Package: cograph 2.3.10

cograph: Analysis and Visualization of Complex Networks

Provides tools for the analysis, visualization, and manipulation of dynamical, social (Saqr et al. (2024) <doi:10.1007/978-3-031-54464-4_10>) and complex networks (Saqr et al. (2025) <doi:10.1145/3706468.3706513>). The package supports multiple network formats and offers flexible tools for heterogeneous, multi-layer, and hierarchical network analysis with simple syntax and extensive toolset.

Authors:Mohammed Saqr [aut, cph], Sonsoles López-Pernas [aut, cre, cph]

cograph_2.3.10.tar.gz
cograph_2.3.10.zip(r-4.7)cograph_2.3.10.zip(r-4.6)cograph_2.3.10.zip(r-4.5)
cograph_2.3.10.tgz(r-4.6-any)cograph_2.3.10.tgz(r-4.5-any)
cograph_2.3.10.tar.gz(r-4.7-any)cograph_2.3.10.tar.gz(r-4.6-any)
cograph_2.3.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cograph/json (API)

# Install 'cograph' in R:

install.packages('cograph', repos = c('https://sonsoleslp.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sonsoleslp/cograph/issues

Pkgdown/docs site:https://sonsoles.me

Datasets:

ai_coding - Human-AI Interaction Coding Sequences
ai_detailed - Human-AI Interaction Coding Sequences
coding - Human-AI Interaction Coding Sequences
coding_detailed - Human-AI Interaction Coding Sequences
human_ai - Human-AI Interaction Coding Sequences
human_ai_detailed - Human-AI Interaction Coding Sequences
student_interactions - Student Interaction Edge List

On CRAN:

6.74 score 4 stars 1 packages 44 scripts 747 downloads 335 exports 19 dependencies

Last updated from:b3a33f6f47. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	253
source / vignettes	OK	344
linux-release-x86_64	OK	272
macos-release-arm64	OK	210
macos-oldrel-arm64	OK	143
windows-devel	OK	268
windows-release	OK	273
windows-oldrel	OK	284
wasm-release	OK	125

