[ADMB Users] C++ code for logistic-normal

Steve Martell SteveM at iphc.int
Mon Dec 2 14:31:35 PST 2013

Hi Dan, Rick,

Here is what I have implemented thus far in iSCAM.  If you save the cpp and header file in your tpl directory, then you'll have to recompile the code using

> admb mycode logistic_normal

I think that works; I use my own makefiles to compile the code.  But if your using the most recent version of ADMB, it should be there.

Note also that the logistic_normal is already in the ADMB source code (I put it there a couple of years ago).  In the API search dmvlogistic.  So you can use that as an alternative.

Note I've implemented it as a class,  to use it inside your tpl, you'll need the following:

  #include "logistic_normal.h"

and in the
  // Instantiate the object with observed matrix(O) and predicted matrix (P)
  logistic_normal cLN_Age(O,P);

  // Get the logistic normal likelihood
  nlvec(k)  = cLN_Age.negative_loglikelihood(atau2(k));

  // Get the normalized residuals for plotting.
  nu          = cLN_Age.standardized_residuals();

On Dec 2, 2013, at 1:53 PM, chris.francis <chris.francis at clear.net.nz> wrote:

> Hi Dan,
> Rick Methot is contemplating implementing the
> logistic-normal likelihood in Stock Synthesis, and asked me
> whether I had any C++ code I could send him to use as a
> prototype for this implementation.
> Would you be able to send him (at the email address above)
> the logistic-normal-related code you inserted into your paua
> model?  That would be great if you could.
> Actually, it would be useful if you could cc your email to
> Steve Martell (address above), who already has LN1 in his
> program (iSCAM), and is wanting to implement LN2-3.
> Cheers,
> Chris


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