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igraph 0.6.5
============
Released February 24, 2013
The version number is not a mistake, we jump to 0.6.5 from 0.6,
for technical reasons.
R: 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 some potential crashes in the DrL layout generator.
- Fixed a bug in the Reingold-Tilford layout when the graph is
directed and mode != ALL.
- Eliminate gap between vertex and edge when plotting an edge without an arrow.
Fixes \#1118448.
- Fixed a bug in has.multiple() that resulted in false negatives for
some undirected graphs.
- Fixed a crash in weighted betweenness calculation.
- R plotting: fixed a bug that caused misplaced arrows at rectangle
vertex shapes.
Python news and fixes
---------------------
- Added bipartite support to the Pajek reader and writer, closes bug
\#1042298.
- Graph.Degree_Sequence() has a new method now: "no_multiple".
- Added the is_degree_sequence() and is_graphical_degree_sequence()
functions.
- rewire() has a new mode: "loops", that can create loop edges.
- Walktrap community detection now handles isolates.
- Added Graph.K_Regular().
- power_law_fit() now uses a C implementation.
- Added support for setting the frame (stroke) width of vertices using the
frame_width attribute or the vertex_frame_width keyword argument in plot()
- Improved Inkscape-friendly SVG output from Graph.write_svg(), thanks to drlog
- Better handling of named vertices in Graph.delete_vertices()
- Added experimental Gephi graph streaming support; see igraph.remote.gephi and
igraph.drawing.graph.GephiGraphStreamingDrawer
- Nicer __repr__ output for Flow and Cut instances
- Arrows are now placed correctly around diamond-shaped nodes on plots
- Added Graph.TupleList, a function that allows one to create graphs with
edge attributes quickly from a list of tuples.
- plot() now also supports .eps as an extension, not only .ps
- Fixed overflow issues in centralization calculations.
- 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 Graph.shortest_paths() (Dijkstra's algorithm.) Thanks to
Martin J Reed.
- Fixed a bug in the NCV setting for ARPACK functions. It cannot be
bigger than the matrix size.
- Fixed a bug in Graph.layout_mds() that resulted vertices on top of each
other.
- Motif finding functions return nan for isomorphism classes that are
not motifs (i.e. not connected). Fixes bug \#1050859.
- Fixed a bug when calculating the largest cliques of a directed
graph. Bug \#1073800.
- Warn for negative weights when calculating PageRank.
- Fixed a bug in Graph.eccentricity() and Graph.radius(), the results were often
simply wrong.
- Fixed a bug in Graph.get.all.shortest.paths() when some edges had zero weight.
- Fixed some potential crashes in the DrL layout generator.
- Fixed a bug in the Reingold-Tilford layout when the graph is
directed and mode != ALL.
- Fixed a bug in Graph.layout_sugiyama() when the graph had no edges.
- Fixed a bug in Graph.community_label_propagation() when initial labels
contained -1 entries. Issue \#1105460.
- Repaired the DescartesCoordinateSystem class (which is not used too frequently
anyway)
- Fixed a bug that caused segfaults when an igraph Graph was used in a thread
forked from the main Python interpreter thread
- Fixed a bug that affected file handles created from Python strings in the
C layer
- Fixed a bug in has_multiple() that resulted in false negatives
for some undirected graphs.
- Fixed a crash in weighted betweenness calculation.
C library news and changes
--------------------------
- Added bipartite support to the Pajek reader and writer, closes bug
\#1042298.
- igraph_layout_mds() uses LAPACK instead of ARPACK.
- igraph_degree_sequence_game has a new method:
IGRAPH_DEGSEQ_SIMPLE_NO_MULTIPLE.
- Added the igraph_is_degree_sequence() and
igraph_is_graphical_degree_sequence() functions.
- igraph_rewire() has a new method: IGRAPH_REWIRING_SIMPLE_LOOPS,
that can create loops.
- Walktrap community detection now handles isolates.
- Added igraph_k_regular_game().
- Added igraph_power_law_fit.
- Fixed a bug in igraph_barabasi_game when outseq was an empty vector.
- Fixed overflow issues in centralization calculations.
