[ADMB Users] ADMB development cycle

Schnute, Jon Jon.Schnute at dfo-mpo.gc.ca
Fri Aug 21 11:32:57 PDT 2009

John - Thanks very much for your helpful reply. I didn't know (or
perhaps had forgotten) about the web site you mentioned:

I'm very impressed with your long term plans and the progress so far.

Perhaps this cartoon expresses how I was feeling:

You're right, I need to be more patient.

Thanks again, and best wishes,
Jon (Impatient Canine, Retired)

PS - It would be great if someone out there would volunteer to be a
cartoonist for the ADMB project. On the subject of dog food, I also
noticed these:

-----Original Message-----
From: John Sibert [mailto:sibert at hawaii.edu] 
Sent: August-20-09 11:09 PM
To: Schnute, Jon; Bolker, Ben
Cc: users at admb-project.org
Subject: Re: ADMB development cycle

Jon, Ben -
Thanks for your feedback and support.

I apologize for your confusion over the source code on code google. We 
regard the current code on this site as an interim step. It was not our 
immediate intention that this code be used for making the libraries. 
Rather it is posted mainly to allow people to study the main parts of 
the ADMB code. Currently some  parts  of the ADMB code need to  be 
modified slightly before the whole package can be released. If you look 
at the ADMB Project workplan at 
http://admb-project.org/community/public-domain, you will see that our 
intention is, and always has been, to make the full source code and make

utilities available in December 2009. We are definitely on track to make

that deadline.

The whole point of an open-source project is sharing breakfast with 
canine colleagues, and that is also one of the purpose of the ADMB 
Project. One could wish that dogs were a more patient species.

Meanwhile, Johnoel has  updated the code.google site so that it reflects

the most recent changes.

We make the Honolulu subversion server available to people who have 
reason to use it, i.e. those who have agreed to take on specific tasks.

In the long run, I'm not sure that we will eliminate the Honolulu 
subersion repository. It may be beneficial to maintain both "production"

and "development" versions.

Thanks again for your comments.

Schnute, Jon wrote:
> John - Thanks for your reply. I'm going to try responding pretty
> honestly, but first let me emphasize that I'm speaking as an
> enthusiastic supporter of the ADMB project who is genuinely trying to
> help. I don't want to criticise anyone, particularly you who played
> continues to play) a key role in making the project possible. I'm sure
> that Ben also comes from that point of view, and we're really lucky to
> have someone like him making contributions. (Users who don't know him
> may wish to check out his web site
> http://people.biology.ufl.edu/bolker/.)
> I was glad to see that Jim Ianelli enjoyed the dog food metaphor. Like
> you, I generally eat my own dog food. I think Ben's point is that the
> more people eating the same food the better. Different people, with
> different tastes, can make constructive suggestions for the recipe,
> after a while the stuff might get really tasty. (Of course, it could
> also get pretty horrible.) Very possibly the ingredients may lead to a
> variety of new recipes.
> In regard to ADMB, I feel as if I have the can of dog food, but no can
> opener. In framework of "open source" software, I honestly don't
> understand the concept of an "official" Honolulu SVN repository that
> isn't publically available. How can people make useful comments and
> contributions without seeing what's really going on? It seems to me
> if you have everything running from your repository (and the binary
> files demonstrate that you do), then you must have quite a few tools,
> such as "make" files that don't appear on the Google Code site. Also,
> see no source code (perhaps originally in Lex/Yacc) for the
> tpl2cpp and tpl2rem. 
> As things currently stand, I get the (possibly false) impression that
> ADMB has a core group of insiders, who really know what's going on,
> a group of outsiders (like me) who don't really see the picture
> >From Ben's comments and his notable record in education, I think he
> wants to learn the tool so that he can adopt it in his courses and
> it to his students. (Ben, sorry if I'm reading you wrong on this.)
> certainly is where I'm coming from, although I just have "colleagues",
> not formal students.
> Could you perhaps open the Honolulu SVN server (read only) to the ADMB
> community and give us the address? Or, if the server can't handle the
> load, could you give me access to the server so that I can post
> files on the Google code site from time to time? It strikes me that
> Google offers many features above and beyond the SVN server itself,
> as an tools for posting problem issues and providing reviews.
> I can understand that you probably have very limited resources in
> Honolulu. If so, I think you can get a lot more help from the user
> community by making the project more open. Everything I've read about
> open source software suggests that this is true.
> Hey, I'm just a retired guy like you. I could be out in the garden
> instead of writing a letter like this one. I'll feel slightly rebuffed
> if this appeal warrants only a cryptic reply with no proposed changes.
> But maybe I'm just a grouchy old guy speaking on a subject of no
> interest to anyone. It might help to hear comments from other ADMB
> about this issue.
> I've had these thoughts for some time, but Ben's comments encouraged
> to speak freely. Am I at the head of a parade, or just trotting along
> far behind everyone else?
> Thanks for reading this, and best wishes,
> Jon
> -----Original Message-----
> From: John Sibert [mailto:sibert at hawaii.edu] 
> Sent: August-19-09 10:36 PM
> To: Schnute, Jon
> Cc: users at admb-project.org
> Subject: Re: [ADMB Users] ADMB development cycle (bug in file f1b2vc1)
> Jon (et al),
> The explanation is simple. The code on code.google has not been kept
> 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
>> file f1b2vc1.cpp, located at:
>> e/f1b2vc1.cpp
>> According to the SVN log on this file, it hasn't changed since
>> 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
>> 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
>> 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
>> 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
>> 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
>> 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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