# Network analysis and visualization

## Documentation for package ‘igraph’ version 0.6.5-2

- DESCRIPTION file.
- Code demos. Use demo() to run them.
- 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 misc

igraph-package | The igraph package

## -- A --

add.edges | Method for structural manipulation of graphs
add.vertex.shape | Various vertex shapes when plotting igraph graphs
add.vertices | Method for structural manipulation of graphs
aging.ba.game | Generate an evolving random graph with preferential attachment and aging
aging.barabasi.game | Generate an evolving random graph with preferential attachment and aging
aging.prefatt.game | Generate an evolving random graph with preferential attachment and aging
algorithm | Functions to deal with the result of network community detection
alpha.centrality | Find Bonacich alpha centrality scores of network positions
are.connected | Gaining information about graph structure
arpack | ARPACK eigenvector calculation
arpack-options | ARPACK eigenvector calculation
arpack.unpack.complex | ARPACK eigenvector calculation
articulation.points | Articulation points of a graph
as.dendrogram.communities | Functions to deal with the result of network community detection
as.directed | Convert between directed and undirected graphs
as.hclust.communities | Functions to deal with the result of network community detection
as.igraph | Conversion to igraph
as.igraph.igraphHRG | Conversion to igraph
as.undirected | Convert between directed and undirected graphs
asPhylo | Functions to deal with the result of network community detection
asPhylo.communities | Functions to deal with the result of network community detection
assortativity | Assortativity coefficient
assortativity.degree | Assortativity coefficient
assortativity.nominal | Assortativity coefficient
asymmetric.preference.game | Trait-based random generation
attribute.combination | How igraph functions handle attributes when the graph changes
attributes | Graph, vertex and edge attributes
authority.score | Kleinberg's centrality scores.
autocurve.edges | Optimal edge curvature when plotting graphs
average.path.length | Shortest (directed or undirected) paths between vertices

## -- B --

ba.game | Generate scale-free graphs according to the Barabasi-Albert model
barabasi.game | Generate scale-free graphs according to the Barabasi-Albert model
betweenness | Vertex and edge betweenness centrality
betweenness.estimate | Vertex and edge betweenness centrality
bibcoupling | Cocitation coupling
biconnected.components | Biconnected components
bipartite.mapping | Decide whether a graph is bipartite
bipartite.projection | Project a bipartite graph
bipartite.projection.size | Project a bipartite graph
blockGraphs | Calculate Cohesive Blocks
blocks | Calculate Cohesive Blocks
bonpow | Find Bonacich Power Centrality Scores of Network Positions

## -- C --

callaway.traits.game | Graph generation based on different vertex types
canonical.permutation | Canonical permutation of a graph
centralization | Centralization of a graph.tmax
centralization.betweenness | Centralization of a graph.tmax
centralization.betweenness.tmax | Centralization of a graph.tmax
centralization.closeness | Centralization of a graph.tmax
centralization.closeness.tmax | Centralization of a graph.tmax
centralization.degree | Centralization of a graph.tmax
centralization.degree.tmax | Centralization of a graph.tmax
centralization.evcent | Centralization of a graph.tmax
centralization.evcent.tmax | Centralization of a graph.tmax
centralize.scores | Centralization of a graph.tmax
cited.type.game | Undocumented and unsupportted igraph functions
citing.cited.type.game | Undocumented and unsupportted igraph functions
clique.number | The functions find cliques, ie. complete subgraphs in a graph
cliques | The functions find cliques, ie. complete subgraphs in a graph
closeness | Closeness centrality of vertices
closeness.estimate | Closeness centrality of vertices
cluster.distribution | Connected components of a graph
clusters | Connected components of a graph
cocitation | Cocitation coupling
code.length | Functions to deal with the result of network community detection
cohesion | Calculate Cohesive Blocks
cohesive.blocks | Calculate Cohesive Blocks
cohesiveBlocks | Calculate Cohesive Blocks
communities | Functions to deal with the result of network community detection
community.le.to.membership | Community structure detecting based on the leading eigenvector of the community matrix
community.to.membership | Common functions supporting community detection algorithms
compare | Compares community structures using various metrics
compare.communities | Compares community structures using various metrics
compare.numeric | Compares community structures using various metrics
connect.neighborhood | Neighborhood of graph vertices
constraint | Burt's constraint
contract.vertices | Contract several vertices into a single one
convex.hull | Convex hull of a set of vertices
count.multiple | Find the multiple or loop edges in a graph
crossing | Functions to deal with the result of network community detection
cutat | Functions to deal with the result of network community detection

