[Developers] Making changes to ADMB

Johnoel Ancheta johnoel at hawaii.edu
Wed Sep 12 12:41:48 PDT 2012

Hi Trevor,

I can help you get going with developing for ADMB.  Please contact me
by email.


On Wed, Sep 12, 2012 at 8:31 AM, Mark Maunder <mmaunder at iattc.org> wrote:

> Trevor,
> Cole could do this himself by getting access to the ADMB code from
> Johnoel, but it might take some learning, or he could suggest it to the
> developers and put it on the Redmine development website. We encourage
> people to get involved in the development of ADMB, so perhaps he could team
> up with one of the developers to implement it. I have copied the developers
> on this e-mail.
> Mark
> -----Original Message-----
> From: Trevor A Branch [mailto:tbranch at uw.edu]
> Sent: Wednesday, September 12, 2012 11:17 AM
> To: Mark Maunder; Cole Monnahan; Ian J. Stewart; Ian Taylor; James Thorson
> Subject: Making changes to ADMB
> Mark:
> How do people go about making changes to ADMB itself? I ask because a
> quantitatively sharp student of mine, Cole Monnahan, worked over the summer
> with Ian Stewart and others at the NWFSC (Ian S is now at the IPHC), to
> improve the MCMC algorithm of ADMB.
> In essence, he is able to take the variance-covariance matrix, read it
> into R, alter it, and write it back, in order to improve MCMC performance.
> As a proof of concept he has shown that replacing correlations greater than
> a particular value with a lower value, greatly improves MCMC convergence
> (by a factor of 10). In his example, he replaces a correlation of -0.94
> with one of -0.5.
> What I am thinking is that it would be amazingly useful to have a command
> line option in ADMB that would look like this:
> model -mcmc 2000000 -mcsave 100 -nohess -noest -relaxed 0.5
> This would replace all correlations with an absolute value greater than
> 0.5, with a value of 0.5. (i.e. -0.9 would become -0.5, and 0.9 would
> become 0.5).
> I think that the R code worked out by Cole could be used as the basis for
> recoding ADMB in this way. I'll leave Cole to explain his method a little
> further.
> Trevor
> --
> Assistant Professor, School of Aquatic and Fisheries Sciences, University
> of Washington, +1-206-221-0776 Organizer, Bevan Series on Sustainable
> Fisheries, Jan-Mar 2013 (Previous Bevan Series:
> http://courses.washington.edu/susfish/schedule.php)
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