Re: [igraph] simple example, graph.incidence skips directed parameter

[Gábor Csárdi]

Jose,

this was a bug for dense matrices only. If you use 'sparse=TRUE', then
the 'directed' argument is fine. For dense matrices you cannot trust
either 'directed' or 'mode'.

But, remember that the 'mode' argument is not fine for sparse matrices.

G.

On Sun, Jun 14, 2009 at 1:25 AM, Jose Quesada<address@hidden> wrote:
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> Hi Gabor,
>
> Well, this is not a solution at all, since I have a large graph reading
> from a sparse matrix; using anything dense will result in the following
> error:
>
> CHOLMOD error: tFď
> Error in asMethod(object) :
>  Cholmod error 'problem too large' at file:../Core/cholmod_dense.c,
> line 106
> Error in as.vector(as(x, "matrix"), mode) :
>  error in evaluating the argument 'x' in selecting a method for
> function 'as.vector'
>
> Still, when I run graph.incidence on a monster network, it seems to at
> least respect 'directed'.
>
>> dg = graph.incidence(m, directed=T, mode="out") # BUG
>>
>>
>> summary(dg)
> Vertices: 3024016
> Edges: 11463075
> Directed: TRUE
> No graph attributes.
> Vertex attributes: type, name.
> No edge attributes.
>
>
> Can I trust this?
>
> Best,
> - -Jose
> Gábor Csárdi wrote:
>> Jose, thanks for the report, this was a bug. I have fixed it, and here
>> is a workaround that works with the currently released version:
>>
>> i <- igraph:::graph.incidence.dense(inc, directed=TRUE, mode="out",
>>                                     weighted=NULL, multiple=FALSE)
>>
>> It is not perfect, because in fact the 'mode' parameter will be always
>> 'out', no matter what you set (for unweighted graphs at least), but
>> you can transpose the incidence matrix and then have the same as you
>> would with mode=="in".
>>
>> Thanks again, best,
>> Gabor
>>
>> On Fri, Jun 5, 2009 at 3:00 PM, Jose Quesada<address@hidden> wrote:
>>> Hi Gabor, Tamar, (all),
>>>
>>> In this simple example, graph.incidence skips directed parameter.
>>>
>>> inc <- matrix(sample(0:1, 15, repl=TRUE), 3, 5)
>>> colnames(inc) <- letters[1:5]
>>> rownames(inc) <- LETTERS[1:3]
>>> i <- graph.incidence(inc, directed=T)
>>> summary(i) # it's not a directed graph
>>>
>>> I have no idea why, because it certainly works on other (bigger)
>>> networks I'm using.
>>> Thoughts?
>>>
>>> Best,
>>> -Jose
>>>
>>> --
>>> Jose Quesada, PhD.
>>> Max Planck Institute,
>>> Center for Adaptive Behavior and Cognition -ABC-,
>>> Lentzeallee 94, office 224, 14195 Berlin
>>> http://www.josequesada.name/
>>>
>>>
>>>
>>> _______________________________________________
>>> igraph-help mailing list
>>> address@hidden
>>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>>
>>
>>
>>
>
> - --
> Jose Quesada, PhD.
> Max Planck Institute,
> Center for Adaptive Behavior and Cognition -ABC-,
> Lentzeallee 94, office 224, 14195 Berlin
> http://www.josequesada.name/
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-- 
Gabor Csardi <address@hidden>     UNIL DGM