Thanks, guys. I just have a follow-up question: Does anyone know of a
way to optimize BLs using optim.pml() while enforcing a molecular
clock?
Thanks!
John
On Thu, Nov 8, 2012 at 6:06 PM, Rob Lanfear rob.lanf...@gmail.com wrote:
Hi John,
Brian's suggestion is a good one.
Another option
Hi Jeremy,
Emmanuel and I had a off-list conversation after that email, so there was
follow-up, we just never told the list about it!
To my knowledge, the issue I was having where not all clades shared were
being detected with prop.clades was unique to 3.0-1. For example, under my
3.0-6 install
Hi John,
optim.pml has an parameter optRooted and you have to set it to TRUE.
If you give the function an ultrametric tree it will optimise the edge
lengths. Unfortunately it is not possible to use tree rearrangements
with this option so far.
Regards,
Klaus
On 11/9/12, john d
Thanks for getting back, Dave! Klaus Schliep had already replied off-list â
he suggested that I make sure the tip labels in the trees under comparison are
in the same order, using a feature in phangorn:
tree2 - phangorn:::checkLabels(tree2, tree1$tip.label)
prop.clades(tree1,tree2)
And that
I would have to see your code to know 100% for certain - but your results make
intuitive sense, so let me just guess. When you have OU under a very high alpha
(which is what you are getting here), then you are modeling a process following
a random walk with an extremely high tendency to be
Hi all
I write to ask a simple question, anyone know how to plot the
parameters obtained by applying the different diversification models
implemented in the program laser of Rabosky ??.
if anyone can guide me would be very nice
cheers!
--
Oscar Inostroza Michael
Biólogo
Laboratorio de