## -- D --

decompose.graph | Decompose a graph into components
degree | Degree and degree distribution of the vertices
degree.distribution | Degree and degree distribution of the vertices
degree.sequence.game | Generate random graphs with a given degree sequence
delete.edges | Method for structural manipulation of graphs
delete.vertices | Method for structural manipulation of graphs
dendPlot | Plot dendrograms
dendPlot.communities | Community structure dendrogram plots
dendPlot.igraphHRG | HRG dendrogram plot
diameter | Diameter of a graph
DL | Reading foreign file formats
dominator.tree | Dominator tree
dyad.census | Dyad census of a graph

## -- E --

E | Vertex and edge sequences and iterators
E<- | Vertex and edge sequences and iterators
eccentricity | Eccentricity and radius
ecount | Gaining information about graph structure
edge | Method for structural manipulation of graphs
edge.betweenness | Vertex and edge betweenness centrality
edge.betweenness.community | Community structure detection based on edge betweenness
edge.betweenness.community.merges | Community structure detection based on edge betweenness
edge.betweenness.estimate | Vertex and edge betweenness centrality
edge.connectivity | Edge connectivity.
edge.disjoint.paths | Edge connectivity.
edges | Method for structural manipulation of graphs
erdos.renyi.game | Generate random graphs according to the Erdos-Renyi model
establishment.game | Graph generation based on different vertex types
evcent | Find Eigenvector Centrality Scores of Network Positions
evolver | Measuring the driving force in evolving networks
evolver.d | Measuring the driving force in evolving networks
exportPajek | Calculate Cohesive Blocks

## -- F --

farthest.nodes | Diameter of a graph
fastgreedy.community | Community structure via greedy optimization of modularity
forest.fire.game | Forest Fire Network Model

## -- G --

get.adjacency | Convert a graph to an adjacency matrix or an edge list
get.adjedgelist | Adjacency lists
get.adjlist | Adjacency lists
get.all.shortest.paths | Shortest (directed or undirected) paths between vertices
get.data.frame | Creating igraph graphs from data frames or vice-versa
get.diameter | Diameter of a graph
get.edge | Gaining information about graph structure
get.edge.attribute | Graph, vertex and edge attributes
get.edge.ids | Find the edge ids based on the incident vertices of the edges
get.edgelist | Convert a graph to an adjacency matrix or an edge list
get.edges | Gaining information about graph structure
get.graph.attribute | Graph, vertex and edge attributes
get.incidence | Incidence matrix of a bipartite graph
get.shortest.paths | Shortest (directed or undirected) paths between vertices
get.stochastic | Stochastic matrix of a graph
get.vertex.attribute | Graph, vertex and edge attributes
getIgraphOpt | Parameters for the igraph package
girth | Girth of a graph
GML | Reading foreign file formats
graph | Various methods for creating graphs
graph.adhesion | Edge connectivity.
graph.adjacency | Create graphs from adjacency matrices
graph.adjlist | Create graphs from adjacency lists
graph.atlas | Various methods for creating graphs
graph.automorphisms | Number of automorphisms
graph.bfs | Breadth-first search
graph.bipartite | Create a bipartite graph
graph.cohesion | Vertex connectivity.
graph.complementer | Graph operators
graph.compose | Graph operators
graph.constructors | Various methods for creating graphs
graph.coreness | K-core decomposition of graphs
graph.count.isomorphisms.vf2 | Graph Isomorphism
graph.count.subisomorphisms.vf2 | Graph Isomorphism
graph.data.frame | Creating igraph graphs from data frames or vice-versa
graph.de.bruijn | De Bruijn graphs.
graph.density | Graph density
graph.dfs | Depth-first search
graph.difference | Graph operators
graph.difference.by.name | Graph operators based on symbolic vertex names
graph.disjoint.union | Graph operators
graph.diversity | Graph diversity
graph.edgelist | Various methods for creating graphs
graph.empty | Various methods for creating graphs
graph.extended.chordal.ring | Various methods for creating graphs
graph.famous | Creating named graphs
graph.formula | Creating (small) graphs via a simple interface
graph.full | Various methods for creating graphs
graph.full.bipartite | Create a full bipartite graph
graph.full.citation | Various methods for creating graphs
graph.get.isomorphisms.vf2 | Graph Isomorphism
graph.get.subisomorphisms.vf2 | Graph Isomorphism
graph.graphdb | Load a graph from the graph database for testing graph isomorphism.
graph.incidence | Create graphs from an incidence matrix
graph.intersection | Graph operators
graph.intersection.by.name | Graph operators based on symbolic vertex names
graph.isoclass | Graph Isomorphism
graph.isoclass.subgraph | Graph Isomorphism
graph.isocreate | Graph Isomorphism
graph.isomorphic | Graph Isomorphism
graph.isomorphic.34 | Graph Isomorphism
graph.isomorphic.bliss | Graph Isomorphism
graph.isomorphic.vf2 | Graph Isomorphism
graph.kautz | Kautz graphs
graph.knn | Average nearest neighbor degree
graph.laplacian | Graph Laplacian
graph.lattice | Various methods for creating graphs
graph.lcf | Creating a graph from LCF notation
graph.maxflow | Maximum flow in a network
graph.mincut | Maximum flow in a network
graph.motifs | Graph motifs
graph.motifs.est | Graph motifs
graph.motifs.no | Graph motifs
graph.neighborhood | Neighborhood of graph vertices
graph.ring | Various methods for creating graphs
graph.star | Various methods for creating graphs
graph.strength | Strength or weighted vertex degree
graph.subisomorphic.vf2 | Graph Isomorphism
graph.tree | Various methods for creating graphs
graph.union | Graph operators
graph.union.by.name | Graph operators based on symbolic vertex names
GraphML | Reading foreign file formats
grg.game | Geometric random graphs
growing.random.game | Growing random graph generation

