Thanks! I didn't see an "edit" button, which is why I asked, but I figured out
that you have to be a user to edit the wiki and made the change.
On 14-05-23 01:48 PM, Sam Price wrote:
Hi Rosemary,
You are correct the wiki has a typo, as it is a wiki so you should be able to
correct yourself!
Sam
---------------------------------------
Samantha Price, Ph.D.
Dept. Evolution & Ecology
1 Shields Ave,
UC Davis
Davis, CA 95616
USA
Tel: +1 530-752-4720
Website: www.evovert.com <http://www.evovert.com>
---------------------------------------
On May 23, 2014, at 9:34 AM, Rosemary McCloskey <[email protected]
<mailto:[email protected]>> wrote:
Hello,
I'm trying to do ancestral reconstruction of a discrete character state using
ace. I'm referencing the Ancestral State Reconstruction HowTo on the R phylo
wiki (http://www.r-phylo.org/wiki/HowTo/Ancestral_State_Reconstruction). It
says how to use a custom model with ace:
"What if you want to use a transition model that isn't hardwired into ace? You can
do so by defining a custom transition matrix. For example, let's create a custom
four-parameter matrix for a three state character, in which the the probability of
transitioning from state 1 to 2 equals the probability of state 2 to 1 (parameter 1), the
probability of transitioning from 1 to 3 equals the probability of transitioning from
state 3 to 1 (parameter 2), but the probability of transitioning from state 2 to 3
(parameter 3) does not necessarily equal the probability of transitioning from state 3 to
2 (parameter 4)."
Right below, on the page, it shows this matrix:
[,1] [,2] [,3]
[1,] 0 1 2
[2,] 1 0 4
[3,] 2 3 0
Isn't this the transpose of how model matrices normally work? I would expect "the
probability of transitioning from state 2 to 3 (parameter 3)" to be in position
[2,3], but it's in position [3,2] here. I realize that it doesn't make a difference in
this case, but in my case I'm trying to define a non-reversible model so it does matter.
So, sorry if this is a dumb question, but I just want to make sure: when passing a custom
rate matrix to ace, does the transition from state i to state j go in position [i,j] of
the matrix, or in position [j,i]? If this is just a typo in the wiki, who do I contact
about correcting it?
Thanks!
Rosemary
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