Hi John, On 7/28/11, John Denton <jden...@amnh.org> wrote: > Hi all, > > I'm using the ape package, and was wondering if there was a method in the > package or code for calculating the diameter > > (http://mathworld.wolfram.com/GraphDiameter.html) > > of phylogenetic tree objects. I had been looking in to exporting trees > from ape into a graph theory package (igraph), but it looks like it would > be more difficult to write a file conversion script than to try something > in ape itself.
Conversion is not hard, look in the source code of phangorn:::plot.networx for an example. > > Also, I have tried installing the phybase package from CRAN but keep > getting errors. Does anyone have or know of a good script for calculating > Robinson-Foulds differences for phy objects? dist.topo in ape and RF.dist and treedist in phangorn compute the Robinson-Foulds or symmetric distance (called Penny-Hendy in dist.topo). Cheers, Klaus > > Thanks! > > ~J > > > > -- > "ORGANIC LIFE beneath the shoreless waves > Was born and nurs'd in ocean's pearly caves; > First forms minute, unseen by spheric glass, > Move on the mud, or pierce the watery mass; > These, as successive generations bloom, > New powers acquire and larger limbs assume; > Whence countless groups of vegetation spring, > And breathing realms of fin and feet and wing." > > ~Erasmus Darwin, The Temple of Nature Canto I.V > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
