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_degree_discount | DegreeDiscountIC and SingleDiscount Rankings |
| centrality_delta_betweenness | Betweenness and closeness variants that carry a tuning parameter |
| centrality_delta_closeness | Betweenness and closeness variants that carry a tuning parameter |
| centrality_diffusion | Diffusion Centrality |
| centrality_diffusion_centrality | Finite-horizon diffusion centrality |
| centrality_dil | Degree and Importance of Lines |
| centrality_distance_entropy | Distance Entropy |
| centrality_diversity | Diversity Centrality |
| centrality_dkgm | DK-based gravity model |
| centrality_dmnc | Density of Maximum Neighborhood Component (DMNC) |
| centrality_dynamical_importance | Dynamical importance by exact vertex deletion |
| centrality_dynamics_sensitive | Dynamics-sensitive centrality |
| centrality_eccentricity | Eccentricity |
| centrality_effective_size | Effective Size (Burt's) |
| centrality_ego_betweenness | Betweenness and closeness variants that carry a tuning parameter |
| centrality_ehcc | Extended hybrid characteristic centrality |
| centrality_eigenvector | Eigenvector Centrality |
| centrality_enrenew | WVoteRank, EnRenew and VoteRank++ |
| centrality_entropy | Entropy Centrality |
| centrality_entropy_variation | Entropy Variation |
| centrality_epc | Local efficiency, s-core, fragmentation, k-path census and EPC |
| centrality_exogenous | Exogenous centrality |
| centrality_expected | Expected Centrality |
| centrality_expected_force | Expected Force centrality |
| centrality_expected_influence_1 | Expected Influence (one-step) |
| centrality_expected_influence_2 | Expected Influence (two-step) |
| centrality_extended_coreness | Extended neighborhood coreness |
| centrality_extended_gravity | Extended gravity centrality |
| centrality_extended_local_bridging | Extended local bridging centrality |
| centrality_extended_mixed_gravity | Extended mixed gravitational centrality |
| centrality_flow_betweenness | Flow Betweenness Centrality |
| centrality_flow_coefficient | Heatmap, Flow Coefficient, Local Entropy, Weighted h-index, Redundancy |
| centrality_fragmentation | Local efficiency, s-core, fragmentation, k-path census and EPC |
| centrality_fuzzy_local_dimension | Fixed-Radius, Fuzzy and Volume Local Dimensions |
| centrality_gateway | Gateway Coefficient |
| centrality_generalized_closeness | Generalized Closeness Centrality |
| centrality_geodesic_kpath | Weighted k-shell, Renewed Coreness and Geodesic k-path |
| centrality_gilschmidt | Gil-Schmidt Power Index |
| centrality_global_structure | Global structure model centrality |
| centrality_godfather | Truss, mixed-degree decomposition and local social-capital measures |
| centrality_graph_regularization | Graph regularization centrality |
| centrality_gravity | Gravity centrality |
| centrality_harary | Harary Centrality |
| centrality_harmonic | Harmonic Centrality |
| centrality_hcc | Hybrid characteristic centrality |
| centrality_heatmap | Heatmap, Flow Coefficient, Local Entropy, Weighted h-index, Redundancy |
| centrality_hide_information | Access and Hide Information |
| centrality_hub | HITS Authority and Hub Scores |
| centrality_hubbell | Hubbell Centrality |
| centrality_hybrid_global_structure | Hybrid global structure model centrality |
| centrality_iec | Immediate Effects Centrality |
| centrality_iira | Improved iterative resource allocation (IIRA) |
| centrality_improved_closeness | Improved closeness centrality |
| centrality_improved_global_structure | Improved global structure model 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_ira | Iterative resource allocation (IRA) |
| centrality_katz | Katz Centrality |
| centrality_ked | KED method centrality |
| centrality_kpath | Local efficiency, s-core, fragmentation, k-path census and EPC |
| centrality_kreach | Geodesic K-Path Centrality |
| centrality_lac | Local Average Connectivity (LAC) |
| centrality_laplacian | Laplacian Centrality |
| centrality_leaderrank | LeaderRank Centrality |
| centrality_length_scaled_betweenness | Betweenness and closeness variants that carry a tuning parameter |
| centrality_leverage | Leverage Centrality |
| centrality_lhc | Lhc Index |
| centrality_lin | Lin Centrality |
| centrality_linerank | LineRank centrality |
| centrality_lnc | Local neighbor contribution centrality |
| centrality_load | Load Centrality |
| centrality_lobby | Lobby Index (H-Index of Neighborhood) |