- Fixed an invalid return value of igraph_vector_ptr_pop_back.
- Fixed a igraph_all_minimal_st_separators() bug, some vertex sets
were incorrectly reported as separators. Bug \#1033045.
- Pajek exporter now always quotes strings, thanks to Elena Tea Russo.
- Fixed a bug with handling small edge weights in
igraph_shortest_paths_dijkstra(), thanks to Martin J Reed.
- Fixed a bug in the NCV setting for ARPACK functions. It cannot be
bigger than the matrix size.
- igraph_layout_merge_dla uses better default parameter values now.
- Fixed a bug in igraph_layout_mds() that resulted vertices on top of
each other.
- Attribute handler table is not thread-local any more.
- Motif finding functions return IGRAPH_NAN for isomorphism classes
that are not motifs (i.e. not connected). Fixes bug \#1050859.
- Fixed a bug when calculating the largest cliques of a directed
graph. Bug \#1073800.
- Fix a bug in degree_sequence_game(), in_seq can be an empty vector as
well instead of NULL, for an undirected graph.
- Fixed a bug in the maximal clique search, closes \#1074402.
- Warn for negative weights when calculating PageRank.
- Fixed a bug in igraph_eccentricity() (and also igraph_radius()),
the results were often simply wrong.
- Fixed a bug in igraph_get_all_shortest_paths_dijkstra() when edges
had zero weight.
- Fixed some potential crashes in the DrL layout generator.
- Fixed a bug in the Reingold-Tilford layout when the graph is
directed and mode != ALL.
- Fixed a bug in igraph_has_multiple() that resulted in false negatives
for some undirected graphs.
- Fixed a crash in weighted betweenness calculation.
igraph 0.6
==========
Released June 11, 2012
See also the release notes at
http://igraph.sf.net/relnotes-0.6.html
R: Major new features
---------------------
- 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.
Input/output and file formats
-----------------------------
- Support the DL file format in graph.read(). See
http://www.analytictech.com/networks/dataentry.htm.
- 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().
- Graph Laplacian calculation (graph.laplacian()) supports edge
weights now.
- Biconnected component calculation, biconnected.components()
now returns the components themselves.
- bipartite.projection() calculates multiplicity of edges.
- Maximum cardinality search: maximum.cardinality.search() and
chordality test: is.chordal()
- Convex hull computation, convex.hull().
- Contract vertices, contract.vertices().
New in the Python interface
---------------------------
TODO
Major changes in the Python interface
-------------------------------------
TODO
New in the C layer
------------------
- Maximum cardinality search: igraph_maximum_cardinality_search() and
chordality test: igraph_is_chordal().
- Support the DL file format, igraph_read_graph_dl(). See
http://www.analytictech.com/networks/dataentry.htm.
- Added generic breadth-first and depth-first search implementations
with many callbacks (igraph_bfs(), igraph_dfs()).
- Centralization scores for degree, closeness, betweenness and
eigenvector centrality, see igraph_centralization().
- Added igraph_sparsemat_t, a type that implements sparse
matrices based on the CXSparse library by Tim Davis.
See http://www.cise.ufl.edu/research/sparse/CXSparse/.
- Personalized Page-Rank scores, igraph_personalized_pagerank() and
igraph_personalized_pagerank_vs().
- Assortativity coefficient, igraph_assortativity(),
igraph_assortativity_nominal(), and igraph_assortativity_degree().
- The multi-level modularity optimization community structure detection
algorithm by Blondel et al. was added, see igraph_community_multilevel().
- Added the igraph_version() function.
- Star layout: igraph_layout_star().
- Function to calculate a non-induced subraph: igraph_subgraph_edges().
- Distance between two community structures: igraph_compare_communities().
- Community structure via exact modularity optimization,
igraph_community_optimal_community().
- More comprehensive maximum flow and minimum cut calculation,
see functions igraph_maxflow(), igraph_mincut(),
igraph_all_st_cuts(), igraph_all_st_mincuts().
- Layout based on multidimensional scaling, igraph_layout_mds().
