Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
R/igraph is an R package of the igraph network analysis library.
Installation
You can install the stable version of R/igraph from CRAN:
install.packages("igraph")
For the development version, you can use Github, with the devtools
package:
Graph id is printed in the header, and a graph_id function was added
Fix edge_attr for some index values
Fix a bfs() bug, restricted argument was zero-based
match_vertices is exported now
%>% is re-exported in a better way, to avoid interference with other
packages
ego_ functions default to order = 1 now
New function igraph_with_opt to run code with temporary igraph
options settings
Fix broken sample_asym_pref function
Fix curve_multiple to avoid warnings for graphs with self-loops.
The NMF package is only suggested now, it is not a hard
dependency
Fix gen_uid.c _SVID_SOURCE issues
Avoid drawing straight lines as Bezier curves
Use the pkgconfig package for options. This allows setting options
on a per-package basis. E.g. a package using igraph can set return.vs.es
to FALSE in its .onLoad() function, and then igraph will return
plain numeric vectors instead of vertex/edge sequences
if called from this package.
igraph_options() returns the old values of the updated options,
this is actually useful, returning the new values was not.
with_igraph_opt() function to temporarily change values of
igraph options.
get.edge() is deprecated, use ends() instead. (This was already the case
for igraph 1.0.0, but we forgot to add a NEWS point for it.)
Do not redefine .Call(), to make native calls faster.
Speed up special cases of indexing vertex sequences.
Removed an anyNA() call, to be compatible with older R versions.
Fixed head_of() and tail_of(), they were mixed up.
Plot: make label.dist independent of label lengths, fixes #63.
Plot: no error for unknown graphical parameters.
Import functions from base packages, to eliminate
R CMD checkNOTEs.
Readd support for edge weights in Fruchterman-Reingold layout
Check membershiph vector in modularity().
Rename str.igraph() to print_all().
Use the igraph version in exported graphs, instread of @[email protected] #75.
Functions that can be used inside a V() or E() indexing
now begin with a dot. Old names are deprecated.
New names: .nei(), .innei(), .outnei(), .inc(), .from(),
.to(). #22
Fix packages that convert graphs to graph::graphNEL: they
don't need to attach 'graph' manually any more.
Fix a bugs in layout_with_dh, layout_with_gem and
layout_with_sugiyama. They crashed in some cases.
igraph 1.0.1
June 26, 2015
Some minor updates:
Documentation fixes.
Do not require a C++-11 compiler any more.
Fedora, Solaris and Windows compilation fixes.
igraph 1.0.0
June 21, 2015
Release notes
This is a new major version of igraph, and then why not call
it 1.0.0. This does not mean that it is ready, it'll never be
ready.
The biggest changes in the release are
the new function names. Most functions were renamed to
make them more consistent and readable. (Relax, old names
can still be used, no need to update any code.)
Better operations for vertex and edge sequences. Most functions
return proper vertex/edge sequences instead of numeric ids.
The versatile make_() and make_graph() functions to
create graphs.
Major changes
Many functions were renamed. Old names are not documented,
but can still be used.
A generic make_graph() function to create graphs.
A generic layout_() (not the underscore!) function
to create graph layouts, see also add_layout_().
The igraph data type has changed. You need to call
upgrade_graph() on graphs created with previous igraph
versions.
Vertex and edge sequence operations: union, intersection, etc.
Vertex and edge sequences can only be used with the graphs they
belong to. This is now strictly checked.
Most functions that return a (sub)set of vertices
or edges return vertex or edge sequences instead.
Vertex and edge sequences have a [[ operator now,
for easy viewing of vertex/edge metadata.
Vertex and edge sequences are implemented as weak references.
See also the as_ids() function to convert them to simple ids.
Vertex order can be specified for the circle layout now.
Davidson-Harel layout algorithm layout_with_dh().
GEM layout algorithm layout_with_gem().
Neighborhood functions have a mindist parameter for the
smallest distance to consider.
all_simple_paths() function to list all simple paths in a graph.
triangles() lists all triangles in a graph.
Fruchterman-Reingold and Kamada-Kawai layout algorithms
rewritten from scratch. They are much faster and follow the
original publications closely.
Nicer printing of graphs, vertex and edge sequences.
local_scan() function calculates scan statistics.
Embeddings: embed_adjacency_matrix() and embed_laplacian_matrix().
Product operator: *, the same graph multiple times. Can be also
used as rep().
Better default colors, color palettes for vertices.
Random walk on a graph: random_walk()
adjacenct_vertices() and incident_edges() functions,
they are vectorized, as opposed to neighhors() and incident().
Convert a graph to a long data frame with as_long_data_frame().
