Re: [igraph] maximal.cliques returns duplicates

[Tony Larson]

OK, 

Here's a toy example (and on the latest igraph) - still not behaving as expected??

> mat <- matrix(sample(c(0,1), 100 * 100, replace = TRUE, prob = c(0.8, 0.2)), 100, 100)

> g <- graph.adjacency(mat, mode = "undirected", weighted = TRUE, diag = FALSE)

> mc <- maximal.cliques(g)

> any(duplicated(unlist(mc)))

[1] TRUE

> g <- simplify(g)

> mc <- maximal.cliques(g)

> any(duplicated(unlist(mc)))

[1] TRUE

> sessionInfo()

R version 3.0.0 (2013-04-03)

Platform: x86_64-unknown-linux-gnu (64-bit)

locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8

 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8

 [7] LC_PAPER=C                 LC_NAME=C

 [9] LC_ADDRESS=C               LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods

[8] base

other attached packages:

 [1] reshape_0.8.4      plyr_1.8           Matrix_1.0-12      lattice_0.20-15

 [5] xcms_1.37.2        Biobase_2.20.1     BiocGenerics_0.6.0 mzR_1.6.1

 [9] Rcpp_0.10.4        igraph_0.6.5-2

loaded via a namespace (and not attached):

[1] codetools_0.2-8 grid_3.0.0      tcltk_3.0.0     tools_3.0.0

>

On 18 November 2013 15:31, Gábor Csárdi <address@hidden> wrote:

Btw. you can also try to remove multiple and loop edges if you have
any. Just a guess, maybe they are not a problem, but it's worth
trying, just call simplify() on the graph.

G.

On Mon, Nov 18, 2013 at 10:27 AM, Tony Larson <address@hidden> wrote:
> Will try and work up a toy example later this afternoon, as the graph I am
> working on is too large to post  (generated from a 4000 x 4000 adjacency
> matrix).
>
> Thanks
> Tony
>
> On 18 Nov 2013 15:06, "Gábor Csárdi" <address@hidden> wrote:
>>
>> Hi!
>>
>> On Mon, Nov 18, 2013 at 10:00 AM, Tony Larson <address@hidden>
>> wrote:
>> > Hi,
>> > I am using igraph 0.6.2 on R.
>>
>> That is 0.6-2, right? Note that there is a newer version. I can't
>> recall any changes in maximal cliques, though, so it won't fix your
>> issue, probably, but it fixes other issues.
>>
>> > When I use maximal.cliques() to get a list of
>> > complete subgraphs back, several have partly duplicated values, e.g
>> >
>> > [1] 1 2 3 4 5
>> > [2] 1 2 3 4 5 7 8
>> > [3] 1 2 3 4 5 6
>> >
>> > If all vertices in each listing are completely connected, then why in
>> > the
>> > example above don't I get  single list entry for indices 1:8?
>>
>> If you do, then this is a bug. Can you please show us an example that
>> reproduces it? Thanks.
>>
>> Gabor
>>
>> > Why do I get
>> > 3? How can I merge these into one list item?
>> >
>> > Thanks
>> > Tony
>> >
>> >
>> > _______________________________________________
>> > igraph-help mailing list
>> > address@hidden
>> > https://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>>
>> _______________________________________________
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>
>
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Dr. Tony R. Larson
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