igraph: Network Analysis and Visualization

> library(igraph)


Attaching package: 'igraph'

The following object is masked from 'package:arules':

    union

The following object is masked from 'package:vegdata':

    parent

The following objects are masked from 'package:sna':

    %c%, betweenness, bonpow, closeness, components, degree,
    dyad.census, evcent, hierarchy, is.connected, neighborhood,
    triad.census

The following object is masked from 'package:BioFTF':

    radius

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:git2r':

    tree

The following object is masked from 'package:magrittr':

    %>%

The following object is masked from 'package:base':

    union

バージョン: 1.0.1

関数名 概略
%>% Magrittr's pipes
+.igraph Add vertices, edges or another graph to a graph
E Edges of a graph
V Vertices of a graph
[.igraph Query and manipulate a graph as it were an adjacency matrix
[[.igraph Query and manipulate a graph as it were an adjacency list
add_edges Add edges to a graph
add_layout_ Add layout to graph
add_vertices Add vertices to a graph
adjacent_vertices Adjacent vertices of multiple vertices in a graph
all_simple_paths List all simple paths from one source
alpha_centrality Find Bonacich alpha centrality scores of network positions
are_adjacent Are two vertices adjacent?
arpack_defaults ARPACK eigenvector calculation
articulation_points Articulation points of a graph
as.directed Convert between directed and undirected graphs
as.igraph Conversion to igraph
as_adj_list Adjacency lists
as_adjacency_matrix Convert a graph to an adjacency matrix
as_data_frame Creating igraph graphs from data frames or vice-versa
as_edgelist Convert a graph to an edge list
as_graphnel Convert igraph graphs to graphNEL objects from the graph package
as_ids Convert a vertex or edge sequence to an ordinary vector
as_incidence_matrix Incidence matrix of a bipartite graph
as_long_data_frame Convert a graph to a long data frame
as_membership Declare a numeric vector as a membership vector
assortativity Assortativity coefficient
authority_score Kleinberg's authority centrality scores.
automorphisms Number of automorphisms
bfs Breadth-first search
biconnected_components Biconnected components
bipartite_mapping Decide whether a graph is bipartite
bipartite_projection Project a bipartite graph
c.igraph.es Concatenate edge sequences
c.igraph.vs Concatenate vertex sequences
canonical_permutation Canonical permutation of a graph
categorical_pal Palette for categories
centr_betw Centralize a graph according to the betweenness of vertices
centr_betw_tmax Theoretical maximum for betweenness centralization
centr_clo Centralize a graph according to the closeness of vertices
centr_clo_tmax Theoretical maximum for closeness centralization
centr_degree Centralize a graph according to the degrees of vertices
centr_degree_tmax Theoretical maximum for degree centralization
centr_eigen Centralize a graph according to the eigenvector centrality of vertices
centr_eigen_tmax Theoretical maximum for betweenness centralization
centralize Centralization of a graph
cliques The functions find cliques, ie. complete subgraphs in a graph
closeness Closeness centrality of vertices
cluster_edge_betweenness Community structure detection based on edge betweenness
cluster_fast_greedy Community structure via greedy optimization of modularity
cluster_infomap Infomap community finding
cluster_label_prop Finding communities based on propagating labels
cluster_leading_eigen Community structure detecting based on the leading eigenvector of the community matrix
cluster_louvain Finding community structure by multi-level optimization of modularity
cluster_optimal Optimal community structure
cluster_spinglass Finding communities in graphs based on statistical meachanics
cluster_walktrap Community strucure via short random walks
cocitation Cocitation coupling
cohesive_blocks Calculate Cohesive Blocks
compare Compares community structures using various metrics
complementer Complementer of a graph
component_distribution Connected components of a graph
component_wise Component-wise layout
compose Compose two graphs as binary relations
consensus_tree Create a consensus tree from several hierarchical random graph models
console The igraph console
constraint Burt's constraint
contract Contract several vertices into a single one
convex_hull Convex hull of a set of vertices
coreness K-core decomposition of graphs
count_isomorphisms Count the number of isomorphic mappings between two graphs
count_motifs Graph motifs
count_subgraph_isomorphisms Count the isomorphic mappings between a graph and the subgraphs of another graph
