Dear Igraph Users,
I am using 2 different square genetic distance matrices (26 rows and columns of animal populations) to build 2 weighted and undirected graphs. I would like to find clusters or communities in each of the graphs and determine how they differ. However, I have a couple of questions.
1) A (mostly) complete graph with genetic distances between all populations (a small number of the distances are 0) clusters much differently than a graph with a reduced edge set. Does anyone know if techniques exist to identify an optimal cutoff distance value for reducing the number of edges?
2) There are a large number of modularity metrics in igraph. I have experimented with both the leading.eigenvector.community and the fast.greedy.community and they seem to give fairly similar results. Are these appropriate metrics for my particular problem?
Thanks for your help!