R/igraph 1.3.0

Announcements
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Our efforts to bring the R interface of igraph closer to the recent developments of the C core continues: we have released R-igraph 1.3.0, which updates the C core of igraph within the R interface to version 0.9.7, which is now only one patch version behind the mainline C core. The update fixes lots of bugs compared to the previous release and adds quite a few new functions.

Due to the underlying changes in the C core of igraph between the 0.8 series and 0.9.7, there are some cases when we needed to make extra efforts in the R interface to keep things compatible with previous releases. For instance, igraph 0.9.7 now interprets zero cutoff in the closeness, betweenness and edge betweenness centrality functions literally, while igraph 0.8 interpreted zero as “no cutoff”. The R interface keeps the old behaviour in such cases but prints a deprecation warning; the old behaviour will be gone in igraph 1.4.0 or 2.0.0, whichever comes first.

A patch release of R/igraph is coming soon in the next few days, which will hopefully (finally) catch up with the 0.9 branch of the C core. We aim to let R/igraph stabilize for a few weeks now while we work on further improvements in the C core.

Even though we tried to do our best not to cause breaking changes for users of igraph from R, we may have made unintentional mistakes, so please keep on reporting issues in the Github issue tracker.

Release Notes

The C core is updated to 0.9.7, fixing a range of bugs and introducing a number of new functions.

Added

  • has_eulerian_path() and has_eulerian_cycle() decides whether there is an Eulerian path or cycle in the graph.
  • eulerian_path() and eulerian_cycle() returns the edges and vertices in an Eulerian path or cycle in the graph.
  • any_loop() checks whether a graph contains at least one loop edge.
  • is_tree() checks whether a graph is a tree and also finds a possible root
  • to_prufer() converts a tree graph into its Prufer sequence
  • make_from_prufer() creates a tree graph from its Prufer sequence
  • sample_tree() to sample labelled trees uniformly at random
  • sample_spanning_tree() to sample spanning trees of an undirected graph uniformly at random
  • automorphisms() and canonical_permutation() now supports vertex colors
  • random_edge_walk() to record the edges traversed during a random walk
  • harmonic_centrality() calculates the harmonic centrality of vertices, optionally with a cutoff on path lengths
  • mean_distance() now supports edge weights and it can also return the number of unconnected vertex pairs when details=TRUE is passed as an argument
  • greedy_vertex_coloring() finds vertex colorings based on a simple greedy algorithm.
  • bridges() finds the bridges (cut-edges) of a graph
  • The frame width of circle, rectangle and square vertex shapes can now be adjusted on plots with the frame.width vertex attribute or the vertex.frame.width keyword argument, thanks to @simoncarrignon. See PR #500 for more details.
  • automorphism_group() returns a possible (not necessarily minimal) generating set of the automorphism group of a graph.
  • global_efficiency() calculates the global efficiency of the graph.
  • local_efficiency() calculates the local efficiency of each vertex in a graph.
  • average_local_efficiency() calculates the average local efficiency across the set of vertices in a graph.
  • rewire(each_edge(...)) now supports rewiring only one endpoint of each edge.
  • realize_degseq() generates graphs from degree sequences in a deterministic manner. It is also available as make_(degseq(..., deterministic=TRUE)).
  • clique_size_counts() counts cliques of different sizes without storing them all.
  • feedback_arc_set() finds a minimum-weight feedback arc set in a graph, either with an exact integer programming algorithm or with a linear-time approximation.
  • make_bipartite_graph() now handles vertices with names.
  • shortest_paths() now supports graphs with negative edge weights.
  • min_cut() now supports s-t mincuts even if value.only=FALSE.
  • as.matrix() now supports converting an igraph graph to an adjacency or edge list matrix representation. See as.matrix.igraph() for more details. This function was migrated from intergraph; thanks to MichaĹ‚ Bojanowski.

Fixed

  • is_connected() now returns FALSE for the null graph
  • Calling length() on a graph now returns the number of vertices to make it consistent with indexing the graph with [[.
  • diameter() now corrently returns infinity for disconnected graphs when unconnected=FALSE. Previous versions returned the number of vertices plus one, which was clearly invalid for weighted graphs.
  • mean_distance() now correctly treats the path length between disconnected vertices as infinite when unconnected=FALSE. Previous versions used the number of vertices plus one, adding a bias towards this number, even if the graph was weighted and the number of vertices plus one was not a path length that could safely have been considered as being longer than any “valid” path.
  • layout_with_sugiyama() now handles the case of exactly one extra virtual node correctly; fixes #85
  • bfs() and dfs() callback functions now correctly receive 1-based vertex indices and ranks; it used to be zero-based in earlier versions
  • Accidentally returning a non-logical value from a bfs() or dfs() callback does not crash R any more
  • Calling print() on a graph with a small max.lines value (smaller than the number of lines needed to print the attribute list and the header) does not raise an error any more; fixes #179
  • as_adjacency_matrix(edges=TRUE, sparse=TRUE) now consistently returns the last edge ID for each cell in the matrix instead of summing them.
  • Using the + and - operators with a path() object consisting of two vertices is now handled correctly; fixes #355
  • topo_sort() now throws an error if the input graph is not acyclic instead of returning an incorrect partial ordering.
  • Weighted transitivity calculations (i.e. transitivity(mode="barrat") now throw an error for multigraphs; the implementation does not work correctly for multigraphs and earlier versions did not warn about this.

Changed

  • The neimode argument of bfs() and dfs() was renamed to mode for sake of consistency with other functions. The old argument name is deprecated and will be removed in 1.4.0.
  • bfs() and dfs() callback functions now correctly receive 1-based vertex indices and ranks; it used to be zero-based in earlier versions. (This is actually a bugfix so it’s also mentioned in the “Fixed” section).
  • closeness(), betweenness() and edge_betweenness() now all take a cutoff argument on their own. estimate_closeness(), estimate_betweenness() and estimate_edge_betweenness() became aliases, with identical signature. They are not deprecated but their implementation might change in future versions to provide proper estimation schemes instead of a simple cutoff-based approximation. If you explicitly need cutoffs and you want your results to be reproducible with future versions, use closeness(), betweenness() and edge_betweenness() in your code with a cutoff argument.
  • closeness() now only considers reachable vertices during the calculation; in other words, closeness centrality is now calculated on a per-component basis for disconnected graphs. Earlier versions considered all vertices.

Deprecated

  • Using cutoff=0 for closeness(), betweenness() and edge_betweenness() is deprecated; if you want exact scores, use a negative cutoff. cutoff=0 will be interpreted literally from igraph 1.4.0.
  • centr_degree_tmax() now prints a warning when it is invoked without an explicit loops argument. loops will be mandatory from igraph 1.4.0.
  • The nexus_list(), nexus_info(), nexus_get() and nexus_search() functions now return an error informing the user that the Nexus graph repository has been taken offline (actually, several years ago). These functions will be removed in 1.4.0.
  • The edges argument of as_adjacency_matrix() is deprecated; it will be removed in igraph 1.4.0.

Removed

  • The deprecated page_rank_old() function and the deprecated power method of page_rank() were removed.
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