count_triangles Find triangles in graphs
curve_multiple Optimal edge curvature when plotting graphs
decompose Decompose a graph into components
degree Degree and degree distribution of the vertices
delete_edge_attr Delete an edge attribute
delete_edges Delete edges from a graph
delete_graph_attr Delete a graph attribute
delete_vertex_attr Delete a vertex attribute
delete_vertices Delete vertices from a graph
dfs Depth-first search
diameter Diameter of a graph
difference Difference of two sets
difference.igraph Difference of graphs
difference.igraph.es Difference of edge sequences
difference.igraph.vs Difference of vertex sequences
dim_select Dimensionality selection for singular values using profile likelihood.
disjoint_union Disjoint union of graphs
distance_table Shortest (directed or undirected) paths between vertices
diverging_pal Diverging palette
diversity Graph diversity
dominator_tree Dominator tree
dyad_census Dyad census of a graph
each_edge Rewires the endpoints of the edges of a graph to a random vertex
eccentricity Eccentricity of the vertices in a graph
edge Helper function for adding and deleting edges
edge_attr Query edge attributes of a graph
edge_attr<- Set one or more edge attributes
edge_attr_names List names of edge attributes
edge_connectivity Edge connectivity.
edge_density Graph density
ego Neighborhood of graph vertices
eigen_centrality Find Eigenvector Centrality Scores of Network Positions
embed_adjacency_matrix Spectral Embedding of Adjacency Matrices
embed_laplacian_matrix Spectral Embedding of the Laplacian of a Graph
ends Incident vertices of some graph edges
erdos.renyi.game Generate random graphs according to the Erdos-Renyi model
estimate_betweenness Vertex and edge betweenness centrality
fit_hrg Fit a hierarchical random graph model
fit_power_law Fitting a power-law distribution function to discrete data
gclust.app Graph Clustering Using NMF (and no SVT) - Apparent Clusters
gclust.rsvt Graph Clustering Using SVT and NMF - Clusters Implied by Singular Value Thresholding
get.edge.ids Find the edge ids based on the incident vertices of the edges
getAICc Compute AIC based on a Poisson Approximation using the output from 'gclust'
`girth Girth of a graph
gorder Order (number of vertices) of a graph
graph_ Convert object to a graph
graph_attr Graph attributes of a graph
graph_attr<- Set all or some graph attributes
graph_attr_names List names of graph attributes
graph_from_adj_list Create graphs from adjacency lists
graph_from_adjacency_matrix Create graphs from adjacency matrices
graph_from_atlas Create a graph from the Graph Atlas
graph_from_edgelist Create a graph from an edge list matrix
graph_from_graphdb Load a graph from the graph database for testing graph isomorphism.
graph_from_graphnel Convert graphNEL objects from the graph package to igraph
graph_from_incidence_matrix Create graphs from an incidence matrix
graph_from_isomorphism_class Create a graph from an isomorphism class
graph_from_lcf Creating a graph from LCF notation
graph_from_literal Creating (small) graphs via a simple interface
graph_version Igraph data structure versions
graphlet_basis Graphlet decomposition of a graph
groups Groups of a vertex partitioning
gsize The size of the graph (number of edges)
head_of Head of the edge(s) in a graph
hrg Create a hierarchical random graph from an igraph graph
hrg-methods Hierarchical random graphs
hrg_tree Create an igraph graph from a hierarchical random graph model
hub_score Kleinberg's hub centrality scores.
identical_graphs Decide if two graphs are identical
igraph-attribute-combination How igraph functions handle attributes when the graph changes
igraph-dollar Getting and setting graph attributes, shortcut
igraph-es-attributes Query or set attributes of the edges in an edge sequence
igraph-es-indexing Indexing edge sequences
igraph-es-indexing2 Select edges and show their metadata
igraph-minus Delete vertices or edges from a graph
igraph-package The igraph package
igraph-vs-attributes Query or set attributes of the vertices in a vertex sequence
igraph-vs-indexing Indexing vertex sequences
igraph-vs-indexing2 Select vertices and show their metadata
igraph.plotting Drawing graphs
igraph_demo Run igraph demos, step by step
igraph_options Parameters for the igraph package
igraph_test Run package tests
igraph_version Query igraph's version string
incident Incident edges of a vertex in a graph
incident_edges Incident edges of multiple vertices in a graph
intersection Intersection of two or more sets
intersection.igraph Intersection of graphs
intersection.igraph.es Intersection of edge sequences
