Re: [igraph] modularity in dense weighted networks with spinglass.community

[Tamas Nepusz]

Hi,

> I'm trying to apply spinglass.community in the R package to dense weighted 
> networks and have some trouble interpreting the modularity value in my 
> results. I'm assuming that $modularity is the value of the Hamiltonian as in 
> the Reichardt/Bornholdt paper.
I'm not quite familiar with the R package of igraph, but I have a feeling that 
$modularity is the value calculated by igraph's modularity() function on the 
obtained partition, which will be equal to the Hamiltonian if using the 
configuration model and gamma is equal to 1.

> But I'm not clear on how these concepts are related for weighted graphs. If I 
> separately get the modularity value of the partition that spinglass gives me, 
> it is different from the modularity value given by spinglass directly.
Did you pass the name of the attribute storing the edge weights to the 
modularity() function? Even if you have a "weight" attribute in each edge of 
your graph, modularity() will still calculate the unweighted modularity unless 
you explicitly tell it to use the "weight" attribute. I guess the same applies 
to the spinglass community detection function: if you tell it to use the 
"weight" attribute, it will use the weights and calculate the modularity 
accordingly, but if you don't, it will stick to the unweighted case. However, 
keep in mind that I'm not that familiar with the R interface, so I might be 
wrong here.

> In a related question, is there any plan to implement the "weighted version" 
> of this method as in Heimo (2008)
Well, if someone sends us a patch, we will be happy to include it in later 
releases ;)

-- 
Tamas