[ADMB Users] ADMB development cycle (bug in file f1b2vc1)

[John Sibert]

Jon (et al),
The explanation is simple. The code on code.google has not been kept up 
to date with the "official" svn repository in Honolulu. We could be a 
bit more diligent I suppose.

I generally eat my own dog food.
John

Schnute, Jon wrote:
> We've had some excellent exchanges among ADMB users recently. In
> particular, according to a message from Dave on August 6 (attached at
> the bottom of this message), Ben found a fatal bug. A few days later
> (August 10), Johnoel announced the release of ADMB 9.0.363 with "various
> fixes to the libraries". I made the assumption that this bug had
> probably been fixed, so I thought I'd check the status of the code at
> http://code.google.com/p/admb-project/. In particular, I looked at the
> file f1b2vc1.cpp, located at:
>
> http://code.google.com/p/admb-project/source/browse/trunk/df1b2-separabl
> e/f1b2vc1.cpp
>
> According to the SVN log on this file, it hasn't changed since release
> 43 on March 31. Also, it appears not to include Dave's suggestion about
> ADUNCONST(dvector,x).
>
> So my question is this: How does the source code site
> http://code.google.com/p/admb-project/ fit into the ADMB development
> cycle? Also, how would I actually build a version of ADMB from the files
> in the trunk subdirectories: df1b2-separable, examples, LICENSE,
> linad99, nh99, and tools99?
>
> I've used SVN to build and track my own local version of the source
> files, but I see from the change log at:
>
> http://code.google.com/p/admb-project/source/list 
>
> that all changes since release 43 have pertained to the Wiki.
>
> Probably, I've failed to notice an explanation somewhere of how all this
> should work, and I suspect that the Google code site is still in
> development. But I know from my own recent experience that the tools
> available at "Google code" can greatly facilitate project development.
> Perhaps the ADMB user community would explore some of the changes Ben
> discussed if they/we had a full understanding of the complete toolkit
> needed to build ADMB from the latest source code.
>
> Thanks,
> Jon
>
> ******************************************
> Jon Schnute
> Pacific Biological Station
> 3190 Hammond Bay Road
> Nanaimo, BC V9T 6N7
> CANADA
>
> NEW email: Jon.Schnute at dfo-mpo.gc.ca 
>  (formerly schnutej at pac.dfo-mpo.gc.ca)
> ******************************************
>
> -----Original Message-----
> From: users-bounces at admb-project.org
> [mailto:users-bounces at admb-project.org] On Behalf Of dave fournier
> Sent: August-06-09 8:30 AM
> To: users at admb-project.org
> Subject: [ADMB Users] bug in file f1b2vc1
>
>
> Thanks Ben you found a fatal bug. Hard to believe that function had
> never been used before. In the file f1b2vc1.cpp
> the line
>
>       ADUNCONST(df1b2vector,x)
>
> should have been
>
>     ADUNCONST(dvector,x)
>
>
>
> df1b2vector operator + (const dvector& _x,const df1b2vector& _y)
>   {
>     ADUNCONST(df1b2vector,x)
>
>    ADUNCONST(df1b2vector,y)
>
>    check_shape(x,y,"operator +");
>
>
>    int mmin=x.indexmin();
>
>    int mmax=x.indexmax();
>
>    df1b2vector tmp;
>
>    tmp.noallocate(mmin,mmax);
>
>
>    for (int i=mmin;i<=mmax;i++)
>     {
>
>      tmp(i)=x(i)+y(i);
>     }
>
>    return tmp;
>
>  }
>
>
> Sorry for that.  The reason for these stupid errors is that every once
> and a while the  compiler police for the various c++ compilers make
> changes that break huge amount of old code so one has to fix it all at
> one go and these sorts of errors  creep in.
>
> Maybe someone can comment on how this can get fixed quickly.
>
> as for just hoping that prob will remain between 0 and 1 -- that is a
> mugs game. It will break at the most inopportune time. I modifed your
> code to put in the bounds. also you need to include the prior for the
> u's
>
> Finally WRT yuo commentabout initial values for the u's being necessary.
> that is inaccurate. default values are provided for all parameters.
> However if you want to supply a *.pin ifle then it must include values
> for all parameters. I have already commented on the easiest way to
> produce such a *.pin file.
>
> Herre is your code as I have modified it.
>
>  //cout << "cvec calc\n";
>  cvec = sigma_c*(Z*u)+c;
>  a1vec = elem_prod(pow(size/d,g),exp(-size/d));
>  //cout << "prob calc\n";
>  prob = 1/(1/(elem_prod(cvec,a1vec))+h*initial);
>
>  dvariable ppen=0.0;
>  dvar_vector pprob=posfun(prob,0.01,ppen);
>  f+=ppen;
>
>  ppen=0.0;
>
>  dvar_vector pprob2=1.0-posfun(1.0-pprob,0.01,ppen);
>
>  f+=ppen;
>
>  f+=0.5*norm2(u);  // prior
>
>  f -= sum( log_comb(initial,killed)+
>           elem_prod(killed,log(pprob2))+
>           elem_prod(initial-killed,log(1-pprob2)));
>
>
>
>
>
>   

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