| centrality_localized_bridging | Localized bridging centrality from ego betweenness |
| centrality_local_bridging | Local Bridging Centrality |
| centrality_local_dimension | Local Dimension |
| centrality_local_dimension_fixed | Fixed-Radius, Fuzzy and Volume Local Dimensions |
| centrality_local_efficiency | Local efficiency, s-core, fragmentation, k-path census and EPC |
| centrality_local_entropy | Heatmap, Flow Coefficient, Local Entropy, Weighted h-index, Redundancy |
| centrality_local_information_dimension | Local Information Dimensionality |
| centrality_local_volume_dimension | Fixed-Radius, Fuzzy and Volume Local Dimensions |
| centrality_malatya | Malatya centrality |
| centrality_map_equation | Map equation centrality with explicit coding and flow conventions |
| centrality_markov | Markov Centrality |
| centrality_mcc | Maximal clique centrality |
| centrality_mcgm | Multi-characteristics gravity model |
| centrality_mdd | Truss, mixed-degree decomposition and local social-capital measures |
| centrality_mixed_gravity | Mixed gravitational centrality |
| centrality_mnc | Maximum Neighborhood Component (MNC) |
| centrality_modified_expected_force | Modified Expected Force centrality |
| centrality_modularity_vitality | Modularity Vitality |
| centrality_ncvoterank | NCVoteRank |
| centrality_neighborhood_connectivity | Neighborhood Connectivity |
| centrality_neighbor_distance | Neighborhood centrality, and its neighbor distance special case |
| centrality_ninl | Node and Neighbor Layer Information centrality |
| centrality_node_contraction | Node Contraction Centrality (IMC and IIMC) |
| centrality_node_contraction_improved | Node Contraction Centrality (IMC and IIMC) |
| 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_proximal_betweenness | Proximal betweenness centrality |
| centrality_radiality | Radiality Centrality |
| centrality_random_walk | Random Walk Centrality |
| centrality_random_walk_decay | Random walk decay centrality |
| centrality_reaching_local | Local Reaching Centrality (Mones, Vicsek & Vicsek 2012) |
| centrality_redundancy | Heatmap, Flow Coefficient, Local Entropy, Weighted h-index, Redundancy |
| centrality_relative_entropy | Relative-Entropy Integrated Evaluation |
| centrality_renewed_coreness | Weighted k-shell, Renewed Coreness and Geodesic k-path |
| centrality_residual_closeness | Residual Closeness Centrality |
| centrality_resistance_curvature | Node resistance curvature |
| centrality_rsp_betweenness | Randomized Shortest Paths Betweenness Centrality |
| centrality_rumor | Rumor Centrality |
| centrality_salsa | SALSA Authority Centrality |
| centrality_semilocal | Semi-Local Centrality |
| centrality_shapley_game1 | Shapley Value Centrality (Games 1, 2 and 3) |
| centrality_shapley_game2 | Shapley Value Centrality (Games 1, 2 and 3) |
| centrality_shapley_game3 | Shapley Value Centrality (Games 1, 2 and 3) |
| centrality_single_discount | DegreeDiscountIC and SingleDiscount Rankings |
| centrality_spectralrank | SpectralRank with optional diagonal prior information |
| centrality_strength | Strength Centrality (Weighted Degree) |
| centrality_stress | Stress Centrality |
| centrality_subgraph | Subgraph Centrality |
| centrality_support | Truss, mixed-degree decomposition and local social-capital measures |
| centrality_s_core | Local efficiency, s-core, fragmentation, k-path census and EPC |
| centrality_s_shell | s-shell Index |
| centrality_topological_coefficient | Topological Coefficient |
| centrality_transitivity | Local Transitivity (Clustering Coefficient) |
| centrality_truss | Truss, mixed-degree decomposition and local social-capital measures |
| centrality_trust_pagerank | Trust-PageRank |
| centrality_two_way_rw | Two-Way Random Walk Betweenness |
| centrality_volume | Volume centrality |
| centrality_voterank | VoteRank Centrality |
| centrality_voterank_plus | WVoteRank, EnRenew and VoteRank++ |
| centrality_weighted_h_index | Heatmap, Flow Coefficient, Local Entropy, Weighted h-index, Redundancy |
| centrality_weighted_kshell | Weighted k-shell, Renewed Coreness and Geodesic k-path |
| centrality_weighted_leaderrank | Weighted LeaderRank centrality |
| centrality_wiener | Wiener Index Centrality |
| centrality_within_module_z | Within-Module Degree Z-Score |
| centrality_wvoterank | WVoteRank, EnRenew and VoteRank++ |
| centrality_x_degree | X-degree centrality |
| centralization | Centralization index |
| cluster_quality | Cluster Quality Metrics |
