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 : > > 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 : > >> > >> > >> 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]]