## -- H --

has.multiple | Find the multiple or loop edges in a graph
hierarchy | Calculate Cohesive Blocks
HRG | Hierarchical random graphs
hrg.consensus | Hierarchical random graphs
hrg.create | Hierarchical random graphs
hrg.dendrogram | Hierarchical random graphs
hrg.fit | Hierarchical random graphs
hrg.game | Hierarchical random graphs
hrg.predict | Hierarchical random graphs
hub.score | Kleinberg's centrality scores.

## -- I --

igraph | The igraph package
igraph.arpack.default | ARPACK eigenvector calculation
igraph.console | The igraph console
igraph.drl.coarsen | The DrL graph layout generator
igraph.drl.coarsest | The DrL graph layout generator
igraph.drl.default | The DrL graph layout generator
igraph.drl.final | The DrL graph layout generator
igraph.drl.refine | The DrL graph layout generator
igraph.from.graphNEL | Convert igraph graphs to graphNEL objects or back
igraph.options | Parameters for the igraph package
igraph.par | Parameters for the igraph package
igraph.plotting | Drawing graphs
igraph.sample | Sampling a random integer sequence
igraph.shape.noclip | Various vertex shapes when plotting igraph graphs
igraph.shape.noplot | Various vertex shapes when plotting igraph graphs
igraph.to.graphNEL | Convert igraph graphs to graphNEL objects or back
igraph.vertex.shapes | Various vertex shapes when plotting igraph graphs
igraphdemo | Run igraph demos, step by step
incident | Gaining information about graph structure
independence.number | Independent vertex sets
independent.vertex.sets | Independent vertex sets
induced.subgraph | Subgraph of a graph
infomap.community | Infomap community finding
interconnected.islands.game | A graph with subgraphs that are each a random graph.
is.bipartite | Create a bipartite graph
is.chordal | Chordality of a graph
is.connected | Connected components of a graph
is.dag | Directed acyclic graphs
is.degree.sequence | Degree sequences of graphs
is.directed | Gaining information about graph structure
is.graphical.degree.sequence | Degree sequences of graphs
is.hierarchical | Functions to deal with the result of network community detection
is.igraph | Is this object a graph?
is.loop | Find the multiple or loop edges in a graph
is.matching | Graph matching
is.maximal.matching | Graph matching
is.minimal.separator | Vertex separators
is.multiple | Find the multiple or loop edges in a graph
is.mutual | Find mutual edges in a directed graph
is.named | Named graphs
is.separator | Vertex separators
is.simple | Simple graphs
is.weighted | Weighted graphs
iterators | Vertex and edge sequences and iterators

