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constrain variables in HyPhy (Read 1965 times)
student_of_evolution
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Curious HyPhy user

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constrain variables in HyPhy
Sep 9th, 2013 at 1:37pm
 
Hi,

I am trying to devise a LRT (or perhaps use the AIC difference) where the null model is neutral evolution and the alternate model is selection.

For example Yang's M1a vs M2a does this (thus allows use of chisquare with df = 2)
M1a (neutral):
parameters: p0, w_0 < 1, w_1 = 1
M2a (selection):
parameters: p0, p1, w_0 < 1, w_1 = 1, w_2 > 1

I was thinking about setting the neutral model (using the general discrete bi variate distribution) to be:
beta_s <= alpha_s for all s
And alternate model is:
beta_s > alpha_s for at least one s

Can you constrain these variables in hyphy?
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Sergei
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Re: constrain variables in HyPhy
Reply #1 - Sep 9th, 2013 at 2:22pm
 
Hi there,

The types of constraints you need can be implemented through ratios, e.g.

Code:
global R_0;

beta_0 := alpha_0 * R_0;

R_0 :< 1;

...

 



Alternatively, you can use the ratio parameterization directly (e.g. see Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login)

Sergei
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