With the help of several people in this community I have been wetting my feet in clustering some social network data using igraph's implementation of modularity-based clustering.
I am having some trouble interpreting the output of this routine and how to use it to generate lists of members of each community detected.
This routine outputs a two-column matrix and a list of modularity values. From the docs:
merges: A matrix with two column, this
represents a dendogram and contains
all the merges the algorithm
performed. Each line is one merge and
it is given by the ids of the two
communities merged. The community ids
are integer numbers starting from zero
and the communities between zero and
the number of vertices (N) minus one
belong to individual vertices. The
first line of the matrix gives the
first merge, this merge creates
community N, the number of vertices,
the second merge creates community
N+1, etc.modularity: A numeric vector
containing the modularity value of the
community structure after performing
every merge.
Working with this explanation and looking at the example at the bottom of the man page, I think the communities in this graph are
1st community: 0 1 2 3 4
2nd community: 10 11 12 13 14
3rd community: 5 6 7 8 9
Can someone who has used this method before confirm whether the right approach produces this result? I have basically (i) ignored the last two merges and (ii) gone over each row in the 'merges' matrix, combining each pair of vertices into a set while watching out for vertex values that are larger than the number of vertices (and therefore refer to another row in the 'merges' matrix).
Best Answer
The function which is used for this purpose: community.to.membership(graph, merges, steps, membership=TRUE, csize=TRUE) this can be used to extract membership based on the fastgreedy.community function results. You have to provide number of steps - how many merges should be performed. The optimal number of steps(merges) is the one which produce the maximal modularity.