[ADMB Users] "xxglobal.tmp" error with tpl2rem
Steve Martell
s.martell at fisheries.ubc.ca
Tue Aug 4 09:53:49 PDT 2009
This line is causing problems in your other model (mccoypred3.tpl);
prob = 1/(1/(elem_prod(cvec,elem_prod(pow(size/d,g),exp(-size/d))))
+h*initial);
specifically, it does not like "pow(size/d,g)" because there does not
appear to be a function that takes the arguments:
'bolker2.cpp:123: error: no matching function for call to
‘pow(data_vector&, df1b2_init_number&)’
You might want to re-write this function in log-space to get it to
work properly.
On 4-Aug-09, at 8:58 AM, Bolker,Benjamin Michael wrote:
>
> thanks for the quick reply.
>
> no luck, though:
>
> ben at bolker-lap2:~/downloads$ ./admb -r ~/students/mccoy/mccoypred3
>
> *** tpl2rem /home/ben/students/mccoy/mccoypred3
> cat: xxalloc4.tmp: No such file or directory
> Error executing command cat xxglobal.tmp xxhtop.tmp header.tmp
> xxalloc1.tmp xxalloc2.tmp xxalloc3.tmp xxalloc4.tmp
> xxalloc5.tmp xxtopm.tmp xxalloc6.tmp > /home/ben/students/
> mccoy/mccoypred3.cpp
>
> is there something boneheaded/obviously wrong with the TPL file?
> it takes me a long time to recognize such things, being so new to
> ADMB.
>
> I did find that the simple2.tpl example posted on the google code
> site, which is
> basically a translation of the example in the ADMB-RE manual (taking
> "simple.tpl" and adding some measurement error) provokes the same
> response. The union.tpl example distributed with ADMB-RE works, but
> I can provoke the same error
> by deleting the following lines from union.tpl:
>
> < PRELIMINARY_CALCS_SECTION
> < cout << setprecision(4);
> <
> < GLOBALS_SECTION
> <
>
> Here's simple2.tpl:
>
> DATA_SECTION
> init_int nobs
> init_vector Y(1,nobs)
> init_vector X(1,nobs)
> PARAMETER_SECTION
> init_number a
> init_number b
> init_number mu
> vector pred_Y(1,nobs)
> init_bounded_number sigma_Y(0.000001,10)
> init_bounded_number sigma_x(0.000001,10)
> random_effects_vector x(1,nobs)
> objective_function_value f
> PROCEDURE_SECTION // This section is pure C++
> f = 0;
> pred_Y=a*x+b; // Vectorized operations
> // Prior part for random effects x
> f += -nobs*log(sigma_x) - 0.5*norm2((x-mu)/sigma_x);
> // Likelihood part
> f += -nobs*log(sigma_Y) - 0.5*norm2((pred_Y-Y)/sigma_Y);
> f += -0.5*norm2((X-x)/0.5);
> f *= -1; // ADMB does minimization!
>
>
> ________________________________________
> From: Steve Martell [s.martell at fisheries.ubc.ca]
> Sent: Tuesday, August 04, 2009 11:35 AM
> To: Bolker,Benjamin Michael
> Cc: users at admb-project.org
> Subject: Re: [ADMB Users] "xxglobal.tmp" error with tpl2rem
>
> Ben,
>
> Try using the scripts that Arni posted at:
>
> http://admb-project.org/community/editing-tools/admb-ide/scripts-linux.zip/view?searchterm=Scripts
>
> Steve
>
> On 3-Aug-09, at 10:09 PM, Bolker,Benjamin Michael wrote:
>
>>
>> I'm just beginning to use AD Model Builder.
>> I have successfully (after some struggles) created a few different
>> likelihood models, with results matching previous model fits in R.
>> Now I'm trying to add a random effect. Versions of the TPL file
>> below compiled OK with tpl2cpp before I added the random effect;
>> now, with tpl2rem, I'm getting
>>
>> cat: xxalloc4.tmp: No such file or directory
>> cat: xxalloc5.tmp: No such file or directory
>> Error executing command cat xxglobal.tmp xxhtop.tmp header.tmp
>> xxalloc1.tmp xxalloc2.tmp xxalloc3.tmp xxalloc4.tmp
>> xxalloc5.tmp xxtopm.tmp xxalloc6.tmp > mccoypred4.cpp
>>
>> There was an issue with similar keywords listed on the ADMB site,
>> but it
>> was listed as "resolved".
>>
>> I'm running on Ubuntu Linux 9.04, with a recent (?? can't find
>> version number ??)
>> version of ADMB. (Maybe 9.0.202 from the google code page?)
>>
>> I'd be happy to provide any other diagnostics/information if that
>> will
>> help solve / diagnose ...
>>
>> sincerely
>> Ben Bolker
>>
>>
>>
>> -------------------------------------
>> DATA_SECTION
>>
>> init_int nobs // # of observations
>> init_int nblock // # of blocks
>> init_vector killed(1,nobs) // # killed per trial
>> init_vector size(1,nobs) // size of individuals
>> init_vector initial(1,nobs) // starting density (# individuals)
>> init_matrix Z(1,nobs,1,nblock) // random-effects model matrix
>>
>> PARAMETER_SECTION
>>
>> init_number c // *mean* c value
>> init_number d
>> init_bounded_number h(0.0,1.0,1)
>> init_number g
>> init_bounded_number sigma_c(0.00001,1.0,1)
>> random_effects_vector u(1,nblock)
>> vector prob(1,nobs)
>> vector cvec(1,nobs)
>> objective_function_value f
>>
>> PROCEDURE_SECTION
>> // compute vector of c values
>> cvec = c + sigma_c*(Z*u)
>> // power-Ricker
>> prob = 1/(1/(elem_prod(cvec,elem_prod(pow(size/d,g),exp(-size/d))))
>> +h*initial);
>> // binomial negative log-likelihood
>> f -= sum( log_comb(initial,killed)+
>> elem_prod(killed,log(prob))+
>> elem_prod(initial-killed,log(1-prob)));
>> _______________________________________________
>> Users mailing list
>> Users at admb-project.org
>> http://lists.admb-project.org/mailman/listinfo/users
>
> Steve Martell
> s.martell at fisheries.ubc.ca
>
>
>
Steve Martell
s.martell at fisheries.ubc.ca
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