~igraph/igraph/0.5-main

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 ans 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

- Weighted modularity calculation

- igraph_permute_vertices added

- Betweenness ans closeness calculations are speeded up

- Startup positions can be supplied to the Kamada-Kawai layout

  algorithms

- igraph_read_graph_* functions 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 a null pointer for edge

  capacities, implying unit capacities for all edges

Bugs corrected in the C library

-------------------------------

- Memory leak fixed in adjacency list handling

- Memory leak fixed in maximal independent vertex set calculation

- Fixed a bug when rewiring undirected graphs with igraph_rewire

- Fixed edge betweenness community structure detection for unconnected graphs

- Make igraph compile with Sun Studio

- Betweenness bug fixed, when not computing for all vertices

- memory usage of clique finding reduced

- Corrected bugs for motif counts when not all motifs were counted,

  but a 'cut' vector was used

- Bugs fixed in trait games and cited type game

- Accept underscore as letter in GML files

- GML file directedness notation reversed, more logical this way