<
address@hidden> wrote:
> Thank you both,
> I'm eager to hear what you find Gabor.
> Best,
> Aaron
>
> On Fri, Mar 5, 2010 at 11:32 PM, Gábor Csárdi <
address@hidden> wrote:
>>
>> Hi Aaron,
>>
>> hmmm, you are right, something strange is going on here, if I run the
>> following:
>>
>> R
>>
>> library(igraph)
>>
>> largest.component <- function(x) {
>> cl <- clusters(x)
>> ss <- which(cl$membership == which.max(cl$csize)-1)-1
>> subgraph(x, ss)
>> }
>>
>> g <- largest.component(erdos.renyi.game(100, p=5/100))
>> E(g)$weight <- runif(ecount(g))
>> sc <- spinglass.community(g, weights=E(g)$weight)
>> sc$modularity
>> modularity(g, sc$membership, weights=E(g)$weight)
>>
>> sc2 <- spinglass.community(g)
>> sc2$modularity
>> modularity(g, sc2$membership)
>>
>> # I get
>>
>> > sc$modularity
>> [1] 0.2808567
>> > modularity(g, sc$membership, weights=E(g)$weight)
>> [1] 0.4861468
>> >
>> > sc2 <- spinglass.community(g)
>> > sc2$modularity
>> [1] 0.2737963
>> > modularity(g, sc2$membership)
>> [1] 0.3635749
>>
>> which is clearly different, both in the weighted and unweighted case.
>> For spinglass.community we just use the modularity value calculated by
>> the community detection code, as implemented by the original author of
>> the algorithm.
>>
>> I will check why the two values are not the same. Thanks for your report!
>>
>> Best,
>> Gabor
>>
>> On Tue, Mar 2, 2010 at 9:05 PM, Aaron Alexander-Bloch
>> <
address@hidden> wrote:
>> > Hi - Thanks in advance for any help.
>> >
>> > 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. As I'm keeping the gamma parameter at 1
>> > and
>> > using the 'config' model, my understanding is that the Hamiltonian is
>> > the
>> > same as Newman's modularity, at least for binary graphs. 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. So my
>> > question is how should the modularity value given by spinglass be
>> > interpreted for weighted graphs?
>> >
>> > In a related question, is there any plan to implement the "weighted
>> > version"
>> > of this method as in Heimo (2008)
>> >
>> >
http://iopscience.iop.org/1742-5468/2008/08/P08007/
>> >
>> > Thanks very much!
>> > Aaron
>> >
>> > _______________________________________________
>> > igraph-help mailing list
>> >
address@hidden
>> >
http://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>> >
>>
>>
>>
>> --
>> Gabor Csardi <
address@hidden> UNIL DGM
>>
>>
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>>
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--
Gabor Csardi <
address@hidden> UNIL DGM
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