On Tue, Oct 22, 2013 at 12:24 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi,
>
> On Tue, Oct 22, 2013 at 9:13 AM, Forst, Christian
> <christian.forst@mssm.edu> wrote:
> > I am looking for an implementation of Edmond's (or better) algorithm to
> calculated a directed minimum spanning tree from a directed graph. I found
> the edmondsOptimumBranching() function in the RBGL package but I am
> struggling in getting my graphs (from edge-lists) in the right format. I
> would guess using addEdge() is not the way to go to read large graphs.
> > I am open for suggestions for other packages.
>
> The igraph package is usually a good place to look for algorithms over
> graphs:
>
> http://igraph.sourceforge.net
>
> There is a `minimum.spanning.tree` function in there:
>
> http://igraph.sourceforge.net/doc/R/minimum.spanning.tree.html
>
> HTH,
> -steve
>
>
Do we need some investment in interoperability with igraph?

Additionally, it seems to me that there has been little rallying around any
given external format for representing graphs -- we had some GXL support in
graph package but GXL seems to have gone stale (web site is dated 2002),
and igraph does not handle it.  Perhaps some tools for GraphML
import/export would be worthwhile?


> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>
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