## -- K --

k.regular.game | Create a random regular graph

## -- L --

label.propagation.community | Finding communities based on propagating labels
largest.cliques | The functions find cliques, ie. complete subgraphs in a graph
largest.independent.vertex.sets | Independent vertex sets
lastcit.game | Undocumented and unsupportted igraph functions
layout | Generate coordinates for plotting graphs
layout.auto | Generate coordinates for plotting graphs
layout.circle | Generate coordinates for plotting graphs
layout.drl | The DrL graph layout generator
layout.fruchterman.reingold | Generate coordinates for plotting graphs
layout.fruchterman.reingold.grid | Generate coordinates for plotting graphs
layout.graphopt | Generate coordinates for plotting graphs
layout.grid | Simple grid layout
layout.grid.3d | Simple grid layout
layout.kamada.kawai | Generate coordinates for plotting graphs
layout.lgl | Generate coordinates for plotting graphs
layout.mds | Graph layout by multidimensional scaling
layout.merge | Merging graph layouts
layout.norm | Generate coordinates for plotting graphs
layout.random | Generate coordinates for plotting graphs
layout.reingold.tilford | Generate coordinates for plotting graphs
layout.sphere | Generate coordinates for plotting graphs
layout.spring | Generate coordinates for plotting graphs
layout.star | Generate coordinates to place the vertices of a graph in a star-shape
layout.sugiyama | The Sugiyama graph layout generator
layout.svd | Generate coordinates for plotting graphs
leading.eigenvector.community | Community structure detecting based on the leading eigenvector of the community matrix
length.cohesiveBlocks | Calculate Cohesive Blocks
length.communities | Functions to deal with the result of network community detection
LGL | Reading foreign file formats
line.graph | Line graph of a graph
list.edge.attributes | Graph, vertex and edge attributes
list.graph.attributes | Graph, vertex and edge attributes
list.vertex.attributes | Graph, vertex and edge attributes

## -- M --

maxcohesion | Calculate Cohesive Blocks
maximal.cliques | The functions find cliques, ie. complete subgraphs in a graph
maximal.independent.vertex.sets | Independent vertex sets
maximum.bipartite.matching | Graph matching
maximum.cardinality.search | Maximum cardinality search
membership | Functions to deal with the result of network community detection
merges | Functions to deal with the result of network community detection
minimal.st.separators | Minimum size vertex separators
minimum.size.separators | Minimum size vertex separators
minimum.spanning.tree | Minimum spanning tree
modularity | Modularity of a community structure of a graph
modularity.communities | Functions to deal with the result of network community detection
modularity.igraph | Modularity of a community structure of a graph
multilevel.community | Finding community structure by multi-level optimization of modularity

## -- N --

neighborhood | Neighborhood of graph vertices
neighborhood.size | Neighborhood of graph vertices
neighbors | Gaining information about graph structure
nexus | Query and download from the Nexus network repository
nexus.get | Query and download from the Nexus network repository
nexus.info | Query and download from the Nexus network repository
nexus.list | Query and download from the Nexus network repository
nexus.search | Query and download from the Nexus network repository
nexusDatasetInfo | Query and download from the Nexus network repository
no.clusters | Connected components of a graph

## -- O --

optimal.community | Optimal community structure

## -- P --

page.rank | The Page Rank algorithm
page.rank.old | The Page Rank algorithm
Pajek | Reading foreign file formats
parent | Calculate Cohesive Blocks
path | Method for structural manipulation of graphs
path.length.hist | Shortest (directed or undirected) paths between vertices
permute.vertices | Permute the vertices of a graph
piecewise.layout | Merging graph layouts
plot.cohesiveBlocks | Calculate Cohesive Blocks
plot.communities | Functions to deal with the result of network community detection
plot.igraph | Plotting of graphs
plotHierarchy | Calculate Cohesive Blocks
power.law.fit | Fitting a power-law distribution function to discrete data
preference.game | Trait-based random generation
print.cohesiveBlocks | Calculate Cohesive Blocks
print.communities | Functions to deal with the result of network community detection
print.igraph | Print graphs to the terminal
print.igraph.es | Vertex and edge sequences and iterators
print.igraph.vs | Vertex and edge sequences and iterators
print.igraphHRG | Hierarchical random graphs
print.igraphHRGConsensus | Hierarchical random graphs
print.nexusDatasetInfo | Query and download from the Nexus network repository
print.nexusDatasetInfoList | Query and download from the Nexus network repository

