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Network Modularity Calculations in R

开发者 https://www.devze.com 2023-02-21 18:37 出处:网络
The equation for Network Modularity is given on its wikipedia page (and in reputable books).I want to see it working in some code.I have found this is possible using the modularity library for igraph

The equation for Network Modularity is given on its wikipedia page (and in reputable books). I want to see it working in some code. I have found this is possible using the modularity library for igraph used with R (The R Foundation for Statistical Computing).

I want to see the example below (or a similar one) used in the code to calculate the modularity. The library gives on example but it isn't really what I want.

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Let us have a set of vertices V = {1, 2, 3, 4, 5} and edges E = {(1,5), (2,3), (2,4), (2,5) (3,5)} that form an undirected graph.

Divide these vertices into two communities: c1 = {2,3} and c2 = {1,4,5}. It is the modularity of these two communities that is to be computed.


library(igraph)
g <- graph(c(1,5,2,3,2,4,2,5,3,5))
membership <- c(1,2,2,1,1)
modularity(g, membership)

Some explanation here:

  1. The vector I use when creating the graph is the edge list of the graph. (In igraph versions older than 0.6, we had to subtract 1 from the numbers because igraph uses zero-based vertex indices at that time, but not any more).

  2. The i-th element of the membership vector membership gives the index of the community to which vertex i belongs.

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