Hi,
I am sorry, but I cannot find RBGL/R/interfaces.R in the R library directory
in my pc.
I found it in svn repository, but I don't understand what I could do with
it...

Davide

2006/12/19, lilong@isb-sib.ch <lilong@isb-sib.ch>:

>
> Hi,
>
> I took a look at the graphs you sent (network{2,3,4}.txt).  I think the
> problem has more to do with output format than with the result.  I used
> "sapply" instead of "lapply" when converting node index to node names,
> which  causes reformatting...
>
> Could you please try to modify maxClique in RBGL/R/interfaces.R to use
> "lapply" instead of "sapply" and look at the result?  Let me know if it
> works.  If so, I'll check in the fix.
>
> Thanks
>
> Li
>
> > Hi Li,
> >
> > thanks for your answer.
> > I cannot send you the full dataset, because it is a MySQL database of
> > various MBs of size, but in the file "data.zip" in attach you find four
> > files with the adjacency matrix (NOTE: for a direct graph, so, for
> > example,
> > 40 19 means there is a link between node 40 and node 19) for package
> > "Graph"
> > in four temporal steps (note: these steps are consecutive) where I found
> > what I described in my first e-mail (but it also happens in other
> > intervals).
> > The first file ("network1.txt"), maxclique found cliques of length 19,
> in
> > the second and third file ("Network2" and "network3") the maximum clique
> > found has length 1. In the fourth file ("network4") length 19.
> > I also send you  the plot of some network indicator:
> > network density ("densita.png")
> > number of active node ("numero_agenti_vivi.png")
> > The total step are 500; the adjacency matrices I sent you are relative
> at
> > steps 429-430-431-432
> > Thanks in advance
> >
> > Davide
> >
> >
> > 2006/12/18, lilong@isb-sib.ch <lilong@isb-sib.ch>:
> >>
> >>
> >> Hi,
> >>
> >> Could you provide the dataset?  Without any further info, it's hard to
> >> judge the results, especially the graph changes dynamically.  For
> >> instance
> >> it's possible that at SOME stage, there is no bigger clicks.
> >>
> >> If you provide a graph that shows the behaviour (that particular
> graph),
> >> we could help further.
> >>
> >> Thanks
> >>
> >> Li
> >>
> >> > Hello everyone,
> >> >
> >> > I am using packages Graph and RBGL 1.8 with R 2.3.1 for finding
> >> cliques
> >> in
> >> > a
> >> > undirected dynamical graph (it changes over time).
> >> > What I do: I load data (adjacency matrix for Graph) from database in
> a
> >> > temporal step.
> >> > I transform the matrix in a direct graph using ftM2graphNEL, I make
> >> some
> >> > analysis (like "degree"), then I transform the
> >> > direct graph in a undirect graph using "ugraph" to use maxClique to
> >> find
> >> > all
> >> > the cliques in this graph (which now is undirect).
> >> > But I found a problem: in some steps the output of maxClique give me
> >> only
> >> > clique of length one...but it is a graph with density
> >> > near at 1! In the step before it gives me one or two cliques of
> lenght
> >> 27
> >> > or
> >> > 28 (the node in the graph are 29).
> >> > I give you some outputs:
> >> >
> >> > step "Before":
> >> >
> >> > $maxCliques
> >> > $maxCliques[[1]]
> >> >  [1] "1"  "3"  "6"  "7"  "8"  "9"  "11" "12" "14" "16" "17" "18" "19"
> >> "20"
> >> > "21"
> >> > [16] "24" "25" "27" "30" "31" "32" "35" "36" "37" "39" "40" "33" "26"
> >> >
> >> > $maxCliques[[2]]
> >> >  [1] "1"  "3"  "6"  "7"  "8"  "9"  "11" "12" "14" "16" "17" "18" "19"
> >> "20"
> >> > "21"
> >> > [16] "24" "25" "27" "30" "31" "32" "35" "36" "37" "39" "40" "22"
> >> >
> >> > the degree (in the undirected graph) of each node is (node are number
> >> from
> >> > 1
> >> > to 40, but in time some node (e.g.  node 2) "dies"):
> >> >
> >> >  1  3  6  7  8  9 11 12 14 16 17 18 19 20 21 22 24 25 26 27 30 31 32
> >> 33
> >> 35
> >> > 36
> >> > 28 28 28 28 28 28 28 28 28 28 28 28 28 28 28 26 28 28 27 28 28 28 28
> >> 27
> >> 28
> >> > 28
> >> > 37 39 40
> >> > 28 28 28
> >> >
> >> > and in the "next" step the output is the following:
> >> >
> >> > $maxCliques
> >> >       [,1] [,2]
> >> >  [1,] "1"  "1"
> >> >  [2,] "3"  "3"
> >> >  [3,] "6"  "6"
> >> >  [4,] "7"  "7"
> >> >  [5,] "8"  "8"
> >> >  [6,] "9"  "9"
> >> >  [7,] "11" "11"
> >> >  [8,] "12" "12"
> >> >  [9,] "14" "14"
> >> > [10,] "16" "16"
> >> > [11,] "17" "17"
> >> > [12,] "18" "18"
> >> > [13,] "19" "19"
> >> > [14,] "20" "20"
> >> > [15,] "21" "21"
> >> > [16,] "24" "24"
> >> > [17,] "25" "25"
> >> > [18,] "26" "26"
> >> > [19,] "27" "27"
> >> > [20,] "30" "30"
> >> > [21,] "31" "31"
> >> > [22,] "32" "32"
> >> > [23,] "35" "35"
> >> > [24,] "36" "36"
> >> > [25,] "37" "37"
> >> > [26,] "39" "39"
> >> > [27,] "40" "40"
> >> > [28,] "33" "22"
> >> >
> >> > The number of node in each cliques in always 1.
> >> >
> >> > degree:
> >> >  1  3  6  7  8  9 11 12 14 16 17 18 19 20 21 22 24 25 26 27 30 31 32
> >> 33
> >> 35
> >> > 36
> >> > 28 28 28 28 28 28 28 28 28 28 28 28 28 28 28 27 28 28 28 28 28 28 28
> >> 27
> >> 28
> >> > 28
> >> > 37 39 40
> >> > 28 28 28
> >> >
> >> > Some ideas?
> >> > Thank-you very much.
> >> >
> >> > Sorry for my english.
> >> >
> >> > Davide
> >> >
> >> >       [[alternative HTML version deleted]]
> >> >
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor@stat.math.ethz.ch
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >
> >>
> >>
> >
>
>

	[[alternative HTML version deleted]]