- It is now possible to access the random number generator(s) via an
API. Multiple RNGs can be used, from external sources as well.
The default RNG is MT19937.
- Added igraph_get_all_shortest_paths_dijkstra, for calculating all
non-negatively weighted shortest paths.
- Check whether a directed graph is a DAG, igraph_is_dag().
- Cohesive blocking, a'la Moody & White, igraph_cohesive_blocks().
- Igraph functions can now print status messages, see igraph_status()
and related functions.
- Support writing the LEDA file format, igraph_write_graph_leda().
- Contract vertices, igraph_contract_vertices().
- The C reference manual has now a lot of example programs.
- Hierarchical random graphs and community finding, porting the code
from Aaron Clauset. See igraph_hrg_game(), igraph_hrg_fit(), etc.
- igraph_has_multiple() to decide whether a graph has multiple edges.
- New layouts igraph_layout_grid() and igraph_layout_grid_3d().
- igraph_integer_t is really an integer now, it used to be a double.
- igraph_minimum_spanning_tree(), calls either the weighted or
the unweighted implementation.
- Eccentricity (igraph_eccentricity()), and radius (igraph_radius())
calculations.
- Several game theory update rules, written by Minh Van Nguyen. See
igraph_deterministic_optimal_imitation(),
igraph_stochastic_imitation(), igraph_roulette_wheel_imitation(),
igraph_moran_process(),
- Sugiyama layout algorithm for layered directed acyclic graphs,
igraph_layout_sugiyama().
- New graph generators: igraph_static_fitness_game(),
igraph_static_power_law_game().
- Added the InfoMAP community finding method, thanks to Emmanuel
Navarro for the code. See igraph_community_infomap().
- Added the Spectral Coarse Graining algorithm, see igraph_scg().
- Added a function to calculate a diversity score for the vertices,
igraph_diversity().
Major changes in the C layer
----------------------------
- Authority (igraph_authority_score()) and hub (igraph_hub_score()) scores
support edge weights now.
- Graph Laplacian calculation (igraph_laplacian()) supports edge
weights now.
- Support edge weights in betweenness (igraph_betweenness()) and closeness
(igraph_closeness()) calculations.
- Support vertex and edge coloring in the VF2 graph isomorphism
algorithm (igraph_isomorphic_vf2(), igraph_count_isomorphisms_vf2(),
igraph_get_isomorphisms_vf2(), igraph_subisomorphic_vf2(),
igraph_count_subisomorphisms_vf2(), igraph_get_subisomorphisms_vf2()).
- Added print operations for the igraph_vector*_t, igraph_matrix*_t and
igraph_strvector_t types.
- Biconnected component calculation (igraph_biconnected_components())
can now return the components themselves.
- Eigenvector centrality calculation, igraph_eigenvector_centrality()
now works for directed graphs.
- Shortest path calculations with get_shortest_paths() and
get_shortest_paths_dijkstra() can now return the edges along the paths.
- Betweenness calculation can now use arbitrarily large integers,
this is required for some lattice-like graphs to avoid overflow.
- igraph_bipartite_projection() calculates multiplicity of edges.
- igraph_barabasi_game() was rewritten and it supports three
algorithms now, the default algorithm does not generate multiple or
loop edges.
- The Watts-Strogatz graph generator, igraph_watts_strogatz() can
now create graphs without loop edges.
- igraph should be now thread-safe, on architectures that support
thread-local storage (Linux and Windows: yes, Mac OSX: no).
We also fixed numerous bugs, too many to include them here, sorry.
You may look at our bug tracker at https://bugs.launchpad.net/igraph
to check whether a bug was fixed or not. Thanks for all the people
reporting bugs. Special thanks to Minh Van Nguyen for a lot of bug
reports, documentation fixes and contributed code!
