Internal igraph vertex ids start from 0 in C, and from 1 in R, and they are never negative. The not very helpful error message is coming from the igraph C library and is a consequence of some other error, probably in the R package, or maybe a bug in igraph.
Your data is not very big, actually, so if you save it with save() and send it to me with the complete code that you used, I can probably help you. Assuming you are allowed to share the data. Gabor On Wed, Nov 13, 2013 at 9:59 PM, <[email protected]> wrote: > I have a problem with the function bipartite.projection() which returns > > Error in bipartite.projection(igraph_bi) : > At structure_generators.c:84 : Invalid (negative) vertex id, Invalid > vertex id > > when trying to project my bipartite graph. > > Unfortunately my graph is very large (IGRAPH DN-B 154626 448387 -- ) so I > can't easily reproduce the error in a minimum working example to share. > > What I tried to do was to have a look at the dataframes that I used to > create the graph object in the first place with > > graph.data.frame(edges, directed=TRUE, vertices=nodes) > > I checked the "id" column of my "nodes" df along with the "from" column of > my "edges" df for negative values. (By the way, both "id" and "from" columns > are character vectors, not numeric). Indeed I found 25 "negative" strings in > my "id" column of the "nodes" df--it depends on the first character, > non-alphanumerics make for a negative value of the string. But still after > removing all the negative strings, and after double-checking again both "id" > and "from" columns, I keep getting the same error from > bipartite.projection() > > Error in bipartite.projection(igraph_bi) : > At structure_generators.c:84 : Invalid (negative) vertex id, Invalid > vertex id > > Now my problem is to understand how to find where the negative values that > trigger the error are hidden. > > Is the value of the column "id" used as id of the node without any > transformation (and same for the column "from" for edges) by the function > graph.data.frame? > > How can I get the id values out of the graph object to check for negative > values? > > _______________________________________________ > 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
