Re: [igraph] How to identify negative vertices in graph

[capitano . nemo]

Hi Frederik

I gave it a try. But apparently my graph is bipartite:

  > is.bipartite(graph)
  [1] TRUE

So the issue is probably somewhere else...

Il 14.11.2013 16:22 Frederik Elwert ha scritto:
> Hello!
>
> I had the same error. It turned out that my graph was not actually
> bipartite: I had one erroneous edge that connected vertices of the same
> type. Maybe that is also the case for your graph? You can check with
> `is.bipartite(graph)`.
>
> I found the wrong edge with a quick-and-dirty test:
>
> for (v in V(G)) {
>   vtype <- V(G)[v]$type
>   for (n in neighbors(G, v)) {
>     if (V(G)[n]$type == vtype) {
>       print(paste('Problem with', V(G)[v]$label, 'and', V(G)[n]$label))
>     }
>   }
> }
>
> (There is surely a better way to test that.)
>
> Maybe igraph should check before it tries the projection, and give a
> more informative message if the graph is not bipartite?
>
> Regards
> Frederik
>
>
>
> Am Do 14 Nov 2013 04:27:09 CET schrieb address@hidden:
> > Great!
> >
> > Should I email it to you?
> >
> >
> > Il 14.11.2013 03:10 Gábor Csárdi ha scritto:
> > > 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,  <address@hidden> 
> > > 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?
> > > >
> > > > _______________________________________________
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> > >
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> >
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