Bug fixes
Too many to list. Please try if your issue was fixed and (re-)report
it if not. Thanks!
igraph 0.7.1
April 21, 2014
Release Notes
Some bug fixes, to make sure that the code included in
'Statistical Analysis of Network Data with R' works. See
https://github.com/kolaczyk/sand
Detailed changes:
Graph drawing: fix labels of curved edges, issue #181.
Graph drawing: allow fixing edge labels at given positions,
issue #181.
Drop the 'type' vertex attribute after bipartite projection,
the projections are not bipartite any more, issue #255.
Print logical attributes in header properly (i.e. encoded by l,
not x, which is for complex attributes. Issue #578.
Add a constructor for communities objects, see create.communities().
Issue #547.
Better error handling in the GraphML parser.
GraphML reader is a bit more lenient now; makes it possible to read
GraphML files saved from yWorks apps.
Fixed a bug in constaint(), issue #580.
Bipartite projection now detects invalid edges instead of giving
a cryptic error, issue #543.
Fixed the simplify argument of graph.formula(), which was
broken, issue #586.
The function crossing() adds better names to the result,
fixes issue #587.
The sir() function gives an error if the input graph is
not simple, fixes issue #582.
Calling igraph functions from igraph callbacks is not allowed now,
fixes issue #571.
igraph 0.7.0
February 4, 2014
Release Notes
There are a bunch of new features in the library itself, and
other important changes in the life of the project. Thanks everyone
for sending code and reporting bugs!
igraph @ github
igraph's development has moved from Launchpad to github.
This has actually happened several month ago, but never
announced officially. The place for reporting bugs is
at https://github.com/igraph/igraph/issues.
New homepage
igraph's homepage is now hosted at http://igraph.org, and it is
brand new. We wanted to make it easier to use and modern.
Better nightly downloads
You can download nightly builds from igraph at
http://igraph.org/nightly. Source and binary R packages (for windows
and OSX), are all built.
New features and bug fixes
Added a demo for hierarchical random graphs, invoke it via
demo(hrg).
Make attribute prefixes optional when writing a GraphML file.
Added function mod.matrix().
Support edge weights in leading eigenvector community detection.
Added the LAD library for checking (sub)graph isomorphism, version 1.
Logical attributes.
Added layout.bipartite() function, a simple two-column layout
for bipartite graphs.
Support incidence matrices in bipartite Pajek files.
Pajek files in matrix format are now directed by default, unless they
are bipartite.
Support weighted (and signed) networks in Pajek when file is in
matrix format.
Fixed a bug in barabasi.game(), algorithm psumtree-multiple
just froze.
Function layout.mds() by default returns a layout matrix now.
Added support for Boolean attributes in the GraphML and GML readers
and writer.
Change MDS layout coordinates, first dim is according to first
eigenvalue, etc.
plot.communities() (plot.igraph(), really) draws a border
around the marked groups by default.
printing graphs now converts the name graph attribute to character
Convenience functions to query and set all attributes at once:
vertex.attriubutes(), graph.attributes() and edge.attributes().
Function graph.disjoint.union() handles attributes now.
Rewrite graph.union() to handle attributes properly.
rewire(): now supports the generation and destruction of loops.
Erdos-Renyi type bipartite random graphs: bipartite.random.game().
Support the new options (predecessors and inbound_edges) of
get_shortest_paths(), reorganized the output of
get.shortest.paths() completely.
Added graphlets() and related functions.
Fix modularity values of multilevel community if there are no merges
at all.
Fixed bug when deleting edges with FALSE in the matrix notation.
Fix bonpow() and alpha.centrality() and make sure that the
sparse solver is called.
tkplot() news: enable setting coordinates from the command line
via tkplot.setcoords() and access to the canvas via
tkplot.canvas().
Fixed a potential crash in igraph_edge_connectivity(), because of an
un-initialized variable in the C code.
Avoiding overflow in closeness() and related functions.
Check for NAs after converting 'type' to logical in
bipartite.projection().
graphNEL conversion functions only load the 'graph' package if it was
not loaded before and they load it at the end of the search path,
to minimize conflicts.
Fixed a bug when creating graphs from adjacency matrices, we now convert
them to double, in case they are integers.
Fixed an invalid memory read (and a potential crash) in the infomap
community detection.
Fixed a memory leak in the functions with attribute combinations.
Removed some memory leaks from the SCG functions.
Fixed some memory leaks in the ray tracer.
Fixed memory leak in graph.bfs() and graph.dfs().
Fix a bug in triad census that set the first element of the result
to NaN.
Fixed a crash in is.chordal().
Fixed a bug in weighted mudularity calculation, sum of the weights
was truncated to an integer.
Fixed a bug in weighted multilevel communtiies, the maximum weight
was rounded to an integer.
