Somewhere I wrote a function that samples at a series of
user-set timepoints and counts the # of lineages crossing
each timepoint -- this is pretty flexible, allows for
increases/decreases in diversity etc., let me know if the
other options aren't working for you I can dig it up...
On
Hi Rob.
Thanks for identifying the bug. This should be fixed, I hope, in the
newest version of phytools (v0.0-6; available:
http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/).
The way this function works is by first computing the heights above the
root of all the nodes (including tip
Hi Liam, Emmanuel, Nick, et al
Thanks for all the help.
Liam, I can confirm that your new function works fine on all the trees I've
tested (about 20). Thanks!
Some of my trees are pretty large (a few thousand taxa), so for interest's
sake I coded up Emmanuel's suggestion too.
The code is below
Hi all,
I'll make a new version of ltt.plot() that treats ultrametric and
non-ultrametric trees. After all, I don't see a logical reason why both
kinds of trees would be treated differently here. I'll add an option
backward (FALSE by default) so the time scale can start from the root,
and
This is implemented in my phytools package. This is not yet on CRAN,
but can be downloaded from
http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/. The function is
ltt(). It is slow, but seems to work. Please let me know if you have
success with this.
- Liam
--
Liam J. Revell
Hi Liam Rob,
You may try using dist.nodes() for this:
x - dist.nodes(phy)
n - Ntip(phy)
ROOT - n + 1
x[ROOT, ]
The last command returns the distance from the root to all nodes and
tips which are ordered in the usual way. So you may create a vector with
+1 for the nodes, -1 for the tips, and