## -- R --

radius | Eccentricity and radius
random.graph.game | Generate random graphs according to the Erdos-Renyi model
read.graph | Reading foreign file formats
reciprocity | Reciprocity of graphs
remove.edge.attribute | Graph, vertex and edge attributes
remove.graph.attribute | Graph, vertex and edge attributes
remove.vertex.attribute | Graph, vertex and edge attributes
revolver | Measuring the driving force in evolving networks
revolver.ad | Measuring the driving force in evolving networks
revolver.ade | Measuring the driving force in evolving networks
revolver.adi | Measuring the driving force in evolving networks
revolver.air | Measuring the driving force in evolving networks
revolver.ar | Measuring the driving force in evolving networks
revolver.d | Measuring the driving force in evolving networks
revolver.d.d | Measuring the driving force in evolving networks
revolver.de | Measuring the driving force in evolving networks
revolver.di | Measuring the driving force in evolving networks
revolver.dl | Measuring the driving force in evolving networks
revolver.e | Measuring the driving force in evolving networks
revolver.el | Measuring the driving force in evolving networks
revolver.error.ad | Measuring the driving force in evolving networks
revolver.error.ade | Measuring the driving force in evolving networks
revolver.error.adi | Measuring the driving force in evolving networks
revolver.error.air | Measuring the driving force in evolving networks
revolver.error.ar | Measuring the driving force in evolving networks
revolver.error.d | Measuring the driving force in evolving networks
revolver.error.de | Measuring the driving force in evolving networks
revolver.error.di | Measuring the driving force in evolving networks
revolver.error.dl | Measuring the driving force in evolving networks
revolver.error.e | Measuring the driving force in evolving networks
revolver.error.el | Measuring the driving force in evolving networks
revolver.error.il | Measuring the driving force in evolving networks
revolver.error.ir | Measuring the driving force in evolving networks
revolver.error.l | Measuring the driving force in evolving networks
revolver.error.r | Measuring the driving force in evolving networks
revolver.il | Measuring the driving force in evolving networks
revolver.ir | Measuring the driving force in evolving networks
revolver.l | Measuring the driving force in evolving networks
revolver.ml.ad | Measuring the driving force in evolving networks
revolver.ml.AD.alpha.a.beta | Measuring the driving force in evolving networks
revolver.ml.AD.dpareto | Measuring the driving force in evolving networks
revolver.ml.AD.dpareto.eval | Measuring the driving force in evolving networks
revolver.ml.ade | Measuring the driving force in evolving networks
revolver.ml.ADE.alpha.a.beta | Measuring the driving force in evolving networks
revolver.ml.ADE.dpareto | Measuring the driving force in evolving networks
revolver.ml.ADE.dpareto.eval | Measuring the driving force in evolving networks
revolver.ml.ADE.dpareto.evalf | Measuring the driving force in evolving networks
revolver.ml.d | Measuring the driving force in evolving networks
revolver.ml.D.alpha | Measuring the driving force in evolving networks
revolver.ml.D.alpha.a | Measuring the driving force in evolving networks
revolver.ml.de | Measuring the driving force in evolving networks
revolver.ml.DE.alpha.a | Measuring the driving force in evolving networks
revolver.ml.df | Measuring the driving force in evolving networks
revolver.ml.f | Measuring the driving force in evolving networks
revolver.ml.l | Measuring the driving force in evolving networks
revolver.p.p | Measuring the driving force in evolving networks
revolver.probs.ad | Measuring the driving force in evolving networks
revolver.probs.ade | Measuring the driving force in evolving networks
revolver.probs.ADE.dpareto | Measuring the driving force in evolving networks
revolver.probs.d | Measuring the driving force in evolving networks
revolver.probs.de | Measuring the driving force in evolving networks
revolver.r | Measuring the driving force in evolving networks
rewire | Graph rewiring
rewire.edges | Rewires the endpoints of the edges of a graph randomly
rglplot | 3D plotting of graphs with OpenGL
rglplot.igraph | 3D plotting of graphs with OpenGL
running.mean | Running mean of a time series

