Self-loops are not properly considered when using modularity

[vtraag]

We ignore all self-loops upon reading a particular network. Although this works fine for CPM (as self-loops have no effect there) this is not entirely correct for modularity. In particular, the problem is that the nodeWeights are calculated using getTotalEdgeWeightPerNodeHelper, but this is called only after we have removed the self-loops. In other words, the nodeWeights reflect the degree without the self-loops.

networkanalysis/src/main/java/nl/cwts/networkanalysis/Network.java

Line 1371 in 42fdd9e

this.nodeWeights = (nodeWeights != null) ? nodeWeights.clone() : (setNodeWeightsToTotalEdgeWeights ? getTotalEdgeWeightPerNodeHelper() : nl.cwts.util.Arrays.createDoubleArrayOfOnes(nNodes));

In addition, we do consider self-loops when calculating the "proper" resolution parameter:

networkanalysis/src/main/java/nl/cwts/networkanalysis/run/RunNetworkClustering.java

Line 405 in 42fdd9e

double resolution2 = useModularity ? (resolution / (2 * network.getTotalEdgeWeight() + network.getTotalEdgeWeightSelfLinks())) : resolution;

Both issues should be corrected in order to make modularity work correctly when self-loops are present in a network.