Rafael,
You should not used the transformation suggested on this wiki (it is a
bit outdated, NPRS has been removed from ape). In most situations, you
should just leave S=1.
chronopl() is not "broken", but maybe not as reliable than Sanderson's
r8s, though I have seen examples where both programmes agree a lot. What
is needed is someone who could spend a few days (full-time) on testing
and improving chronopl in depth (which I cannot at the moment).
Cheers,
Emmanuel
Rafael Maia wrote on 09/04/2011 04:36:
hello list,
I have been trying to work with chronopl to obtain molecular dating and
ultrametricize a couple trees obtained from Mr. Bayes (at this point, I'm
trying to learn what these functions and methods do, the differences between
them, and follow examples from published papers). I followed the instructions
in the R phylo wiki on my datasets, in order to obtain mean substitution
numbers:
mytree$edge.length = mytree$edge.length * N
where N is the number of sites.
After doing this, I followed the cross validation method to obtain the
smoothing parameter, which was of 1 for one tree and 10 for the other.
However, when I plot the trees, they are identical. In fact, if I use
ridiculously small (0.000001) or large (1000000) values of lambda, they are
still identical.
This does not happen if I use the original edge.length of the tree, but I'm guessing this is probably nonsensical given how the likelihood function is calculated.
I have noticed that the version of chronopl I'm using (ape v.2.6-2) has an S
argument. if I use the original edge.length and specify S=N, then the results
are in fact affected by the value of lambda, and are very different than if I
use the modified edge.length as specified above (indeed, the cross-validation
result for lambda is also different).
Looking online for information, I read that the chronopl function is "broken",
not realiable/not working. Is this still true? Am I not supposed to alter the branch
lengths as specified in the wiki? Should I use the S argument?
Many thanks for any help!
Abraços,
Rafael Maia
---
webpage: http://gozips.uakron.edu/~rm72
"A little learning is a dangerous thing; drink deep, or taste not the Pierian
spring." (A. Pope)
Graduate Student - Integrated Bioscience
University of Akron
http://gozips.uakron.edu/~shawkey/
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Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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