Great, Rosemary! If you encounter a problem with editing something on the
wiki, do let me know.
-hilmar
On Fri, May 23, 2014 at 5:29 PM, Rosemary McCloskey rmcclosk.m...@gmail.com
wrote:
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
rmcclosk.m...@gmail.commailto:
rmcclosk.m...@gmail.com 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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