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
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--
Klaus Schliep
Université Paris 6 (Pierre et Marie Curie)
9, Quai Saint-Bernard, 75005 Paris
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