Exports:abbrev_label aggregate_layers aggregate_weights as_cograph as_mcml as_tna assortativity assortativity_attribute centrality centrality_alpha centrality_authority centrality_average_distance centrality_barycenter centrality_betweenness centrality_bottleneck centrality_bridging centrality_brokerage_coordinator centrality_brokerage_gatekeeper centrality_brokerage_itinerant centrality_brokerage_liaison centrality_brokerage_representative centrality_centroid centrality_closeness centrality_closeness_vitality centrality_clusterrank centrality_communicability centrality_communicability_betweenness centrality_constraint centrality_coreness centrality_cross_clique centrality_current_flow_betweenness centrality_current_flow_closeness centrality_dangalchev centrality_decay centrality_degree centrality_diffusion centrality_diversity centrality_dmnc centrality_eccentricity centrality_effective_size centrality_eigenvector centrality_entropy centrality_expected centrality_expected_influence_1 centrality_expected_influence_2 centrality_flow_betweenness centrality_gateway centrality_generalized_closeness centrality_gilschmidt centrality_harary centrality_harmonic centrality_hub centrality_hubbell centrality_incloseness centrality_indegree centrality_ineccentricity centrality_information centrality_inharmonic centrality_instrength centrality_integration centrality_katz centrality_kreach centrality_lac centrality_laplacian centrality_leaderrank centrality_leverage centrality_lin centrality_load centrality_lobby centrality_local_bridging centrality_markov centrality_mnc centrality_outcloseness centrality_outdegree centrality_outeccentricity centrality_outharmonic centrality_outstrength centrality_pagerank centrality_pairwisedis centrality_participation centrality_percolation centrality_power centrality_prestige_domain centrality_prestige_domain_proximity centrality_radiality centrality_random_walk centrality_reaching_local centrality_residual_closeness centrality_salsa centrality_semilocal centrality_strength centrality_stress centrality_subgraph centrality_topological_coefficient centrality_transitivity centrality_voterank centrality_wiener centrality_within_module_z centralization cluster_quality cluster_significance cnet cograph CographLayout CographNetwork CographTheme color_communities com_consensus com_eb com_fg com_fl com_im com_ld com_le com_lp com_lv com_op com_sg com_wt communities community_consensus community_edge_betweenness community_fast_greedy community_fluid community_infomap community_label_propagation community_leading_eigenvector community_leiden community_louvain community_optimal community_sizes community_spinglass community_walktrap compare_communities core_periphery cqual csig csum degree_distribution detect_communities disparity_filter dispersion edge_betweenness edge_centrality edge_reciprocity estrada_index extract_interlayer extract_layer extract_motifs extract_triads filter_edges filter_nodes fit_degree_distribution from_qgraph from_tna get_data get_edge_list get_edges get_groups get_labels get_layout get_meta get_nodes get_shape get_source get_theme ggplot_robustness group_centrality homophily htna is_bipartite is_directed is_tna_network k_shortest_paths label_abbrev lagg layer_degree_correlation layer_similarity layer_similarity_matrix layout_circle layout_groups layout_oval layout_spring ldegcor list_layouts list_palettes list_shapes list_svg_shapes list_themes lsim lsim_matrix mcml membership mlna motif_census motifs mtna n_communities n_edges n_nodes neighborhood_overlap network_bridges network_clique_size network_cut_vertices network_girth network_global_efficiency network_local_efficiency network_radius network_rich_club network_small_world network_summary network_vertex_connectivity nodes overlay_communities palette_blues palette_colorblind palette_diverging palette_pastel palette_rainbow palette_reds palette_viridis panel_layout plot_alluvial plot_bootstrap_forest plot_centrality plot_centrality_compare plot_centrality_distribution plot_centrality_heatmap plot_chord plot_compare plot_comparison_heatmap plot_degree_correlation plot_edge_diff_forest plot_edge_weights plot_group_permutation plot_heatmap plot_htna plot_mcml plot_mixed_network plot_ml_heatmap plot_mlna plot_motifs plot_mtna plot_net_bootstrap_group plot_net_stability plot_netobject_group plot_netobject_ml plot_network_evolution plot_permutation plot_robustness plot_simplicial plot_temporal plot_tna plot_trajectories plot_transitions project_bipartite reaching_global register_layout register_shape register_svg_shape register_theme rich_club rich_club_local robustness robustness_auc robustness_summary select_bridges select_component select_edges select_edges_between select_edges_involving select_neighbors select_nodes select_top select_top_edges set_edges set_groups set_layout set_nodes shortest_paths simmelian_strength simplify sn_edges sn_ggplot sn_layout sn_nodes sn_palette sn_render sn_save sn_save_ggplot sn_theme soplot splot splot.boot_glasso splot.cograph_communities splot.group_tna_permutation splot.net_bootstrap splot.net_mlvar splot.net_permutation splot.netobject splot.tna_bootstrap splot.tna_communities splot.tna_disparity splot.tna_permutation splot.wtna_mixed subgraphs subset_edges subset_nodes summarize_clusters summarize_network supra supra_adjacency supra_interlayer supra_layer theme_cograph_classic theme_cograph_colorblind theme_cograph_dark theme_cograph_gray theme_cograph_minimal theme_cograph_nature theme_cograph_viridis to_cograph to_data_frame to_df to_igraph to_matrix to_network tplot triad_census trophic_incoherence unregister_svg_shape verify_igraph verify_with_igraph vulnerability wagg

Dependencies:cli cpp11 farver ggplot2 glue gtable isoband labeling lattice lifecycle Matrix R6 RColorBrewer rlang S7 scales vctrs viridisLite withr

