Re: [igraph] contract.vertices() generates error "s tructure_generators.c:84 : Invalid (negative) verte x id, Invalid vertex id"

[capitano . nemo]

But then the projected graph is only nominally bipartite but does not 
contain any nodes of a different type. Then the fact that it is 
bipartite shouldn't effect any community detection algorithm.
Is this correct?

Il 21.11.2013 01:38 Gábor Csárdi ha scritto:
> You cannot eliminate negative vertex ids from an igraph graph, as it
> can _never_ contain vertices with negative ids.
>
> As for contract.vertices() I guess you are calling it with a wrong
> 'mapping' argument, but we would need to see you complete code to be
> sure.
>
> As for the projection of the bipartite graph, yes, it would make sense
> to make it unipartite:
> https://github.com/igraph/igraph/issues/255
>
> Gabor
>
> On Wed, Nov 20, 2013 at 6:56 AM,  <address@hidden> wrote:
> > Hello list,
> >
> > I already got the same error with bipartite.projection(). At that step 
> > I was
> > able to solve the problem by
> > 1) eliminating few negative ids and
> > 2) eliminating few edges between same type nodes (the graph was then
> > actually not truly bipartite).
> >
> > After correcting the bipartite graph I executed with no errors
> >
> >     > igraph_onemode <- bipartite.projection(igraph_bi)
> >     > igraph_onemode
> >     IGRAPH UNWB 75439 50375688 --
> >     attr: ...
> >     > igraph_onemode_threads <- igraph_onemode$proj2
> >     > category_attr <- get.vertex.attribute(igraph_onemode_threads,
> > "category")
> >     > # Map categories to integers, empty attribute is mapped to 4
> >     > map = setNames(c(1:4), c("category1",
> >                              "category2",
> >                              "category3",
> >                              ""))
> >
> > And finally
> >
> >     > igraph_category <- contract.vertices(igraph_onemode_threads,
> > category_attr)
> >     Error in contract.vertices(igraph_onemode_threads, category_attr) 
> > :
> >       At structure_generators.c:84 : Invalid (negative) vertex id, 
> > Invalid
> > vertex id
> >
> > But this error is quite unexpected since the vertex id went through
> > bipartite.projection() which also check for negative values. Can still 
> > be a
> > problem with edges between the nodes of the same type?
> >
> > I am more than happy to share data and code (only the
> > 'igraph_onemode_threads' is 460MB) if can be help.
> >
> > PS: BTW, how come the graph returned from the one-mode projection is
> > bipartite?
> >
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