Hello, Tamas thanks you for reply.
I have tried to write a script to calculate the conductance in genenal case. I have used the definition of conductance from the paper http://cs.stanford.edu/people/jure/pubs/comscore-icdm12.pdf My code is shown below. I have the error: "in `[.data.frame`(tmp, c("X1", "X2")) : undefined columns selected" on the line: "long <- ....." But code is working. I would like to fix this error and than to test the code on some dataset. Could someone please give remarks, comments to the code? library(igraph) g <- make_graph( ~ A-B-C-D-A, E-A:B:C:D, F-G-H-I-F, J-F:G:H:I, K-L-M-N-K, O-K:L:M:N, P-Q-R-S-P, T-P:Q:R:S, B-F, E-J, C-I, L-T, O-T, M-S, C-P, C-L, I-L, I-P) comm <- walktrap.community(g) mS <- vector() # the number of edges in S cS <- vector() # the number of edges on the boundary of S m <- vector() сond <-vector() for (s in 0: nrow(comm$merges)) { memb <- cutat(comm, steps=s) m <- c(m, modularity (g, memb, weights=NULL)) g2<-make_clusters(g, memb) # intra-cluster edges mS <- sapply(unique(membership(g2)), function(i) { vs<- which(membership(g2)==i) subg1<-induced.subgraph(g, vs) ecount(subg1) }) # inter-cluster edges dcs <- data.frame(combn(unique(membership(g2)), 2)) cS <- sapply(dcs, function(x) { es<-E(g)[V(g)[membership(g2)==x[1]] %--% V(g)[membership(g2)==x[2]]] length(es) }) tmp <- data.frame(t(dcs[1,]), t(dcs[2,]), cS) long <- cbind(tmp["cS"], stack(tmp[c("X1","X2")]), row.names = NULL) # Error in `[.data.frame`(tmp, c("X1", "X2")) : undefined columns selected cS <- with( long, tapply(cS, values, sum)) # Conductance сond <- c(сond, min(cS/(2*mS + cS))) } par(mfrow=c(1:2)) plot(0:(length(m)-1), m, col="blue",xlab="Steps",ylab="Modularity") plot(0:(length(сond)-1), сond, col="blue",xlab="Steps",ylab="Conductance") 2016-04-03 23:01 GMT+07:00 <[email protected]>: > Hi, > > There is no error in your implementation, although the way you define > conductance is not exactly the way it is usually defined in the graph > theory literature. (As far as I know, conductance is usually > calculated for a cut of a graph, i.e. a partitioning into two disjoint > sets, and the conductance of a graph is simply the minimum conductance > over all possible cuts). The way you defined conductance is simply the > ratio of the number of edges between clusters and the number of edges > within clusters. Now, before the first merge, obviously all the edges > are between clusters, so you divide a nonzero value with zero, hence > you get infinity. After having performed all the merges, obviously all > the edges are within clusters, so you divide zero with a nonzero > value, getting zero in the end. > > So, there's nothing wrong with your code, but the way you defined > conductance is not suitable for selecting an "optimal" number of > clusters based on its extrema. > > T. > > > On Sat, Apr 2, 2016 at 4:03 AM, MikeS <[email protected]> wrote: >> Tamas, thanks you for reply. >> My code does not have syntactical error now. >> But I concerned about the result, I think I have a logical error. >> >> A modularity curve has the maximum value 0.4583 inside the steps' >> range (on step with no.=18), but conductance curve has extremum 0 on >> the right boundary. >> >>> max(m) >> [1] 0.4583333 # index =18 >>> max(con) >> [1] 0 # index = 20 _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