Introduction to cograph

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-06-11
Started: 2026-01-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Abbreviate Labels	abbrev_label label_abbrev
Aggregate Layers	aggregate_layers lagg
Aggregate Edge Weights	aggregate_weights wagg
Convert to Cograph Network	as_cograph to_cograph
Convert to mcml	as_mcml as_mcml.cluster_summary as_mcml.default as_mcml.group_tna as_mcml.mcml
Convert cluster_summary to tna Objects	as_tna as_tna.cluster_summary as_tna.default as_tna.mcml
Degree Assortativity Coefficient	assortativity
Attribute Assortativity (Homophily)	assortativity_attribute homophily
Calculate Network Centrality Measures	centrality
Alpha (Katz) Centrality	centrality_alpha
HITS Authority and Hub Scores	centrality_authority centrality_hub
Average Distance Centrality	centrality_average_distance
Barycenter Centrality	centrality_barycenter
Betweenness Centrality	centrality_betweenness
Bottleneck Centrality	centrality_bottleneck
Bridging Centrality	centrality_bridging
Gould-Fernandez Brokerage — Coordinator Role	centrality_brokerage_coordinator
Gould-Fernandez Brokerage — Gatekeeper Role	centrality_brokerage_gatekeeper
Gould-Fernandez Brokerage — Itinerant (Consultant) Role	centrality_brokerage_itinerant
Gould-Fernandez Brokerage — Liaison Role	centrality_brokerage_liaison
Gould-Fernandez Brokerage — Representative Role	centrality_brokerage_representative
Centroid Value	centrality_centroid
Closeness Centrality	centrality_closeness centrality_incloseness centrality_outcloseness
Closeness Vitality	centrality_closeness_vitality
ClusterRank Centrality	centrality_clusterrank
Communicability Centrality	centrality_communicability
Communicability Betweenness Centrality	centrality_communicability_betweenness
Burt's Constraint	centrality_constraint
K-Core Decomposition (Coreness)	centrality_coreness
Cross-Clique Connectivity	centrality_cross_clique
Current Flow Betweenness Centrality	centrality_current_flow_betweenness
Current Flow Closeness Centrality	centrality_current_flow_closeness
Dangalchev Closeness Centrality	centrality_dangalchev
Decay Centrality	centrality_decay
Degree Centrality	centrality_degree centrality_indegree centrality_outdegree
Diffusion Centrality	centrality_diffusion
Diversity Centrality	centrality_diversity
Density of Maximum Neighborhood Component (DMNC)	centrality_dmnc
Eccentricity	centrality_eccentricity centrality_ineccentricity centrality_outeccentricity
Effective Size (Burt's)	centrality_effective_size
Eigenvector Centrality	centrality_eigenvector
Entropy Centrality	centrality_entropy
Expected Centrality	centrality_expected
Expected Influence (one-step)	centrality_expected_influence_1
Expected Influence (two-step)	centrality_expected_influence_2
Flow Betweenness Centrality	centrality_flow_betweenness
Gateway Coefficient	centrality_gateway
Generalized Closeness Centrality	centrality_generalized_closeness
Gil-Schmidt Power Index	centrality_gilschmidt
Harary Centrality	centrality_harary
Harmonic Centrality	centrality_harmonic centrality_inharmonic centrality_outharmonic
Hubbell Centrality	centrality_hubbell
Information Centrality (Stephenson-Zelen)	centrality_information
Integration Centrality	centrality_integration
Katz Centrality	centrality_katz
Geodesic K-Path Centrality	centrality_kreach
Local Average Connectivity (LAC)	centrality_lac
Laplacian Centrality	centrality_laplacian
LeaderRank Centrality	centrality_leaderrank
Leverage Centrality	centrality_leverage
Lin Centrality	centrality_lin
Load Centrality	centrality_load
Lobby Index (H-Index of Neighborhood)	centrality_lobby
Local Bridging Centrality	centrality_local_bridging
Markov Centrality	centrality_markov
Maximum Neighborhood Component (MNC)	centrality_mnc
