About igraph releases and other things

R/igraph 0.5.2

Release Notes

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

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.

The label propagation community finding algorithm

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.

3D version of the DrL layout generator

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.

R GUI (limited)

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 shortest path algorithm

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.

Average nearest neighbor degree

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.

Curved edges in R plots

Both plot() and tkplot() supports curved edges. See ?igraph.plotting for more details.

Several bugs and memory leaks corrected

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

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.,
  • 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 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
  • 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