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.

R: 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.
• Removed functions graph.intersection.by.name(), graph.union.by.name(), graph.difference.by.name().
• The + operator on graphs now calls graph.union() if both argument graphs are named, and calls graph.disjoint.union() otherwise.
• Added function igraph.version().
• Generate graphs from a stochastic block model: sbm.game().
• Do not suggest the stats, XML, jpeg and png packages any more.
• Fixed a set.vertex/edge.attribute bug that changed both graph objects, after copying (#533)
• Fixed a bug in barabasi.game that caused crashes.
• We use PRPACK to calculate PageRank scores see https://github.com/dgleich/prpack
• 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).