Re: [igraph] Wierd behavior of graph.adjacency ?

[Gábor Csárdi]

Hi Ester,

I am sorry for the delay. This is a known bug:
https://bugs.launchpad.net/igraph/+bug/1019624

It happens because graph.adjacency does not work if the input matrix
contains integers. The workaround is to convert your matrix to
"numeric" (which means "double", really) before calling
graph.adjacency:

mode(mat) <- "numeric"
graph.adjacency(mat, ...)

Best,
Gabor

On Tue, Jul 10, 2012 at 3:51 AM, Ester Lopez <address@hidden> wrote:
> Hi all,
>
> I'm trying to read some directed graphs from a file which looks like:
>
>>> > cat losses1/257-data.826460.84-2419_10_3net.in
>>>
>>> 1 0 3 0 0 0 3 0 3 0
>>>
>>> 0 1 0 0 0 3 0 0 0 3
>>>
>>> 3 0 0 0 0 0 0 0 0 0
>>>
>>> 0 0 0 0 3 0 0 0 0 0
>>>
>>> 0 0 0 3 1 3 0 3 0 0
>>>
>>> 0 3 0 0 3 1 3 0 0 0
>>>
>>> 3 0 0 0 0 3 0 0 0 0
>>>
>>> 0 0 0 0 3 0 0 0 0 0
>>>
>>> 3 0 0 0 0 0 0 0 1 0
>>>
>>> 0 3 0 0 0 0 0 0 0 0
>
>
>  Which represents the weighted adjacency matrix. When I read the file in R:
>
>> > mat <- read.table('losses1/257-data.826460.84-2419_10_3net.in')
>> > mat <- read.table('losses1/257-data.826460.84-2419_10_3net.in')
>> > mat <- as.matrix(mat)
>> > mat
>>       V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
>>  [1,]  1  0  3  0  0  0  3  0  3   0
>>  [2,]  0  1  0  0  0  3  0  0  0   3
>>  [3,]  3  0  0  0  0  0  0  0  0   0
>>  [4,]  0  0  0  0  3  0  0  0  0   0
>>  [5,]  0  0  0  3  1  3  0  3  0   0
>>  [6,]  0  3  0  0  3  1  3  0  0   0
>>  [7,]  3  0  0  0  0  3  0  0  0   0
>>  [8,]  0  0  0  0  3  0  0  0  0   0
>>  [9,]  3  0  0  0  0  0  0  0  1   0
>> [10,]  0  3  0  0  0  0  0  0  0   0
>> > gr <- graph.adjacency(mat, weighted=TRUE)
>> > get.adjacency(gr, sparse=FALSE)
>>     V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
>> V1   1  1  0  1  1  1  1  0  1   0
>> V2   1  0  1  0  0  1  1  1  1   1
>> V3   0  0  1  1  0  1  1  1  1   1
>> V4   1  0  1  0  0  1  1  1  1   1
>> V5   1  0  0  0  1  1  1  1  1   0
>> V6   1  0  1  0  1  1  1  1  1   1
>> V7   0  0  0  0  0  1  0  1  0   1
>> V8   1  1  1  1  0  1  1  1  1   1
>> V9   0  0  1  0  0  1  1  1  1   1
>> V10  1  0  0  0  0  1  1  1  1   1
>>
>> > E(gr)[2]$weight
>> [1] 1.482197e-323
>
>
> I've tried creating by my own the same matrix manually and it works just
> fine, but Im not sure why, when I load it from the file it behaves like
> this. Also the results slightly differ if I change the dimnames(mat), but
> yet not the correct ones.
>
> I'm using igraph "0.6-2" version.
>
> Any idea about what I'm doing wrong?
>
> Thanks a lot,
> Ester
>
>
>
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>



-- 
Gabor Csardi <address@hidden>     MTA KFKI RMKI