[ADMB Users] MVN Example?

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[ADMB Users] MVN Example? Chris Gast 3/14/12 2:50 PM
Hello,

Does anyone have some code to compute the log-likelihood for a multivariate normal model that they're willing to share? I'm having trouble getting matrix determinants and inverses to work.

I found a link to a previous discussion, indicating such an example would be available in Roa's article "A Likelihood-Based Model of Fish Growth With Multiple Length Frequency Data" in JABES, but I'm having trouble accessing the supplementary material.

If I can get this working (a weighted LMM with autocorrelated residuals and spatially-correlated random effects), I'd be happy to add it to the examples list, since I can't seem to find a MVN likelihood example there either.

Thanks,

Chris






-----------------------------
Chris Gast
cmg...@gmail.com
Re: [ADMB Users] MVN Example? Mollie Brooks 3/14/12 4:39 PM
Hi Chris,
I'm doing an MVN model. My procedure section looks like this
PROCEDURE_SECTION
for(int i=1; i<=ncoeffs; i++)
{
coeffs(i)=ucoeffs(i)*scale(i);
}
nLL=0;
for(int p=1; p<=nponds; p++)
{
calc_predictions(p);
calc_varcov(p);
dvar_vector diff=predictions(p)-obs(p);
dvar_matrix tmp_varcov=varcov(p);
nLL+=.5*(nobs(p)*log(2*M_PI)+ln_det(tmp_varcov)+ diff*solve2(tmp_varcov,diff));
}

The first for loop scales all my coefficients to make it conditioned better.
Then I have observations of a bunch of ponds and each pond is assumed to be independent of the others.
I defined functions calc_predictions() and calc_varcov() to fill in those objects; the code in these is pretty specific to my problem. The important thing fir efficiency is that my covariates are in a design matrix created using model.matrix() in R.

Try using solve() where I have solve2(). If you have a problem with solve, I'll explain the complications of why I used this version.

I hope this helps.
cheers,
Mollie

Mollie Brooks
Ph.D. Candidate
NSF IGERT Fellow
Biology Department
University of Florida
mbr...@ufl.edu
http://people.biology.ufl.edu/mbrooks




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Re: [ADMB Users] MVN Example? Chris Gast 3/14/12 4:52 PM
Thanks, Mollie.  For some reason, ADMB can't seem to find the ln_det() function.

test_mat.obj:test_mat.cpp:(.text+0x13af): undefined reference to `ln_det(df1b2matrix&)'

I'll keep playing with it and see if I can figure it out.


Chris





-----------------------------
Chris Gast
cmg...@gmail.com
Re: [ADMB Users] MVN Example? Chris Gast 3/14/12 5:55 PM
After changing line 1978 in df1b2fun.h to match the correct function header on line 220 of  df1b2ludcmp.cpp, I got your syntax working successfully.

I'm not sure who specifically to address regarding making this correction, but hopefully they're reading this thread already....?

Mollie: I'm interested in what complications you experienced with solve(). Is this related to some speed issues which I found noted on previous admb-users posts?



Thanks Mollie (and Jim Ianelli for an off-list reply).

Chris




-----------------------------
Chris Gast
cmg...@gmail.com
Re: [ADMB Users] MVN Example? Rubén Roa 3/15/12 3:30 AM


Rubén H. Roa-Ureta, Ph. D.
AZTI Tecnalia, Txatxarramendi Ugartea z/g,
Sukarrieta, Bizkaia, SPAIN

Hi Chris,

I've told the JABES people that the link to sup. mat. is broken, to no avail it seems.
I'll send you the code later.

Ruben