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

[Gábor Csárdi]

On Thu, Nov 14, 2013 at 11:22 AM, Frederik Elwert
<address@hidden> wrote:
[...]
> Maybe igraph should check before it tries the projection, and give a
> more informative message if the graph is not bipartite?

Indeed, the error message should be better, I'll improve it.

Thanks, Best,
Gabor

> 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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