igraph 0.5.3
============
Released November 22, 2009
Bugs corrected in the R interface
---------------------------------
- Some small changes to make 'R CMD check' clean
- Fixed a bug in graph.incidence, the 'directed' and 'mode' arguments
were not handled correctly
- Betweenness and edge betweenness functions work for graphs with
many shortest paths now (up to the limit of long long int)
- When compiling the package, the configure script fails if there is
no C compiler available
- igraph.from.graphNEL creates the right number of loop edges now
- Fixed a bug in bipartite.projection() that caused occasional crashes
on some systems
New in the Python interface
---------------------------
- Added support for weighted diameter
- get_eid() considers edge directions by default from now on
- Fixed a memory leak in the attribute handler
- 'NaN' and 'inf' are treated correctly now
Bugs corrected in the C layer
-----------------------------
- Betweenness and edge betweenness functions work for graphs with
many shortest paths now (up to the limit of long long int)
- The configure script fails if there is no C compiler available
- Fixed a bug in igraph_community_spinglass, when csize was a NULL
pointer, but membership was not
- Fixed a bug in igraph_bipartite_projection that caused occasional
crashes on some systems
igraph 0.5.2
============
Released April 10, 2009
See also the release notes at
http://igraph.sf.net/relnotes-0.5.2.html
New in the R interface
----------------------
- 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"
New in the Python interface
---------------------------
- Speeded up betweenness estimation
- Johnson's shortest paths algorithm added (selected automatically
by Graph.shortest_paths() if needed)
- Weighted degree (also called strength) calculation, Graph.strength()
- Some new methods to support bipartite graphs: Graph.Bipartite(),
Graph.is_bipartite(), Graph.get_indicence(), Graph.Incidence(),
Graph.bipartite_projection(), Graph.bipartite_projection_size()
- Added the label propagation community detection algorithm by
Raghavan et al., Graph.community_label_propagation()
- Added a function to "unfold" a tree, Graph.unfold_tree()
- setup.py script improvements
- Graph plotting now supports edge_arrow_size and edge_arrow_width
- Added Graph.Formula to create small graphs from a simple notation
- VertexSeq and EdgeSeq objects can now be indexed by slices
New in the C layer
------------------
- Added progress bar support to igraph_betweenness() and
igraph_betweenness_estimate(), igraph_layout_drl()
- Speeded up igraph_betweenness_estimate(), igraph_get_eid(),
igraph_are_connected(), igraph_get_eids()
- Added igraph_get_eid2()
- Johnson's shortest path algorithm added:
igraph_shortest_paths_johnson()
- Average nearest neighbor degree calculation,
igraph_avg_nearest_neighbor_degree()
- Weighted degree (also called strength) calculation,
igraph_strength()
- Some functions to support bipartite graphs: igraph_full_bipartite(),
igraph_bipartite_projection(), igraph_create_bipartite(),
igraph_incidence(), igraph_get_incidence(),
igraph_bipartite_projection_size(), igraph_is_bipartite()
- Added the label propagation community detection algorithm by
Raghavan et al., igraph_community_label_propagation()
- Added an example that shows how to set the random number generator's
seed from C (examples/simple/random_seed.c)
- Added a function to "unfold" a tree, igraph_unfold_tree()
- C attribute handler updates: added functions to query many
vertices/edges at once
- Three dimensional DrL layout, igraph_layout_drl_3d()
Bugs corrected in the C layer
-----------------------------
- Fixed a bug in igraph_isomorphic_function_vf2(), affecting all VF2
graph isomorphism functions
- VL graph generator in igraph_degree_sequence_game() checks now that
the sum of the degrees is even
- Many small corrections to make igraph compile with Microsoft Visual
Studio 2003, 2005 and 2008
- Many fixes for supporting various compilers, e.g. GCC 4.4 and Sun's
C compiler
- Fix a bug when a graph was imported from LGL and exported to NCOL
format (\#289596)
- Fixed memory leaks in igraph_automorphisms(),
igraph_shortest_paths_bellman_ford(),
igraph_independent_vertex_sets()
- 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
igraph_community_leading_eigenvector()
- Fixed a bug in igraph_path_length_hist(), 'unconnected' was wrong
for unconnected and undirected graphs.
igraph 0.5.1
============
Released July 14, 2008
See also the release notes at
http://igraph.sf.net/relnotes-0.5.1.html
New in the R interface
----------------------
- A new layout generator called DrL.
- Uniform sampling of random connected undirected graphs with a
given degree sequence.