intersection.igraph.vs Intersection of vertex sequences
is_bipartite Create a bipartite graph
is_chordal Chordality of a graph
is_dag Directed acyclic graphs
is_degseq Check if a degree sequence is valid for a multi-graph
is_directed Check whether a graph is directed
is_graphical Is a degree sequence graphical?
is_igraph Is this object an igraph graph?
is_matching Graph matching
is_min_separator Minumal vertex separators
is_named Named graphs
is_separator Vertex separators
is_weighted Weighted graphs
isomorphic Decide if two graphs are isomorphic
isomorphism_class Isomorphism class of a graph
isomorphisms Calculate all isomorphic mappings between the vertices of two graphs
ivs Independent vertex sets
keeping_degseq Graph rewiring while preserving the degree distribution
knn Average nearest neighbor degree
laplacian_matrix Graph Laplacian
layout.fruchterman.reingold.grid Grid Fruchterman-Reingold layout, this was removed from igraph
layout.reingold.tilford Deprecated layout functions
layout.spring Spring layout, this was removed from igraph
layout.svd SVD layout, this was removed from igraph
layout_ Graph layouts
layout_as_bipartite Simple two-row layout for bipartite graphs
layout_as_star Generate coordinates to place the vertices of a graph in a star-shape
layout_as_tree The Reingold-Tilford graph layout algorithm
layout_in_circle Graph layout with vertices on a circle.
layout_nicely Choose an appropriate graph layout algorithm automatically
layout_on_grid Simple grid layout
layout_on_sphere Graph layout with vertices on the surface of a sphere
layout_randomly Randomly place vertices on a plane or in 3d space
layout_with_dh The Davidson-Harel layout algorithm
layout_with_drl The DrL graph layout generator
layout_with_fr The Fruchterman-Reingold layout algorithm
layout_with_gem The GEM layout algorithm
layout_with_graphopt The graphopt layout algorithm
layout_with_kk The Kamada-Kawai layout algorithm
layout_with_lgl Large Graph Layout
layout_with_mds Graph layout by multidimensional scaling
layout_with_sugiyama The Sugiyama graph layout generator
local_scan Compute local scan statistics on graphs
make_ Make a new graph
make_chordal_ring Create an extended chordal ring graph
make_clusters Creates a communities object.
make_de_bruijn_graph De Bruijn graphs
make_empty_graph A graph with no edges
make_full_bipartite_graph Create a full bipartite graph
make_full_citation_graph Create a complete (full) citation graph
make_full_graph Create a full graph
make_graph Create an igraph graph from a list of edges, or a notable graph
make_kautz_graph Kautz graphs
make_lattice Create a lattice graph
make_line_graph Line graph of a graph
make_ring Create a ring graph
make_star Create a star graph, a tree with n vertices and n - 1 leaves
make_tree Create tree graphs
match_vertices Match Graphs given a seeding of vertex correspondences
max_cardinality Maximum cardinality search
max_flow Maximum flow in a graph
membership Functions to deal with the result of network community detection
merge_coords Merging graph layouts
min_cut Minimum cut in a graph
min_separators Minimum size vertex separators
min_st_separators Minimum size vertex separators
modularity.igraph Modularity of a community structure of a graph
motifs Graph motifs
mst Minimum spanning tree
neighbors Neighboring (adjacent) vertices in a graph
norm_coords Normalize coordinates for plotting graphs
normalize Normalize layout
page_rank The Page Rank algorithm
path Helper function to add or delete edges along a path
permute Permute the vertices of a graph
plot.igraph Plotting of graphs
plot.sir Plotting the results on multiple SIR model runs
plot_dendrogram Community structure dendrogram plots
plot_dendrogram.igraphHRG HRG dendrogram plot
power_centrality Find Bonacich Power Centrality Scores of Network Positions
predict_edges Predict edges based on a hierarchical random graph model
print.igraph Print graphs to the terminal
print.igraph.es Print an edge sequence to the screen
print.igraph.vs Show a vertex sequence on the screen
print.igraphHRG Print a hierarchical random graph model to the screen
print.igraphHRGConsensus Print a hierarchical random graph consensus tree to the screen
print.nexusDatasetInfo Query and download from the Nexus network repository
r_pal The default R palette
radius Radius of a graph
random_walk Random walk on a graph
read_graph Reading foreign file formats
reciprocity Reciprocity of graphs
rep.igraph Replicate a graph multiple times
rev.igraph.es Reverse the order in an edge sequence
rev.igraph.vs Reverse the order in a vertex sequence
rewire Rewiring edges of a graph
