Thank you Etienne, this seems to work like a charm. Also thanks to the rest of you for your help.
Henrik On 11 June 2010 13:51, Cuvelier Etienne <ecuscim...@gmail.com> wrote: > > > Le 11/06/2010 12:45, Henrik Aldberg a écrit : > > I have a directed graph which is represented as a matrix on the form >> >> >> 0 4 0 1 >> >> 6 0 0 0 >> >> 0 1 0 5 >> >> 0 0 4 0 >> >> >> Each row correspond to an author (A, B, C, D) and the values says how many >> times this author have cited the other authors. Hence the first row says >> that author A have cited author B four times and author D one time. Thus >> the >> matrix represents two groups of authors: (A,B) and (C,D) who cites each >> other. But there is also a weak link between the groups. In reality this >> matrix is much bigger and very sparce but it still consists of distinct >> groups of authors. >> >> >> My problem is that when I cluster the matrix using pam, clara or agnes the >> algorithms does not find the obvious clusters. I have tried to turn it >> into >> a dissimilarity matrix before clustering but that did not help either. >> >> >> The layout of the clustering is not that important to me, my primary >> interest is the to get the right nodes into the right clusters. >> >> >> >> >> > Hello Henrik, > You can use a graph clustering using the igraph package. > Example: > > library(igraph) > simM<-NULL > simM<-rbind(simM,c(0, 4, 0, 1)) > simM<-rbind(simM,c(6, 0, 0, 0)) > simM<-rbind(simM,c(0, 1, 0, 5)) > simM<-rbind(simM,c(0, 0, 4, 0)) > G <- graph.adjacency( simM,weighted=TRUE,mode="directed") > plot(G,layout=layout.kamada.kawai) > > ### walktrap.community > wt <- walktrap.community(G, modularity=TRUE) > wmemb <- community.to.membership(G, wt$merges, > steps=which.max(wt$modularity)-1) > > V(G)$color <- rainbow(3)[wmemb$membership+1] > plot(G) > > I hope it helps > > Etienne > > Sincerely >> >> >> Henrik >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >> >> > [[alternative HTML version deleted]]
______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
