PS, one final command is the following, i.e. without any weights argument passed to the modularity function, gives this (so it’s the default output). I am wondering therefore what is the ‘right’ answer, 0.031 or 0.055, and what the difference is
> modularity(net,membership(cluster_leading_eigen(net, weights = > E(net)$weight))) [1] 0.03061224 > On 25 May 2017, at 10:43, Edmund Hunt <[email protected]> wrote: > > Hi Gabor, > > Thanks for your reply. > > Here are 4 different commands and their result, I guess I am just a bit > confused how they relate to each other. > > The first two are using the cluster_leading_eigen alone, the second two use > that command to find the communities and then the modularity function to get > the modularity value out of it > > Would I be right in understanding that cluster_leading_eigen only uses the > weights argument after the communities have been found - but then why does it > return the same value below for the first two commands - and why is it > different to the third command > > Thanks > > > cluster_leading_eigen(net, weights = E(net)$weight) > IGRAPH clustering leading eigenvector, groups: 2, mod: 0.055 > + groups: > $`1` > [1] "YV" "B" "P" > > $`2` > [1] "DG" "V" > > > > cluster_leading_eigen(net, weights = NULL) > IGRAPH clustering leading eigenvector, groups: 2, mod: 0.055 > + groups: > $`1` > [1] "YV" "B" "P" > > $`2` > [1] "DG" "V" > > > modularity(net,membership(cluster_leading_eigen(net, weights = > > E(net)$weight)),weights=NULL) > [1] 0.03061224 > > > modularity(net,membership(cluster_leading_eigen(net, weights = > > E(net)$weight)),weights=E(net)$weight) > [1] 0.0546875 > > > >> On 25 May 2017, at 06:51, Gábor Csárdi <[email protected] >> <mailto:[email protected]>> wrote: >> >> IIRC the original algorithm can be extended easily to take weights >> into account. >> >> If you think the igraph is not doing that (and the docs say that it >> would), can you please provide a small example that gives you the same >> results with or without (large enough) weights? Thanks. >> >> Gabor >> >> On Wed, May 24, 2017 at 10:11 AM, Edmund Hunt <[email protected] >> <mailto:[email protected]>> wrote: >>> Hello, >>> >>> I have a question/comment about the leading.eigenvector.community function >>> in igraph >>> >>> It has an argument for weights, but this seems to make no difference to the >>> calculated clusters/resulting modularity >>> >>> Indeed I don’t think Newman’s algorithm takes edge weights into account? >>> >>> Is it the case that the weights are only used after the community detection >>> has taken place, to calculate a modularity value? Is it appropriate to use >>> the weights to calculate modularity, can anyone advise me what is the >>> ‘right’ thing to do with a weighted, undirected network - is it definitely >>> to use the weights in the modularity calculation, or is there a free choice >>> >>> Perhaps these issues could be made clearer in the function help >>> >>> Thanks >>> >>> _______________________________________________ >>> igraph-help mailing list >>> [email protected] <mailto:[email protected]> >>> https://lists.nongnu.org/mailman/listinfo/igraph-help >>> >> >> _______________________________________________ >> igraph-help mailing list >> [email protected] <mailto:[email protected]> >> https://lists.nongnu.org/mailman/listinfo/igraph-help >
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