- Edge labels are plotted at 1/3 of the edge, this is better if
the graph has mutual edges.
- Initial and experimental vertex shape support in 'plot'.
- New function, 'graph.adjlist' creates igraph graphs from
adjacency lists.
- Conversion to/from graphNEL graphs, from the 'graph' R package.
- Fastgreedy community detection can utilize edge weights now, this
was missing from the R interface.
- The 'arrow.width' graphical parameter was added.
- graph.data.frame has a new argument 'vertices'.
- graph.adjacency and get.adjacency support sparse matrices,
the 'Matrix' package is required to use this functionality.
- graph.adjacency adds column/row names as 'name' attribute.
- Weighted shortest paths using Dijkstra's or the Belmann-Ford
algorithm.
- Shortest path functions return 'Inf' for unreachable vertices.
- New function 'is.mutual' to find mutual edges in a directed graph.
- Added inverse log-weighted similarity measure (a.k.a. Adamic/Adar
similarity).
- 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.
- Hub & authority score calculations initialize ARPACK parameters now.
- Fixed a bug in the Walktrap community detection routine, when applied
to unconnected graphs.
- Several small memory leaks were removed, and a big one from the Spinglass
community structure detection function
New in the Python interface
---------------------------
- A new layout generator called DrL.
- Uniform sampling of random connected undirected graphs with a
given degree sequence.
- Methods parameters accepting igraph.IN, igraph.OUT and igraph.ALL
constants now also accept these as strings ("in", "out" and "all").
Prefix matches also allowed as long as the prefix match is unique.
- Graph.shortest_paths() now supports edge weights (Dijkstra's and
Bellman-Ford algorithm implemented)
- Graph.get_shortest_paths() also supports edge weights
(only Dijkstra's algorithm yet)
- Added Graph.is_mutual() to find mutual edges in a directed graph.
- Added inverse log-weighted similarity measure (a.k.a. Adamic/Adar
similarity).
- preference.game and asymmetric.preference.game were
rewritten, they are O(|V|+|E|) now, instead of O(|V|^2).
- ARPACK options can now be modified from the Python interface
(thanks to Kurt Jacobson)
- Layout.to_radial() added -- now you can create a top-down tree
layout by the Reingold-Tilford algorithm and then turn it to a
radial tree layout
- Added Graph.write_pajek() to save graphs in Pajek format
- Some vertex and edge related methods can now also be accessed via
the methods of VertexSeq and EdgeSeq, restricted to the current
vertex/edge sequence of course
- Visualisations now support triangle shaped vertices
- Added Graph.mincut()
- Added Graph.Weighted_Adjacency() to create graphs from weighted
adjacency matrices
- Kamada-Kawai and Fruchterman-Reingold layouts now accept initial
vertex positions
- Graph.Preference() and Graph.Asymmetric_Preference() were
rewritten, they are O(|V|+|E|) now, instead of O(|V|^2).
Bugs corrected in the Python interface
--------------------------------------
- Graph.constraint() now properly returns floats instead of integers
(thanks to Eytan Bakshy)
- Graphs given by adjacency matrices are now finally loaded and saved
properly
- Graph.Preference() now accepts floats in type distributions
- A small bug in Graph.community_edge_betweenness() corrected
- Some bugs in numeric attribute handling resolved
- VertexSeq and EdgeSeq objects can now be subsetted by lists and
tuples as well
- Fixed a bug when dealing with extremely small layout sizes
- Eigenvector centality now always return positive values
- Graph.authority_score() now really returns the authority scores
instead of the hub scores (blame copypasting)
- 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 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.
- Hub & authority score calculations initialize ARPACK parameters now.
- Fixed a bug in the Walktrap community detection routine, when applied
to unconnected graphs.
- Several small memory leaks were removed, and a big one from the Spinglass
community structure detection function
New in the C layer
------------------
- A new layout generator called DrL.
- Uniform sampling of random connected undirected graphs with a
given degree sequence.
- Some stochastic test results are ignored (for spinglass community
detection, some Erdos-Renyi generator tests)
- Weighted shortest paths, Dijkstra's algorithm.