Fixed a bug in centralization.closeness.tmax().
Reimplement push-relabel maximum flow with gap heuristics.
Maximum flow functions now return some statistics about the push
relabel algorithm steps.
Function arpack() now gives error message if unknown options are
given.
Fixed missing whitespace in Pajek writer when the ID attribute was
numeric.
Fixed a bug that caused the GML reader to crash when the ID
attribute was non-numeric.
Fixed issue #500, potential segfault if the two graphs in BLISS
differ in the number of vertices or edges.
Added igraphtest() function.
Fix dyad census instability, sometimes incorrect results were
reported.
Dyad census detects integer overflow now and gives a warning.
Function add.edges() does not allow now zeros in the vertex set.
Added a function to count the number of adjacent triangles:
adjacenct.triangles().
Added graph.eigen() function, eigenproblems on adjacency matrices.
Added some workarounds for functions that create a lot of
graphs, decompose.graph() and graph.neighborhood() use it.
Fixes issue #508.
Added weights support for optimal.community(), closes #511.
Faster maximal clique finding.
Added a function to count maximum cliques.
Set operations: union, intersection, disjoint, union, difference,
compose now work based on vertex names (if they are present) and
keep attributes, closes #20.
Added'which argument to bipartite.projection (#307).
Add normalized argument to closeness functions, fixes issue #3.
R: better handling of complex attributes, [[ on vertex/edge sets,
fixes #231.
Implement the start argument in hrg.fit (#225).
Set root vertex in Reingold-Tilford layout, solves #473.
Fix betweenness normalization for directed graphs.
Fixed a bug in graph.density that resulted in incorrect values for
undirected graphs with loops
Fixed a bug when many graphs were created in one C call
(e.g. by graph.decompose), causing #550.
Fixed sparse graph.adjacency bugs for graphs with one edge,
and graphs with zero edges.
Fixed a bug that made Bellman-Ford shortest paths calculations fail.
Fixed a graph.adjacency bug for undirected, weighted graphs and
sparse matrices.
main, sub, xlab and ylab are proper graphics parameters
now (#555).
graph.data.frame coerces arguments to data frame (#557).
Fixed a minimum cut bug for weighted undirected graphs (#564).
Functions for simulating epidemics (SIR model) on networks,
see the sir function.
Fixed argument ordering in graph.mincut and related functions.
Avoid copying attributes in query functions and print (#573),
these functions are much faster now for graphs with many
vertices/edges and attributes.
Speed up writing GML and GraphML files, if some attributes are
integer. It was really-really slow.
Fix multiple root vertices in graph.bfs (#575).
igraph 0.6.6
Released Oct 28, 2013
Some bugs fixed:
Fixed a potential crash in the infomap.community() function.
Various fixed for the operators that work on vertex names (#136).
Fixed an example in the arpack() manual page.
arpack() now gives error message if unknown options
are supplied (#492).
Better arpack() error messages.
Fixed missing whitespace in Pajek writer when ID attribute
was numeric.
Fixed dyad census instability, sometimes incorrect
results were reported (#496).
Fixed a bug that caused the GML reader to crash when the ID
attribute was non-numeric
Fixed a potential segfault if the two graphs in BLISS
differ in the number of vertices or edges (#500).
Added the igraphtest() function to run tests from R (#485).
Dyad census detects integer overflow now and gives a warning (#497).
R: add.edges() does not allow now zeros in the vertex set (#503).
Add C++ namespace to the files that didn't have one.
Fixes some incompatibility with other packages (e.g. rgl)
and mysterious crashes (#523).
Fixed a bug that caused a side effect in set.vertex.attributes(),
set.edge.attributes() and set.graph.attributes() (#533).
Fixed a bug in degree.distribution() and cluster.distribution()
(#257).
igraph 0.6.5-2
Released May 16, 2013
Worked two CRAN check problems, and a gfortran bug (string bound
checking does not work if code is called from C and without string
length arguments at the "right" place).
Otherwise identical to 0.6.5-1.
igraph 0.6.5-1
Released February 27, 2013
Fixing an annoying bug, that broke two other packages on CRAN:
Setting graph attributes failed sometimes, if the attributes were
lists or other complex objects.
igraph 0.6.5
Released February 24, 2013
This is a minor release, to fix some very annoying bugs in 0.6.4:
igraph should now work well with older R versions.
Eliminate gap between vertex and edge when plotting an edge without an arrow.
Fixes #1118448.
Fixed an out-of-bounds array indexing error in the DrL layout, that
potentially caused crashes.
Fixed a crash in weighted betweenness calculation.
