I would like to apply network measures (such as betweenness centrality, upper boundedness, etc.) to a weighted graph with non-integer weights, defined by a euclidean distance matrix. The package sna provides the measures that I want to use, but seems only to operate on binary graphs. I have read work by Mark Newman (http://aps.arxiv.org/abs/cond-mat/0407503/), who suggests that a weighted graph can be transformed into an unweighted multigraph, to which such measures can be applied. It seems that the package giRaph contains a function to handle multigraphs, but there is no example in the manual to show how it is used. I am also not sure whether this multigraph structure can be used as input into the relevant functions in the sna package. Can anyone advise? Many thanks, Andrew Wilson
Dear Andrew, we've created a package called igraph, but the current version does not really support weighted graphs, so it's not much good for you. It can do weighted minimum spanning tree, but this is probably all. Also it can't handle multigraphs. I'm writing this email because if you end up writing these routines for yourself, you might consider to extend igraph. igraph contains many routines for non-weighted graphs and might be easier for you to use these as a baseline. Most routined are written in C because we need speed for very large graphss but you can also add your extensions in R if you like. Just an option. Also, we will add routines for weigthed graphs, but currently this is not the current direction of the development, so it might take a few months. (Although the direction changes quite often.....) Multigraph support is not planned and very unlikely to be added. See http://cran.at.r-project.org/src/contrib/Descriptions/igraph.html and http://cneurocvs.rmki.kfki.hu/igraph FYI, Gabor On Wed, Mar 01, 2006 at 08:53:06AM -0000, Wilson, Andrew wrote:> I would like to apply network measures (such as betweenness centrality, > upper boundedness, etc.) to a weighted graph with non-integer weights, > defined by a euclidean distance matrix. The package sna provides the > measures that I want to use, but seems only to operate on binary graphs. > I have read work by Mark Newman > (http://aps.arxiv.org/abs/cond-mat/0407503/), who suggests that a > weighted graph can be transformed into an unweighted multigraph, to > which such measures can be applied. It seems that the package giRaph > contains a function to handle multigraphs, but there is no example in > the manual to show how it is used. I am also not sure whether this > multigraph structure can be used as input into the relevant functions in > the sna package. Can anyone advise? > > Many thanks, > Andrew Wilson > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html-- Csardi Gabor <csardi at rmki.kfki.hu> MTA RMKI, ELTE TTK
Hi,
Some implementations are available in the packages graph and RBGL from
Bioconductor (www.bioconductor.org). I think you will find that they do
what you would like, but let the maintainers know if not.
best wishes
Robert
Wilson, Andrew wrote:> I would like to apply network measures (such as betweenness centrality,
> upper boundedness, etc.) to a weighted graph with non-integer weights,
> defined by a euclidean distance matrix. The package sna provides the
> measures that I want to use, but seems only to operate on binary graphs.
> I have read work by Mark Newman
> (http://aps.arxiv.org/abs/cond-mat/0407503/), who suggests that a
> weighted graph can be transformed into an unweighted multigraph, to
> which such measures can be applied. It seems that the package giRaph
> contains a function to handle multigraphs, but there is no example in
> the manual to show how it is used. I am also not sure whether this
> multigraph structure can be used as input into the relevant functions in
> the sna package. Can anyone advise?
>
> Many thanks,
> Andrew Wilson
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org