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

[Jose Quesada]

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Hi Gabor,


Now I'm confused

Gábor Csárdi wrote:
> 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'.
> 

graph.incidence has no sparse parameter. Right?

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

Is this the second bug I mentioned? or something else?


Best,
- -Jose


> G.
> 
> On Sun, Jun 14, 2009 at 1:25 AM, Jose Quesada<address@hidden> wrote:
> 
> 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: tF
> 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
>>>>>
>>>>
>>>>
>>
>>
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- --
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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