rglplot 3D plotting of graphs with OpenGL
running_mean Running mean of a time series
sample_ Sample from a random graph model
sample_bipartite Bipartite random graphs
sample_correlated_gnp Generate a new random graph from a given graph by randomly adding/removing edges
sample_correlated_gnp_pair Sample a pair of correlated G(n,p) random graphs
sample_degseq Generate random graphs with a given degree sequence
sample_dirichlet Sample from a Dirichlet distribution
sample_dot_product Generate random graphs according to the random dot product graph model
sample_fitness Random graphs from vertex fitness scores
sample_fitness_pl Scale-free random graphs, from vertex fitness scores
sample_forestfire Forest Fire Network Model
sample_gnm Generate random graphs according to the G(n,m) Erdos-Renyi model
sample_gnp Generate random graphs according to the G(n,p) Erdos-Renyi model
sample_grg Geometric random graphs
sample_growing Growing random graph generation
sample_hierarchical_sbm Sample the hierarchical stochastic block model
sample_hrg Sample from a hierarchical random graph model
sample_islands A graph with subgraphs that are each a random graph.
sample_k_regular Create a random regular graph
sample_last_cit Random citation graphs
sample_motifs Graph motifs
sample_pa Generate scale-free graphs according to the Barabasi-Albert model
sample_pa_age Generate an evolving random graph with preferential attachment and aging
sample_pref Trait-based random generation
sample_sbm Sample stochastic block model
sample_seq Sampling a random integer sequence
sample_smallworld The Watts-Strogatz small-world model
sample_sphere_surface Sample vectors uniformly from the surface of a sphere
sample_sphere_volume Sample vectors uniformly from the volume of a sphere
sample_traits_callaway Graph generation based on different vertex types
scan_stat Scan statistics on a time series of graphs
scg All-in-one Function for the SCG of Matrices and Graphs
scg-method Spectral Coarse Graining
scg_eps Error of the spectral coarse graining (SCG) approximation
scg_group SCG Problem Solver
scg_semi_proj Semi-Projectors
sequential_pal Sequential palette
set_edge_attr Set edge attributes
set_graph_attr Set a graph attribute
set_vertex_attr Set vertex attributes
shapes Various vertex shapes when plotting igraph graphs
similarity Similarity measures of two vertices
simplified Constructor modifier to drop multiple and loop edges
simplify Simple graphs
spectrum Eigenvalues and eigenvectors of the adjacency matrix of a graph
split_join_distance Split-join distance of two community structures
srand Deprecated function, used to set random seed of the C library's RNG
st_cuts List all (s,t)-cuts of a graph
st_min_cuts List all minimum (s,t)-cuts of a graph
stochastic_matrix Stochastic matrix of a graph
strength Strength or weighted vertex degree
subcomponent In- or out- component of a vertex subgraph Subgraph of a graph
subgraph_centrality Find subgraph centrality scores of network positions
subgraph_isomorphic Decide if a graph is subgraph isomorphic to another one
subgraph_isomorphisms All isomorphic mappings between a graph and subgraphs of another graph
tail_of Tails of the edge(s) in a graph
time_bins.sir SIR model on graphs
tkigraph Experimental basic igraph GUI
tkplot Interactive plotting of graphs
topo_sort Topological sorting of vertices in a graph
transitivity Transitivity of a graph
triad_census Triad census, subgraphs with three vertices
unfold_tree Convert a general graph into a forest
union Union of two or more sets
union.igraph Union of graphs
union.igraph.es Union of edge sequences
union.igraph.vs Union of vertex sequences
unique.igraph.es Remove duplicate edges from an edge sequence
unique.igraph.vs Remove duplicate vertices from a vertex sequence
upgrade_graph Igraph data structure versions
`vertex Helper function for adding and deleting vertices
vertex.shape.pie Using pie charts as vertices in graph plots
vertex_attr Query vertex attributes of a graph
vertex_attr<- Set one or more vertex attributes
vertex_attr_names List names of vertex attributes
vertex_connectivity Vertex connectivity.
which_multiple Find the multiple or loop edges in a graph
which_mutual Find mutual edges in a directed graph
with_edge_ Constructor modifier to add edge attributes
with_graph_ Constructor modifier to add graph attributes
with_vertex_ Constructor modifier to add vertex attributes
without_attr Construtor modifier to remove all attributes from a graph
without_loops Constructor modifier to drop loop edges
without_multiples Constructor modifier to drop multiple edges
write_graph Writing the graph to a file in some format