- The unweigthed shortest path routine returns 'Inf' for unreachable
vertices.
- New function, igraph_adjlist can create igraph graphs from
adjacency lists.
- New function, igraph_weighted_adjacency can create weighted graphs
from weight matrices.
- New function, igraph_is_mutual to search for mutual edges.
- Added inverse log-weighted similarity measure (a.k.a. Adamic/Adar
similarity).
- igraph_preference_game and igraph_asymmetric_preference_game were
rewritten, they are O(|V|+|E|) now, instead of O(|V|^2).
- The Bellman-Ford shortest path algorithm was added.
- Added weighted variant of igraph_get_shortest_paths, based on
Dijkstra's algorithm.
- Several small memory leaks were removed, and a big one from the Spinglass
community structure detection function
Bugs corrected in the C layer
-----------------------------
- Several bugs were corrected in the (still experimental) C attribute
handler.
- 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.)
- Some code polish to make igraph compile with GCC 4.3
- 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.
- Hub & authority score calculations initialize ARPACK parameters now.x
- Fixed a bug in the Walktrap community detection routine, when applied
to unconnected graphs.
igraph 0.5
=========
Released February 14, 2008
See also the release notes at http://igraph.sf.net/relnotes-0.5.html
New in the R interface
----------------------
- 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
New in the Python interface
---------------------------
- Added shell interface: igraph can now be invoked by calling the script called
igraph from the command line. The script launches the Python interpreter and
automatically imports igraph functions into the main namespace
- Pickling (serialization) support for Graph objects
- Plotting functionality based on the Cairo graphics library (so you need to
install python-cairo if you want to use it). Currently the following
objects can be plotted: graphs, adjacency matrices and dendrograms. Some
crude support for plotting histograms is also implemented. Plots can be
saved in PNG, SVG and PDF formats.
- Unified Graph.layout method for accessing layout algorithms
- Added interfaces to walktrap community detection and the BLISS isomorphism
algorithm
- Added dyad and triad census functionality and motif counting
- VertexSeq and EdgeSeq objects can now be restricted to subsets of the
whole network (e.g., you can select vertices/edges based on attributes,
degree, centrality and so on)
New in the C library
--------------------
- Many types (stack, matrix, dqueue, etc.) are templates now
They were also rewritten to provide a better organized interface
- 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
igraph_canonical_permutation, igraph_isomorphic_bliss
- We use ARPACK for eigenvalue/eigenvector calculation. This means that the
following functions were rewritten: igraph_pagerank,
igraph_community_leading_eigenvector_\*. New functions based on
ARPACK: igraph_eigenvector_centrality, igraph_hub_score,
igraph_authority_score, igraph_arpack_rssolve, igraph_arpack_rnsolve
- Experimental C attribute interface added. I.e. it is possible to use
graph/vertex/edge attributes from C code now.
- Edge weights for Fruchterman-Reingold layout.
- Line graph calculation.
- Kautz and de Bruijn graph generators
- Support for writing graphs in DOT format
- Jaccard and Dice similarity coefficients added
- igraph_count_multiple added
- igraph_is_loop and igraph_is_multiple "return" boolean vectors
- The graphopt layout algorithm was added, igraph_layout_graphopt
- Generation of "famous" graphs, igraph_famous
- Create graphs from LCF notation, igraph_lcf, igraph_lcf_vector
- igraph_add_edge adds a single edge to the graph
- Dyad census and triad cencus functions added
- igraph_is_simple added
- progress handlers are allowed to stop calculation
- igraph_full_citation to create full citation networks
- igraph_path_length_hist, create a histogram of path lengths
- forest fire model added
- DIMACS reader can handle different file types now
- Adjacency list types made public now (igraph_adjlist_t, igraph_adjedgelist_t)
- Biconnected components and articulation points can be computed
- Eigenvector centrality computation
- Kleinberg's hub and authority scores
- igraph_to_undirected handles attributes now
- Geometric random graph generator can return the coordinates of the vertices
- Function added to convert leading eigenvector community structure result to
a membership vector (igraph_le_community_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