Plotting: fixed a bug that caused misplaced arrows at rectangle
vertex shapes.
igraph 0.6.4
Released February 2, 2013
The version number is not a mistake, we jump to 0.6.4 from 0.6,
for technical reasons. This version was actually never really
released, but some R packages of this version were uplodaded to
CRAN, so we include this version in this NEW file.
New features and bug fixes
Added a vertex shape API for defining new vertex shapes, and also
a couple of new vertex shapes.
Added the get.data.frame() function, opposite of graph.data.frame().
Added bipartite support to the Pajek reader and writer, closes bug
#1042298.
degree.sequence.game() has a new method now: "simple_no_multiple".
Added the is.degree.sequence() and is.graphical.degree.sequence()
functions.
rewire() has a new method: "loops", that can create loop edges.
Walktrap community detection now handles isolates.
layout.mds() returns a layout matrix now.
layout.mds() uses LAPACK instead of ARPACK.
Handle the '~' character in write.graph and read.graph. Bug
#1066986.
Added k.regular.game().
Use vertex names to plot if no labels are specified in the function
call or as vetex attributes. Fixes issue #1085431.
power.law.fit() can now use a C implementation.
Fixed a bug in barabasi.game() when out.seq was an empty vector.
Fixed a bug that made functions with a progress bar fail if called
from another package.
Fixed a bug when creating graphs from a weighted integer adjacency
matrix via graph.adjacency(). Bug #1019624.
Fixed overflow issues in centralization calculations.
Fixed a minimal.st.separators() bug, some vertex sets were incorrectly
reported as separators. Bug #1033045.
Fixed a bug that mishandled vertex colors in VF2 isomorphism
functions. Bug #1032819.
Pajek exporter now always quotes strings, thanks to Elena Tea Russo.
Fixed a bug with handling small edge weights in shortest paths
calculation in shortest.paths() (Dijkstra's algorithm.) Thanks to
Martin J Reed.
Weighted transitivity uses V(graph) as 'vids' if it is NULL.
Fixed a bug when 'pie' vertices were drawn together with other
vertex shapes.
Speed up printing graphs.
Speed up attribute queries and other basic operations, by avoiding
copying of the graph. Bug #1043616.
Fixed a bug in the NCV setting for ARPACK functions. It cannot be
bigger than the matrix size.
layout.merge()'s DLA mode has better defaults now.
Fixed a bug in layout.mds() that resulted vertices on top of each
other.
Fixed a bug in layout.spring(), it was not working properly.
Fixed layout.svd(), which was completely defunct.
Fixed a bug in layout.graphopt() that caused warnings and on
some platforms crashes.
Fixed community.to.membership(). Bug #1022850.
Fixed a graph.incidence() crash if it was called with a non-matrix
argument.
Fixed a get.shortest.paths bug, when output was set to "both".
Motif finding functions return NA for isomorphism classes that are
not motifs (i.e. not connected). Fixes bug #1050859.
Fixed get.adjacency() when attr is given, and the attribute has some
complex type. Bug #1025799.
Fixed attribute name in graph.adjacency() for dense matrices. Bug
#1066952.
Fixed erratic behavior of alpha.centrality().
Fixed igraph indexing, when attr is given. Bug #1073705.
Fixed a bug when calculating the largest cliques of a directed
graph. Bug #1073800.
Fixed a bug in the maximal clique search, closes #1074402.
Warn for negative weights when calculating PageRank.
Fixed dense, unweighted graph.adjacency when diag=FALSE. Closes
issue #1077425.
Fixed a bug in eccentricity() and radius(), the results were often
simply wrong.
Fixed a bug in get.all.shortest.paths() when some edges had zero weight.
graph.data.frame() is more careful when vertex names are numbers, to
avoid their scientific notation. Fixes issue #1082221.
Better check for NAs in vertex names. Fixes issue #1087215
Fixed a potential crash in the DrL layout generator.
Fixed a bug in the Reingold-Tilford layout when the graph is
directed and mode != ALL.
Vertices and edges are numbered from 1 instead of 0.
Note that this makes most of the old R igraph code incompatible
with igraph 0.6. If you want to use your old code, please use
the igraph0 package. See more at http://igraph.sf.net/relnotes-0.6.html.
The '[' and '[[' operators can now be used on igraph graphs,
for '[' the graph behaves as an adjacency matrix, for '[[' is
is treated as an adjacency list. It is also much simpler to
manipulate the graph structure, i.e. add/remove edges and vertices,
with some new operators. See more at ?graph.structure.
In all functions that take a vector or list of vertices or edges,
vertex/edge names can be given instead of the numeric ids.
New package 'igraphdata', contains a number of data sets that can
be used directly in igraph.
Igraph now supports loading graphs from the Nexus online data
repository, see nexus.get(), nexus.info(), nexus.list() and
nexus.search().