PageRank Centrality	centrality_pagerank
Pairwise Disconnectivity (Potapov et al. 2008)	centrality_pairwisedis
Participation Coefficient	centrality_participation
Percolation Centrality	centrality_percolation
Bonacich Power Centrality	centrality_power
Domain Prestige	centrality_prestige_domain
Domain Proximity Prestige	centrality_prestige_domain_proximity
Radiality Centrality	centrality_radiality
Random Walk Centrality	centrality_random_walk
Local Reaching Centrality (Mones, Vicsek & Vicsek 2012)	centrality_reaching_local
Residual Closeness Centrality	centrality_residual_closeness
SALSA Authority Centrality	centrality_salsa
Semi-Local Centrality	centrality_semilocal
Strength Centrality (Weighted Degree)	centrality_instrength centrality_outstrength centrality_strength
Stress Centrality	centrality_stress
Subgraph Centrality	centrality_subgraph
Topological Coefficient	centrality_topological_coefficient
Local Transitivity (Clustering Coefficient)	centrality_transitivity
VoteRank Centrality	centrality_voterank
Wiener Index Centrality	centrality_wiener
Within-Module Degree Z-Score	centrality_within_module_z
Centralization index	centralization
Cluster Quality Metrics	cluster_quality cqual
Test Significance of Community Structure	cluster_significance csig
Create a Network Visualization	cograph
CographLayout R6 Class	CographLayout
CographNetwork R6 Class	CographNetwork
CographTheme R6 Class	CographTheme
Color Nodes by Community	color_communities
Community Detection	communities
Consensus Community Detection	community_consensus com_consensus
Edge Betweenness Community Detection	community_edge_betweenness com_eb
Fast Greedy Community Detection	community_fast_greedy com_fg
Fluid Communities Detection	community_fluid com_fl
Infomap Community Detection	community_infomap com_im
Label Propagation Community Detection	community_label_propagation com_lp
Leading Eigenvector Community Detection	community_leading_eigenvector com_le
Leiden Community Detection	community_leiden com_ld
Louvain Community Detection	community_louvain com_lv
Optimal Community Detection	community_optimal com_op
Get Community Sizes	community_sizes
Spinglass Community Detection	community_spinglass com_sg
Walktrap Community Detection	community_walktrap com_wt
Compare Community Structures	compare_communities
Detect Core-Periphery Structure	core_periphery
Cluster Summary Statistics	csum
Degree Distribution Visualization	degree_distribution
Detect Communities in a Network	detect_communities
Disparity Filter	disparity_filter disparity_filter.cograph_network disparity_filter.default disparity_filter.igraph disparity_filter.matrix disparity_filter.tna
Dispersion (Backstrom-Kleinberg 2014)	dispersion
Calculate Edge Centrality Measures	edge_betweenness edge_centrality
Edge Reciprocity	edge_reciprocity
Estrada Index	estrada_index
Filter Edges by Metadata	filter_edges subset_edges
Filter Nodes by Metadata or Centrality	filter_nodes subset_nodes
Fit Statistical Distributions to Degree Sequence	fit_degree_distribution
Convert a qgraph object to cograph parameters	from_qgraph
Convert a tna object to cograph parameters	from_tna
Get Original Data from Cograph Network	get_data
Extract Raw Edge List from TNA Model	get_edge_list
Get Edges from Cograph Network	get_edges
Get Node Groups from Cograph Network	get_groups
Get Labels from Cograph Network	get_labels
Get a Registered Layout	get_layout
Get Metadata from Cograph Network	get_meta
Get Nodes from Cograph Network	get_nodes
Get a Registered Shape	get_shape
Get Source Type from Cograph Network	get_source
Get a Registered Theme	get_theme
Compare Network Robustness (ggplot2)	ggplot_robustness
Group Centrality (Everett-Borgatti 1999)	group_centrality
