[ADMB Users] Random effects model with integration in the likelihood

[Jeff Laake]

Thanks for the thought and work on this. Do I use adhmodel.h that you
modified for the admb project or do I make that change locally to my
machine. What is s.htp? It has been a long time since I programmed with c
and I'm still quite new with admb. I'm still in process of reading the
manuals to understand more thoroughly. The re component of admb is really
useful and I want to use it to expand the role of fitting models with
random effects in distance sampling and capture-recapture data. I believe
both could widen the influence and role of admb in ecological research.

regards --jeff


On Sat, Nov 10, 2012 at 9:21 AM, dave fournier <davef at otter-rsch.com> wrote:

>
>
>
> -------- Original Message --------  Subject: Re: [ADMB Users] Random
> effects model with integration in the likelihood  Date: Sat, 10 Nov 2012
> 09:17:59 -0800  From: dave fournier <davef at otter-rsch.com><davef at otter-rsch.com>  To:
> users at admb-project.org
>
> When I want to try and understand something like this I try and let
> the compiler do the work. So I run tpl2rem on your tpl (after
> getting rid of the sigma thing for now).
> An immediate problem is
>
>    df1b2variable sigma=exp(beta+eps);
>     mu=adromb(&model_parameters::fct,0,width,8);
>     f -= -0.5*square(u);
>
> Need to change that to
> > mu=adromb(&df1b2_parameters::fct,0,width,8);
> That is a problem with the sed scripts in tpl2rem
>
> Now compile again and you get
>   undefined reference to df1b2_pre_parameters::adromb(df1b2variable
> (df1b2_parameters::*)(df1b2variable const&), int, data_number&, int)
>
> So give it what it want. Put this in s.htp
>
> class df1b2_parameters;
>
> class df1b2_pre_parameters : public model_parameters
> {
> public:
>    df1b2_pre_parameters(int sz,int argc, char * argv[]) :
>      model_parameters(sz,argc,argv){;}
>    re_objective_function_value  f;
>    void begin_df1b2_funnel(void);
>    void setup_quadprior_calcs(void);
>    void end_df1b2_funnel(void);
>   void ll_j(const int j, const funnel_init_df1b2variable& beta,const
> funnel_init_df1b2variable& sigeps,const funnel_init_df1b2variable& u);
>    df1b2variable df1b2_pre_parameters::adromb(df1b2variable
> (df1b2_parameters::*)(const df1b2variable&), int, data_number&, int);
> };
>
> Now it compiles and returns a link error for this function. So now we
> understand the hierarchy.
> So where is the difficulty?  What we would like to do is to put this
> function in a base class, in this
> case function_minimizer. that is where the dvariable form lives.  It
> almost works, but
> the problem is that function_minimizer does not know about
> df1b2variables so you can't return one
> because at that time it wont know what the size on the stack is.
>
> Anyway that is the idea.  To fix this we can pass the df1b2variable as a
> reference to the function
> instead of returning it and make the function void. So in admodel.h I added
>
> #if defined(USE_LAPLACE)
>    class df1b2variable;
>    class init_df1b2vector;
>    class df1b2vector;
>    class df1b2_parameters;
>    typedef df1b2variable (df1b2_parameters::*DFPMF) (const df1b2variable&);
> #endif
>
>
> class function_minimizer
> {
>     // stuff  ...
>
> #if defined(USE_LAPLACE)
>    void adromb(DFPMF,double a,double b,const df1b2variable& _v,int ns=9);
> #endif
>
>
> This is all the information the compiler needs.
>
> We can put the code for the actual function in a place where it knows
> about df1b2variables.
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