Oh, yeah, that is a bug I fixed recently in the dev tree, zero vertices are just ignored silently. So it was an igraph bug after all.
Gabor On Fri, Jul 12, 2013 at 10:47 AM, <[email protected]> wrote: > Sorry for not posting sample data, > however I have found the problem: for some reason, igraph ignored zeros in > the matrix. There were four zeros, which resulted in two missing pairs. > When I increase the ids of vertices by one from (0 to 2403) to (1 to > 2404), it works. > Plus you were right, that putting not transposed matrix as edgelist just > took it as a vector > > Thanks, > Zbynek > > > [email protected] napsal(a): ----- > Komu: Help for igraph users <[email protected]> > Od: Gábor Csárdi ** > Odesílatel: [email protected] > Datum: 12.7.2013 15:24 > Předmět: Re: [igraph] edges "disapear", when creating graph in R > > > On Fri, Jul 12, 2013 at 8:23 AM, <[email protected]> wrote: > >> Hello, >> I have encountered following problem in R: >> I construct graph from a matrix of edges, but resulting graph has fewer >> edges than there is rows in the matrix. >> >> # edges are stored in a matrix M >> >> > head(M) >> USEK1 USEK2 >> [1,] 985 866 >> [2,] 982 866 >> [3,] 1062 1039 >> [4,] 1088 1119 >> [5,] 1061 1088 >> [6,] 1060 1061 >> >> # matrix stores 3244 edges >> > dim(M) >> [1] 3244 2 >> >> # number of vertices >> > max(M)+1 >> [1] 2404 >> >> > g <- graph.empty(n=max(M)+1,directed=T) >> > g <- add.edges(g,M) >> > > Aer you sure this works? I think it'll just take the matrix as a vector, > column-wise, which is probably not what you want. > > >> > g >> IGRAPH D--- 2404 3242 -- >> >> ######### >> >> there are two edges missing. >> Can anyone explain, what it the source of this behavior, and how can I >> fix it? >> > > Maybe you have NAs in the matrix and they are ignored. But this is just a > guess, as you did not provide a reproducible example that I could try. > Maybe it is a bug in igraph, although I would say that is unlikely. > > Best, > Gabor > > >> >> Best Regards, >> >> Zbynek Janoska >> Transport Research Centre >> Olomouc, Czech Republic >> [email protected] >> >> _______________________________________________ >> 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 > >
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