All the community structure finding algorithm return a 'communities'
object now, which has a bunch of useful operations, see
?communities for details.
Vertex and edge attributes are handled much better now. They
are kept whenever possible, and can be combined via a flexible API.
See ?attribute.combination.
R now prints igraph graphs to the screen in a more structured and
informative way. The output of summary() was also updated
accordingly.
R: Other new features
It is possible to mark vertex groups on plots, via
shading. Communities and cohesive blocks are plotted using this by
default.
Some igraph demos are now available, see a list via
'demo(package="igraph")'.
igraph now tries to select the optimal layout algorithm, when
plotting a graph.
Added a simple console, using Tcl/Tk. It contains a text area
for status messages and also a status bar. See igraph.console().
Reimplemented igraph options support, see igraph.options() and
getIgraphOpt().
Igraph functions can now print status messages.
R: New or updated functions
Community detection
The multi-level modularity optimization community structure detection
algorithm by Blondel et al. was added, see multilevel.community().
Distance between two community structures: compare.communities().
Community structure via exact modularity optimization,
optimal.community().
Hierarchical random graphs and community finding, porting the code
from Aaron Clauset. See hrg.game(), hrg.fit(), etc.
Added the InfoMAP community finding method, thanks to Emmanuel
Navarro for the code. See infomap.community().
Shortest paths
Eccentricity (eccentricity()), and radius (radius()) calculations.
Shortest path calculations with get.shortest.paths() can now
return the edges along the shortest paths.
get.all.shortest.paths() now supports edge weights.
Centrality
Centralization scores for degree, closeness, betweenness and
eigenvector centrality. See centralization.scores().
Personalized Page-Rank scores, see page.rank().
Subgraph centrality, subgraph.centrality().
Authority (authority.score()) and hub (hub.score()) scores support
edge weights now.
Support edge weights in betweenness and closeness calculations.
bonpow(), Bonacich's power centrality and alpha.centrality(),
Alpha centrality calculations now use sparse matrices by default.
Eigenvector centrality calculation, evcent() now works for
directed graphs.
Betweenness calculation can now use arbitrarily large integers,
this is required for some lattice-like graphs to avoid overflow.
Support writing the LEDA file format in write.graph().
Plotting and layouts
Star layout: layout.star().
Layout based on multidimensional scaling, layout.mds().
New layouts layout.grid() and layout.grid.3d().
Sugiyama layout algorithm for layered directed acyclic graphs,
layout.sugiyama().
Graph generators
New graph generators: static.fitness.game(), static.power.law.game().
barabasi.game() was rewritten and it supports three algorithms now,
the default algorithm does not generate multiple or loop edges.
The graph generation process can now start from a supplied graph.
The Watts-Strogatz graph generator, igraph_watts_strogatz() can
now create graphs without loop edges.
Others
Added the Spectral Coarse Graining algorithm, see scg().
The cohesive.blocks() function was rewritten in C, it is much faster
now. It has a nicer API, too. See demo("cohesive").
Added generic breadth-first and depth-first search implementations
with many callbacks, graph.bfs() and graph_dfs().
Support vertex and edge coloring in the VF2 (sub)graph isomorphism
functions (graph.isomorphic.vf2(), graph.count.isomorphisms.vf2(),
graph.get.isomorphisms.vf2(), graph.subisomorphic.vf2(),
graph.count.subisomorphisms.vf2(), graph.get.subisomorphisms.vf2()).
Assortativity coefficient, assortativity(), assortativity.nominal()
and assortativity.degree().
Vertex operators that work by vertex names:
graph.intersection.by.name(), graph.union.by.name(),
graph.difference.by.name(). Thanks to Magnus Torfason for
contributing his code!
Function to calculate a non-induced subraph: subgraph.edges().
More comprehensive maximum flow and minimum cut calculation,
see functions graph.maxflow(), graph.mincut(), stCuts(), stMincuts().
Check whether a directed graph is a DAG, is.dag().
has.multiple() to decide whether a graph has multiple edges.
Added a function to calculate a diversity score for the vertices,
graph.diversity().
Added progress bar support to beweenness() and
betweenness.estimate(), layout.drl()
Speeded up betweenness estimation
Speeded up are.connected()
Johnson's shortest paths algorithm added
shortest.paths() has now an 'algorithm' argument to choose from the
various implementations manually
Always quote symbolic vertex names when printing graphs or edges
Average nearest neighbor degree calculation, graph.knn()
Weighted degree (also called strength) calculation, graph.strength()
Some new functions to support bipartite graphs: graph.bipartite(),
is.bipartite(), get.indicence(), graph.incidence(),
bipartite.projection(), bipartite.projection.size()
Support for plotting curved edges with plot.igraph() and tkplot()
Added support for weighted graphs in alpha.centrality()
Added the label propagation community detection algorithm by
Raghavan et al., label.propagation.community()
cohesive.blocks() now has a 'cutsetHeuristic' argument to choose
between two cutset algorithms
Added a function to "unfold" a tree, unfold.tree()
New tkplot() arguments to change the drawing area
Added a minimal GUI, invoke it with tkigraph()
The DrL layout generator, layout.drl() has a three dimensional mode
now.
