About igraph releases and other things

April 10, 2009

This is another bug fix release, with a couple of new features. Here are the important ones. See at the end for the complete list of changes.

Bipartite graphs have two kinds of vertices and edges are only allowed to connect opposite kinds. Think of the Hollywood movie graph with actors and movies. igraph 0.5.2 now contains some functions to deal with these kind of networks.

This is a simple and intuitive community finding algorithm, published by Raghavan et al. in 2007 (see docs for full citation). It works by assigning labels to the vertices and then updating the labels based on majority voting among the neighbors.

The DrL layout generator was extended to generate three dimensional layouts. Albeit slower than the regular 2D version, this is a nice addition for those who do visualization in 3D.

A minimal, supported GUI is included now in the R package. It contains
only a small fraction of igraph capabilities, but can be still useful,
e.g. in teaching. You can start it by typing `tkigraph()`

,
after loading the igraph package of course.

Johnson's algorithm is a good choice for finding all shortest paths in a network that has some negative edge weights, but no negative cycles.

A new function was added to calculate the average degree of the neighbors of all or some vertices. It supports the edge weighted version of the measure as well.

Both `plot()`

and `tkplot()`

supports curved
edges. See `?igraph.plotting`

for more details.

Apart from the bug fixes, some functions were rewritten to speed them up.

- 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.

- 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`