| cluster_significance | Test Significance of Community Structure |
| 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 |
| complement_network | Complement of a Network |
| 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 |
| contract_nodes | Contract Nodes into Groups |
| 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) |
| dyad_census | Dyad Census |
-- E --
| edge_betweenness | Calculate Edge Centrality Measures |
| edge_centrality | Calculate Edge Centrality Measures |
| edge_reciprocity | Edge Reciprocity |
| ego_networks | Ego-Network Metrics |
| estrada_index | Estrada Index |
| extract_interlayer | Extract Inter-Layer Block |
| extract_layer | Extract Layer from Supra-Adjacency Matrix |
| extract_motifs | Extract Motifs from Network Data |
| extract_triads | Extract Triads with Node Labels |
-- 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 --
| invert_weights | Invert Edge Weights (Similarity to Distance and Back) |
| 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_saqr | Saqr Layout (Start/End transition flow) |
| layout_spring | Fruchterman-Reingold Spring Layout |
| layout_target | Target Layout (focal-node, topological) |
| ldegcor | Degree Correlation Between Layers |
| list_centralities | Catalogue of the Centrality Measures |
| 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 |
| motif_census | Network Motif Analysis |
| mtna | Multi-Cluster TNA Network Plot |
| mutate_edges | Add or Change Edge Attributes |
| mutate_nodes | Add or Change Node Attributes |
-- 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 |
| network_wrangling | Network Wrangling Verbs |
| nodes | Get Nodes from Cograph Network (Deprecated) |
| normalize_weights | Normalize Edge Weights |
| 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 |
| panel_layout | Configure a custom multi-panel layout |
| 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.tna_bootstrap | Plot Bootstrap Results |
| plot.tna_disparity | Plot Disparity Filter Result |
| plot_alluvial | Plot Alluvial Diagram |
| plot_bootstrap_forest | Forest Plot for Bootstrap Network Results |
| plot_bootstrap_forest.boot_glasso | Forest Plot for Bootstrap Network Results |
| plot_bootstrap_forest.net_bootstrap | Forest Plot for Bootstrap Network Results |
| plot_bootstrap_forest.net_bootstrap_group | Forest Plot for Bootstrap Network Results |
| plot_bootstrap_forest.tna_bootstrap | 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_compare | Plot Network Difference (alias of plot_difference) |
| plot_comparison_heatmap | Plot Comparison Heatmap |
| plot_degree_correlation | Plot Degree-Degree Correlation |
| plot_difference | Plot Network Difference |
| 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_motifs | Plot a motif/subgraph result |
| 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_motifs | Network Motif Analysis |
| print.cograph_motif_analysis | Extract Motifs from Network Data |
| 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 |
| regulation_net | Learning Regulation Transition Network |
| remove_edges | Remove Edges from a Network |
| remove_isolates | Remove Isolated Nodes |
| remove_nodes | Remove Nodes from a Network |
| rename_nodes | Rename Nodes |
| render-ggplot | ggplot2 Conversion |
| render-grid | Grid Rendering |
| reorder_nodes | Reorder the Nodes of a Network |
| reverse_edges | Reverse Edge Direction |
| 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_k_core | Select the k-Core of a Network |
| 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 |
| spanning_tree | Minimum or Maximum Spanning Tree |
| split_components | Split a Network into Its Connected Components |
| 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_clusters | Build MCML from Raw Transition Data |
| 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 |
| symmetrize | Symmetrize a Directed Network |
-- 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 |
| threshold_edges | Threshold Edges by Weight, Count, Proportion or Density |
| 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_directed | Convert an Undirected Network to Directed |
| to_igraph | Convert Network to igraph Object |
| to_matrix | Convert Network to Adjacency Matrix |
| to_network | Convert Network to statnet network Object |
| to_undirected | Convert a Directed Network to Undirected |
| tplot | TNA-Style Network Plot (qgraph Compatible) |
| triad_census | Triad Census |
| 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 |