Bugs corrected in the R interface
Fixed a bug in VF2 graph isomorphism functions
Fixed a bug when a sparse adjacency matrix was requested in
get.adjacency() and the graph was named
VL graph generator in degree.sequence.game() checks now that
the sum of the degrees is even
Many fixes for supporting various compilers, e.g. GCC 4.4 and Sun's
C compiler
Fixed memory leaks in graph.automorphisms(), Bellman-Ford
shortest.paths(), independent.vertex.sets()
Fix a bug when a graph was imported from LGL and exported to NCOL
format (#289596)
cohesive.blocks() creates its temporary file in the session
temporary directory
write.graph() and read.graph() now give error messages when unknown
arguments are given
The GraphML reader checks the name of the attributes to avoid adding
a duplicate 'id' attribute
It is possible to change the 'ncv' ARPACK parameter for
leading.eigenvector.community()
Fixed a bug in path.length.hist(), 'unconnected' was wrong
for unconnected and undirected graphs
Better handling of attribute assingment via iterators, this is now
also clarified in the manual
Better error messages for unknown vertex shapes
Make R package unload cleanly if unloadNamespace() is used
Fixed a bug in plotting square shaped vertices (#325244)
Fixed a bug in graph.adjacency() when the matrix is a sparse matrix
of class "dgTMatrix"
preference.game and asymmetric.preference.game were
rewritten, they are O(|V|+|E|) now, instead of O(|V|^2).
Edge weight support in function 'get.shortest.paths', it uses
Dijkstra's algorithm.
Bugs corrected in the R interface
A bug was corrected in write.pajek.bgraph.
Several bugs were corrected in graph.adjacency.
Pajek reader bug corrected, used to segfault if '*Vertices'
was missing.
Directedness is handled correctly when writing GML files.
(But note that 'correct' conflicts the standard here.)
Corrected a bug when calculating weighted, directed PageRank on an
undirected graph. (Which does not make sense anyway.)
Several bugs were fixed in the Reingold-Tilford layout to avoid
edge crossings.
A bug was fixed in the GraphML reader, when the value of a graph
attribute was not specified.
Fixed a bug in the graph isomorphism routine for small (3-4 vertices)
graphs.
Corrected the random sampling implementation (igraph_random_sample),
now it always generates unique numbers. This affects the
Gnm Erdos-Renyi generator, it always generates simple graphs now.
The basic igraph constructor (igraph_empty_attrs, all functions
are expected to call this internally) now checks whether the number
of vertices is finite.
The LGL, NCOL and Pajek graph readers handle errors properly now.
The non-symmetric ARPACK solver returns results in a consistent form
now.
The fast greedy community detection routine now checks that the graph
is simple.
The LGL and NCOL parsers were corrected to work with all
kinds of end-of-line encodings.
The 'rescale', 'asp' and 'frame' graphical parameters were added
Create graphs from a formula notation (graph.formula)
Handle graph attributes properly
Calculate the actual minimum cut for undirected graphs
Adjacency lists, get.adjlist and get.adjedgelist added
Eigenvector centrality computation is much faster now
Proper R warnings, instead of writing the warning to the terminal
R checks graphical parameters now, the unknown ones are not just
ignored, but an error message is given
plot.igraph has an 'add' argument now to compose plots with multiple
graphs
plot.igraph supports the 'main' and 'sub' arguments
layout.norm is public now, it can normalize a layout
It is possible to supply startup positions to layout generators
Always free memory when CTRL+C/ESC is pressed, in all operating
systems
plot.igraph can plot square vertices now, see the 'shape' parameter
graph.adjacency rewritten when creating weighted graphs
We use match.arg whenever possible. This means that character scalar
options can be abbreviated and they are always case insensitive
VF2 graph isomorphism routines can check subgraph isomorphism now,
and they are able to return matching(s)
The BLISS graph isomorphism algorithm is included in igraph now. See
canonical.permutation, graph.isomorphic.bliss
We use ARPACK for eigenvalue/eigenvector calculation. This means that the
following functions were rewritten: page.rank,
leading.eigenvector.community.*, evcent. New functions based on
ARPACK: hub.score, authority.score, arpack.
Edge weights for Fruchterman-Reingold layout (layout.fruchterman.reingold).