## -- S --

SCG | Spectral Coarse Graining
scg | All-in-one Function for the SCG of Matrices and Graphs
scgGrouping | SCG Problem Solver
scgNormEps | SCG Extra Functions
scgSemiProjectors | Semi-Projectors
set.edge.attribute | Graph, vertex and edge attributes
set.graph.attribute | Graph, vertex and edge attributes
set.vertex.attribute | Graph, vertex and edge attributes
shortest.paths | Shortest (directed or undirected) paths between vertices
showtrace | Functions to deal with the result of network community detection
similarity.dice | Similarity measures of two vertices
similarity.invlogweighted | Similarity measures of two vertices
similarity.jaccard | Similarity measures of two vertices
simplify | Simple graphs
sizes | Functions to deal with the result of network community detection
spinglass.community | Finding communities in graphs based on statistical meachanics
static.fitness.game | Random graphs from vertex fitness scores
static.power.law.game | Scale-free random graphs, from vertex fitness scores
stCuts | List all (s,t)-cuts of a graph
stMincuts | List all minimum (s,t)-cuts of a graph
str.igraph | Print graphs to the terminal
subcomponent | In- or out- component of a vertex
subgraph | Subgraph of a graph
subgraph.centrality | Find subgraph centrality scores of network positions
subgraph.edges | Subgraph of a graph
summary.cohesiveBlocks | Calculate Cohesive Blocks
summary.igraph | Print graphs to the terminal
summary.nexusDatasetInfoList | Query and download from the Nexus network repository

## -- T --

tkigraph | Experimental basic igraph GUI
tkplot | Interactive plotting of graphs
tkplot.center | Interactive plotting of graphs
tkplot.close | Interactive plotting of graphs
tkplot.export.postscript | Interactive plotting of graphs
tkplot.fit.to.screen | Interactive plotting of graphs
tkplot.getcoords | Interactive plotting of graphs
tkplot.off | Interactive plotting of graphs
tkplot.reshape | Interactive plotting of graphs
tkplot.rotate | Interactive plotting of graphs
topological.sort | Topological sorting of vertices in a graph
transitivity | Transitivity of a graph
triad.census | Triad census, subgraphs with three vertices

## -- U --

UCINET | Reading foreign file formats
unfold.tree | Convert a general graph into a forest

## -- V --

V | Vertex and edge sequences and iterators
V<- | Vertex and edge sequences and iterators
vcount | Gaining information about graph structure
vertex | Method for structural manipulation of graphs
vertex.connectivity | Vertex connectivity.
vertex.disjoint.paths | Vertex connectivity.
vertex.shape.pie | Using pie charts as vertices in graph plots
vertex.shapes | Various vertex shapes when plotting igraph graphs
vertices | Method for structural manipulation of graphs

## -- W --

walktrap.community | Community strucure via short random walks
watts.strogatz.game | The Watts-Strogatz small-world model
write.graph | Writing the graph to a file in some format

## -- misc --

$.igraph.es | Vertex and edge sequences and iterators
$.igraph.vs | Vertex and edge sequences and iterators
$<-.igraph.es | Vertex and edge sequences and iterators
$<-.igraph.vs | Vertex and edge sequences and iterators
%--% | Vertex and edge sequences and iterators
%->% | Vertex and edge sequences and iterators
%<-% | Vertex and edge sequences and iterators
%c% | Graph operators
%du% | Graph operators
%m% | Graph operators
%s% | Graph operators
%u% | Graph operators
+.igraph | Method for structural manipulation of graphs
-.igraph | Method for structural manipulation of graphs
[.igraph | Method for structural manipulation of graphs
[.igraph.es | Vertex and edge sequences and iterators
[.igraph.vs | Vertex and edge sequences and iterators
[<-.igraph | Method for structural manipulation of graphs
[<-.igraph.es | Vertex and edge sequences and iterators
[<-.igraph.vs | Vertex and edge sequences and iterators
[[.igraph | Method for structural manipulation of graphs