Human-AI Interaction Coding Sequences	ai_coding ai_detailed coding coding_detailed hai_datasets human_ai human_ai_detailed
Check if a Matrix Could Be Bipartite	is_bipartite
Check if Network is Directed	is_directed
Check if Network is TNA-based	is_tna_network
Find K Shortest Loopless Paths (Yen's Algorithm)	k_shortest_paths
Degree Correlation Between Layers	layer_degree_correlation ldegcor
Layer Similarity	layer_similarity lsim
Pairwise Layer Similarities	layer_similarity_matrix lsim_matrix
Circular Layout	layout_circle
Group-based Layout	layout_groups
Oval Layout	layout_oval
Fruchterman-Reingold Spring Layout	layout_spring
List Available Layouts	list_layouts
List Available Color Palettes	list_palettes
List Available Shapes	list_shapes
List Registered SVG Shapes	list_svg_shapes
List Available Themes	list_themes
Get Community Membership	membership
Network Motif Analysis	motifs plot.cograph_motif_result print.cograph_motif_result
Get Number of Communities	n_communities
Get Number of Edges	n_edges
Get Number of Nodes	n_nodes
Neighborhood Overlap (Jaccard) for Each Edge	neighborhood_overlap
Bridge Edges	network_bridges
Largest Clique Size	network_clique_size
Cut Vertices (Articulation Points)	network_cut_vertices
Network Girth (Shortest Cycle Length)	network_girth
Global Efficiency	network_global_efficiency
Local Efficiency	network_local_efficiency
Network Radius	network_radius
Rich Club Coefficient	network_rich_club
Small-World Coefficient (Sigma)	network_small_world
Network-Level Summary Statistics	network_summary
Network Vertex Connectivity	network_vertex_connectivity
Get Nodes from Cograph Network (Deprecated)	nodes
Overlay Community Blobs on a Network Plot	overlay_communities
Blues Palette	palette_blues
Colorblind-friendly Palette	palette_colorblind
Diverging Palette	palette_diverging
Pastel Palette	palette_pastel
Rainbow Palette	palette_rainbow
Reds Palette	palette_reds
Viridis Palette	palette_viridis
Color Palettes	palettes
Configure a custom multi-panel layout	panel_layout
Plot Alluvial Diagram	plot_alluvial
Plot Centrality	plot_centrality
Plot Centrality Comparison	plot_centrality_compare
Plot Centrality Distribution	plot_centrality_distribution
Plot Centrality Heatmap	plot_centrality_heatmap
Chord Diagram	plot_chord
Plot Network Difference	plot_compare
Plot Comparison Heatmap	plot_comparison_heatmap
Plot Degree-Degree Correlation	plot_degree_correlation
Forest Plot for Bootstrap Edge Differences	plot_edge_diff_forest plot_edge_diff_forest.boot_glasso
Plot Edge Weight Distribution	plot_edge_weights
Plot Network as Heatmap	plot_heatmap
Plot Heterogeneous TNA Network (Multi-Group Layout)	htna plot_htna
Plot Multi-Cluster Multi-Layer Network	plot_mcml
Plot Mixed Network	plot_mixed_network
Multilayer Network Heatmap	plot_ml_heatmap
Multilevel Network Visualization	mlna plot_mlna
Plot a motif/subgraph result	plot_motifs
Multi-Cluster TNA Network Plot	mtna plot_mtna
Plot a Group Bootstrap Result	plot.net_bootstrap_group plot_net_bootstrap_group
Plot Centrality Stability Results	plot_net_stability
Plot a Group of Nestimate netobjects	plot.netobject_group plot_netobject_group
Plot a Multilevel Nestimate netobject	plot.netobject_ml plot_netobject_ml
Plot Network Evolution (Small Multiples)	plot_network_evolution
Plot Network Robustness	plot_robustness
Simplicial Complex Visualization	plot_simplicial
Temporal Network Prism (3D Glass Box)	plot_temporal
TNA-Style Network Plot (qgraph Compatible)	plot_tna tplot
Plot Individual Trajectories	plot_trajectories
Plot Transitions Between States	plot_transitions
Plot Cluster Significance	plot.cograph_cluster_significance
Plot Community Structure	plot.cograph_communities
Plot Core-Periphery Structure	plot.cograph_core_periphery
Plot method for cograph_degree_fit	plot.cograph_degree_fit
