# Analysis and Visualization of Complex Networks

## Documentation for package ‘cograph’ version 2.3.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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
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_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_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_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
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.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 | 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
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_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_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