On 25 May 2017 at 19:43, 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" > > > > $`2` > [1] "DG" "V"
According to the documentation, you need to supply weights=NA, and not weights=NULL, to ignore any existing weight values in the graph. > >> modularity(net,membership(cluster_leading_eigen(net, weights = >> E(net)$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]> 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]> 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] > https://lists.nongnu.org/mailman/listinfo/igraph-help > > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > > > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
