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Optimal community structure

Source: R/community.R
cluster_optimal.Rd

This function calculates the optimal community structure of a graph, by maximizing the modularity measure over all possible partitions.

Usage

cluster_optimal(graph, weights = NULL)

Arguments

graph

The input graph. It may be undirected or directed.

weights

The weights of the edges. It must be a positive numeric vector, NULL or NA. If it is NULL and the input graph has a ‘weight’ edge attribute, then that attribute will be used. If NULL and no such attribute is present, then the edges will have equal weights. Set this to NA if the graph was a ‘weight’ edge attribute, but you don't want to use it for community detection. A larger edge weight means a stronger connection for this function.

Value

cluster_optimal() returns a communities() object, please see the communities() manual page for details.

Details

This function calculates the optimal community structure for a graph, in terms of maximal modularity score.

The calculation is done by transforming the modularity maximization into an integer programming problem, and then calling the GLPK library to solve that. Please the reference below for details.

Note that modularity optimization is an NP-complete problem, and all known algorithms for it have exponential time complexity. This means that you probably don't want to run this function on larger graphs. Graphs with up to fifty vertices should be fine, graphs with a couple of hundred vertices might be possible.

Examples



## Zachary's karate club
g <- make_graph("Zachary")

## We put everything into a big 'try' block, in case
## igraph was compiled without GLPK support

## The calculation only takes a couple of seconds
oc <- cluster_optimal(g)

## Double check the result
print(modularity(oc))
print(modularity(g, membership(oc)))

## Compare to the greedy optimizer
fc <- cluster_fast_greedy(g)
print(modularity(fc))

References

Ulrik Brandes, Daniel Delling, Marco Gaertler, Robert Gorke, Martin Hoefer, Zoran Nikoloski, Dorothea Wagner: On Modularity Clustering, IEEE Transactions on Knowledge and Data Engineering 20(2):172-188, 2008.

See also

communities() for the documentation of the result, modularity(). See also cluster_fast_greedy() for a fast greedy optimizer.

Community detection as_membership(), cluster_edge_betweenness(), cluster_fast_greedy(), cluster_fluid_communities(), cluster_infomap(), cluster_label_prop(), cluster_leading_eigen(), cluster_leiden(), cluster_louvain(), cluster_spinglass(), cluster_walktrap(), compare(), groups(), make_clusters(), membership(), modularity.igraph(), plot_dendrogram(), split_join_distance(), voronoi_cells()

Author

Gabor Csardi csardi.gabor@gmail.com