1. Any graph-theoretic algorithm can be coded in R using the "graph" package as a basis.
2. I don't know whether graphviz is capable of doing the advanced visualizations that pigale is, since some things are "unpublished". 3. "graph" itself is "generic" and "non-biological", as are many of the supporting tools in the Bioconductor repository. 4. Even better, if you're willing to do a bit of heavy lifting, R has the capability of calling arbitrary C/C++ code, sending and receiving information from it, etc., and such code could be packaged to work as a library within R! This means that pigale could be made into an R extension package. As you've probably guessed, I'm a shameless R bigot. I don't know the folks who built pigale -- I went to the web site and saw the feature set you posted. It's all way over my head; my usage of graph theory is strictly limited to the structures that arise in computer performance analysis -- stochastic Petri nets and their reachability graphs, for example. I haven't found many GPL packages for the *advanced* performance analysis domain. PEPA is the best I've uncovered. If all you care about is steady-state queuing models, Neil Gunther's "PDQ" is great, but it can't do the really advanced stuff. I'm not even sure PEPA can do transient analysis; for that, I think you have to roll your own. There are quite a few good packages in the academic arena that are free to academic researchers, but they all have steep price tags for commercial users. I'm working on a GPL R package to do what these tools do, and it will use "graph" and "graphviz" and a number of other existing R packages. And yes, I will submit it to Portage as an ebuild. :) David Grant wrote: >Can graph and graphviz do all this? in a generic non-biological way? > > > -- [email protected] mailing list