Line graph calculation (line.graph)
Kautz and de Bruijn graph generators (graph.kautz, graph.de.bruijn)
Support for writing graphs in DOT format
Jaccard and Dice similarity coefficients added (similarity.jaccard,
similarity.dice)
Counting the multiplicity of edges (count.multiple)
The graphopt layout algorithm was added, layout.graphopt
Generation of "famous" graphs (graph.famous).
Create graphs from LCF notation (graph.cf).
Dyad census and triad cencus functions (dyad.census, triad.census)
Cheking for simple graphs (is.simple)
Create full citation networks (graph.full.citation)
Create a histogram of path lengths (path.length.hist)
Forest fire model added (forest.fire.game)
DIMACS reader can handle different file types now
Biconnected components and articulation points (biconnected.components,
articulation.points)
Kleinberg's hub and authority scores (hub.score, authority.score)
as.undirected handles attributes now
Geometric random graph generator (grg.game) can return the
coordinates of the vertices
Function added to convert leading eigenvector community structure result to
a membership vector (community.le.to.membership)
Weighted fast greedy community detection
Weighted page rank calculation
Functions for estimating closeness, betweenness, edge betweenness by
introducing a cutoff for path lengths (closeness.estimate,
betweenness.estimate, edge.betweenness.estimate)
Weighted modularity calculation
Function for permuting vertices (permute.vertices)
Betweenness and closeness calculations are speeded up
read.graph can handle all possible line terminators now (\r, \n, \r\n, \n\r)
Error handling was rewritten for walktrap community detection,
the calculation can be interrupted now
The maxflow/mincut functions allow to supply NULL pointer for edge
capacities, implying unit capacities for all edges
Bugs corrected in the R interface
Fixed a bug in cohesive.blocks, cohesive blocks were sometimes not
calculated correctly
igraph 0.4.5
Released January 1, 2008
New:
Cohesive block finding in the R interface, thanks to Peter McMahan
for contributing his code. See James Moody and Douglas R. White,
2003, in Structural Cohesion and Embeddedness: A Hierarchical
Conception of Social Groups American Sociological Review 68(1):1-25
Biconnected components and articulation points.
R interface: better printing of attributes.
R interface: graph attributes can be used via '$'.
Bug fixed:
Erdos-Renyi random graph generators rewritten.
igraph 0.4.4
Released October 3, 2007
This release should work seemlessly with the new R 2.6.0 version.
Some other bugs were also fixed:
A bug was fixed in the Erdos-Renyi graph generator, which sometimes
added an extra vertex.
igraph 0.4.3
Released August 13, 2007
The next one in the sequence of bugfix releases. Thanks to many people
sending bug reports. Here are the changes:
Some memory leaks removed when using attributes from R or Python.
GraphML parser: entities and character data in multiple chunks are
now handled correctly.
A bug corrected in edge betweenness community structure detection,
it failed if called many times from the same program/session.
Edge betweeness community structure: handle unconnected graphs properly.
Fixed bug related to fast greedy community detection in unconnected graphs.
Use a different kind of parser (Push) for reading GraphML
files. This is almost invisible for users but fixed a
nondeterministic bug when reading in GraphML files.
R interface: plot now handles properly if called with a vector as
the edge.width argument for directed graphs.
R interface: bug (typo) corrected for walktrap.community and
weighted graphs.
igraph 0.4.2
Released June 7, 2007
This is another bugfix release, as there was a serious bug in the
R package of the previous version: it could not read and write graphs
to files in any format under MS Windows.
Some other bits added:
circular Reingold-Tilford layout generator for trees
corrected a bug, Pajek files are written properly under MS Windows now.
arrow.size graphical edge parameter added in the R interface.
igraph 0.4.1
Released May 23, 2007
This is a minor release, it corrects a number of bugs, mostly in the
R package.
igraph 0.4
Released May 21, 2007
The major new additions in this release is a bunch of community
detection algorithms and support for the GML file format. Here
is the complete list of changes:
New in the R interface
as the internal representation changed, graphs stored with 'save'
with an older igraph version cannot be read back with the new
version reliably.