Plot Motif Analysis Results	plot.cograph_motif_analysis
Plot Network Motifs	plot.cograph_motifs
Plot cograph_network Object	plot.cograph_network
Plot Rich Club Results	plot.cograph_rich_club
Plot Node Vulnerability	plot.cograph_vulnerability
Plot Bootstrap Results	plot.tna_bootstrap splot.tna_bootstrap
Plot Disparity Filter Result	plot.tna_disparity
Print Community Structure	print.cograph_communities
Print method for cograph_degree_fit	print.cograph_degree_fit
Print cograph_network Object	print.cograph_network
Project Bipartite Network to One-Mode	project_bipartite
Global Reaching Centrality (Mones, Vicsek & Vicsek 2012)	reaching_global
Register a Custom Layout	register_layout
Register a Custom Shape	register_shape
Register Custom SVG Shape	register_svg_shape
Register a Custom Theme	register_theme
ggplot2 Conversion	render-ggplot
Grid Rendering	render-grid
Rich Club Coefficient	rich_club
Local Rich Club Score	rich_club_local
Network Robustness Analysis	robustness
Calculate Area Under Robustness Curve (AUC)	robustness_auc
Summary of Robustness Analysis	robustness_summary
Select Bridge Edges	select_bridges
Select Connected Component	select_component
Select Edges with Lazy Computation	select_edges
Select Edges Between Node Sets	select_edges_between
Select Edges Involving Nodes	select_edges_involving
Select Node Neighbors (Ego Network)	select_neighbors
Select Nodes with Lazy Centrality Computation	select_nodes
Select Top N Nodes by Centrality	select_top
Select Top N Edges	select_top_edges
Set Edges in Cograph Network	set_edges
Set Node Groups	set_groups
Set Layout in Cograph Network	set_layout
Set Nodes in Cograph Network	set_nodes
Compute Shortest Path Distances	shortest_paths
Simmelian Strength (Triangle Count per Edge)	simmelian_strength
Simplify a Network	simplify simplify.cograph_network simplify.default simplify.igraph simplify.matrix simplify.tna
Set Edge Aesthetics	sn_edges
Convert Network to ggplot2	sn_ggplot
Apply Layout to Network	sn_layout
Set Node Aesthetics	sn_nodes
Apply Color Palette to Network	sn_palette
Save Network Visualization	sn_save
Save as ggplot2	sn_save_ggplot
Apply Theme to Network	sn_theme
Plot Cograph Network	sn_render soplot
Plot Group Permutation Test Results	plot_group_permutation splot.group_tna_permutation
Plot Nestimate Bootstrap Results	splot splot.boot_glasso splot.cograph_communities splot.netobject splot.net_bootstrap splot.net_mlvar splot.net_permutation splot.tna_communities splot.wtna_mixed
Plot Disparity Results with splot	splot.tna_disparity
Plot Permutation Test Results	plot_permutation splot.tna_permutation
Student Interaction Edge List	student_interactions
Extract Specific Motif Instances (Subgraphs)	subgraphs
Build MCML from Raw Transition Data	summarize_clusters
Summarize Network by Clusters	cnet summarize_network
Summary of cograph_network Object	summary.cograph_network
Supra-Adjacency Matrix	supra supra_adjacency
Extract Inter-Layer Block	extract_interlayer supra_interlayer
Extract Layer from Supra-Adjacency Matrix	extract_layer supra_layer
Classic Theme	theme_cograph_classic
Colorblind-friendly Theme	theme_cograph_colorblind
Dark Theme	theme_cograph_dark
Grayscale Theme	theme_cograph_gray
Minimal Theme	theme_cograph_minimal
Nature Theme	theme_cograph_nature
Viridis Theme	theme_cograph_viridis
Built-in Themes	themes-builtin
Export Network as Edge List Data Frame	to_data_frame to_df
Convert Network to igraph Object	to_igraph
Convert Network to Adjacency Matrix	to_matrix
Convert Network to statnet network Object	to_network
Trophic Incoherence Parameter	trophic_incoherence
Unregister SVG Shape	unregister_svg_shape
Verify Against igraph	verify_igraph verify_with_igraph
Node Vulnerability	vulnerability