Comments and Ratings

has anyone had success installing this toolbox with MATLAB v7.5 Release R2007b (on Win XP Pro)

I unzipped the files to the /toolbox/local/ folder and tried adding the new @graph folder to path-- however I get this message:

"Warning: Method directories not allowed in MATLAB path: ...."

Any pointers? Thanks.

Does these coded work for directed, weighted graph?

Hi,
I am interested in using the graph package for calculation of the modularity of a complex network. I work with adjacency matrix, but the input in modularity is in other format. So, can you tell me the input format of the network to calculate its modularity.
Thanks in advance,
Igor Mishkovski

I believe there might be several errors in the code for computing the clustering coefficient in clusteringcoeff.m

Currently lines of the code read:
        for k1 = 1:a
        for k2 = k1+1:a
            if adj(k1,k2) | adj(k2,k1)
                E = E + 1;
            end
        end
    end

But
 1. if the nested for loops are meant to cover all possible pairs, technically it should be 'for k1 = 1:(a-1)' though if the original matrix did not have self-loops, this will not affect the result. The check for non-self loops in 'neighbours' only removes the self-loop of the node, not self-loops among its neighbors so if the adjacency matrix has self-loops, this code would be incorrect - unless I am mistaken about the calculation of the clustering coefficient? Given that the calculation counts the 'denominator' as 'all possible pairs' (a(a-1)/2), this makes me think that the authors assume no self loops in the graph. In that case, the code is incorrect.
  3. a is meant to be the number of neighbors and k1, k2 to enumerate over the SET of neighbors, not be the IDENTITY of the neighbors so the line
    'if adj(k1,k2) | adj(k2,k1)'
should instead read
     if adj(neighbours(k1), neighbours(k2)) | adj(neighbours(k2), neighbours(k1))
to access the actual indices of the neighbors, not just the nodes 1:a....

I believe the correct version of this segment of code should be:
    for k1 = 1:(a-1)
        for k2 = k1+1:a
            if adj(neighbours(k1),neighbours(k2)) | adj(neighbours(k2),neighbours(k1))
                E = E + 1;
            end
        end
    end

Hi,

I am interested to do some experiments using
your Graph package for molecular biologist.
I you appreciate some examples on how to uses it.
Regards,
saad

The code fails under R12.1
Please update the informations about the Matlab release.

Thanks! I have been looking for this for my Final Year Project!!

good tool,however may be some extra drawing utilities such as line,circle.. can be cool,
thanx..