neighbors returns ordered lists
is.loop and is.multiple were added
topological sorting
VF2 isomorphism algorithm
support for reading graphs from the Graph Database for isomorphism
graph.mincut can calculate the actual minimum cut
girth calculation added, thanks to Keith Briggs
support for reading and writing GML files
Walktrap community detection algorithm added, thanks to Matthieu Latapy
and Pascal Pons
edge betweenness based community detection algorithm added
fast greedy algorithm for community detection by Clauset et al. added
thanks to Aaron Clauset for sharing his code
leading eigenvector community detection algorithm by Mark Newman added
functions for creating dendrograms from the output of the
community detection algorithms added
community.membership supporting function added, creates
a membership vector from a community structure merge tree
modularity calculation added
graphics parameter handling is completely rewritten, uniform handling
of colors and fonts, make sure you read ?igraph.plotting
new plotting parameter for edges: arrow.mode
a bug corrected when playing a nonlinear barabasi.game
better looking plotting in 3d using rglplot: edges are 3d too
rglplot layout is allowed to be two dimensional now
rglplot suspends updates while drawing, this makes it faster
loop edges are correctly plotted by all three plotting functions
better printing of attributes when printing graphs
summary of a graph prints attribute names
is.igraph rewritten to make it possible to inherit from the 'igraph' class
somewhat better looking progress meter for functions which support it
Others
many functions benefit from the new internal representation and are
faster now: transitivity, reciprocity, graph operator functions like
intersection and union, etc.
Bugs corrected
corrected a bug when reading Pajek files: directed graphs were read
as undirected
igraph 0.3.2
Released Dec 19, 2006
This is a new major release, it contains many new things:
Changes in the R interface
bonpow function ported from SNA to calculate Bonacich power centrality
get.adjacency supports attributes now, this means that it sets the
colnames and rownames attributes and can return attribute values in
the matrix instead of 0/1
grg.game, geometric random graphs
graph.density, graph density calculation
edge and vertex attributes can be added easily now when added new
edges with add.edges or new vertices with add.vertices
graph.data.frame creates graph from data frames, this can be used to
create graphs with edge attributes easily
plot.igraph and tkplot can plot self-loop edges now
graph.edgelist to create a graph from an edge list, can also handle
edge lists with symbolic names
get.edgelist has now a 'names' argument and can return symbolic
vertex names instead of vertex ids, by default id uses the 'name'
vertex attribute is returned
printing graphs on screen also prints symbolic symbolic names
(the 'name' attribute if present)
maximum flow and minimum cut functions: graph.maxflow, graph.mincut
vertex and edge connectivity: edge.connectivity, vertex.connectivity
edge and vertex disjoint paths: edge.disjoint.paths,
vertex.disjoint.paths
White's cohesion and adhesion measure: graph.adhesion, graph.cohesion
dimacs file format added
as.directed handles attributes now
constraint corrected, it handles weighted graphs as well now
weighted attribute to graph.adjacency
spinglass-based community structure detection, the Joerg Reichardt --
Stefan Bornholdt algorithm added: spinglass.community
graph.extended.chordal.ring, extended chordal ring generation
no.clusters calculates the number of clusters without calculating
the clusters themselves
minimum spanning tree functions updated to keep attributes
transitivity can calculate local transitivity as well
neighborhood related functions added: neighborhood,
neighborhood.size, graph.neighborhood
new graph generators based on vertex types: preference.game and
asymmetric.preference.game
Bugs corrected
attribute handling bug when deleting edges corrected
GraphML escaping and NaN handling corrected
bug corrected to make it possible compile the R package without the
libxml2 library
a bug in Erdos-Renyi graph generation corrected: it had problems
with generating large directed graphs
bug in constraint calculation corrected, it works well now
fixed memory leaks in the GraphML reader
error handling bug corrected in the GraphML reader
bug corrected in R version of graph.laplacian when normalized
Laplacian is requested
memory leak corrected in get.all.shortest.paths in the R package
igraph 0.2.1
Released Aug 23, 2006
This is a bug-fix release. Bugs fixed:
reciprocity corrected to avoid segfaults
some docs updates
various R package updates to make it conform to the CRAN rules
igraph 0.2
Released Aug 18, 2006
Release time at last! There are many new things in igraph 0.2, the
most important ones:
reading writing Pajek and GraphML formats with attributes
(not all Pajek and GraphML files are supported, see documentation
for details)
the RANDEDU fast motif search algorithm is implemented
many new graph generators, both games and regular graphs
many new structural properties: transitivity, reciprocity, etc.
graph operators: union, intersection, difference, structural holes, etc.
conversion between directed and undirected graphs
new layout algorithms for trees and large graphs, 3D layouts
and many more.
New things specifically in the R package:
support for CTRL+C
new functions: Graph Laplacian, Burt's constraint, etc.
vertex/edge sequences totally rewritten, smart indexing (see manual)
new R manual and tutorial: `Network Analysis with igraph', still
under development but useful
very basic 3D plotting using OpenGL
Although this release was somewhat tested on Linux, MS Windows, Mac
OSX, Solaris 8 and FreeBSD, no heavy testing was done, so it might
contain bugs, and we kindly ask you to send bug reports to make igraph
better.
igraph 0.1
Released Jan 30, 2006
After about a year of development this is the first "official" release
of the igraph library. This release should be considered as beta
software, but it should be useful in general. Please send your
questions and comments.