[R-sig-ME] error in glmmTMB when adding glmmTMBControl: unused arguments

[Mollie Brooks]

Yes, I agree that the control argument (as you specified it) appears to be working on the development version of glmmTMB.
For example
(m3 <- glmmTMB(count~spp + mined + (1|site), 
  zi=~spp + mined, 
  family=nbinom2, Salamanders, control = glmmTMBControl(optCtrl = list(iter.max = 1000,
eval.max = 1000), profile = TRUE, collect = FALSE)))

The error you get 
>> 
>> Error in optimHess(par.fixed, obj$fn, obj$gr) :
>>  gradient in optim evaluated to length 1 not 14
>> In addition: There were 11 warnings (use warnings() to see them)
>> 

should have produced a message including "See vignette('troubleshooting')". If it didn’t, then something is broken, so please report it in the issue tracker on GitHub or let me know.

thanks,
Mollie

———————————
Mollie E. Brooks, Ph.D.
Research Scientist
National Institute of Aquatic Resources
Technical University of Denmark

> On 12Feb 2018, at 13:48, Ben Bolker <bbolker at gmail.com> wrote:
> 
> A reproducible example would be useful.  This works (with the
> development version
> of glmmTMB, but I'd be surprised if it broke since the last CRAN release ...)
> 
> library(glmmTMB)
> 
> m1 <- glmmTMB(count~ mined + (1|site),
>              zi=~mined,
>              family=poisson, data=Salamanders,
>  control=glmmTMBControl(optCtrl=list(iter.max=1e3,
>                                      eval.max=1e3),
>                         profile=TRUE))
> 
> what's your sessionInfo()?
> 
> Maybe obvious, but it would probably be efficient to do some
> troubleshooting/model-checking on a
> smaller subset of your data, if you haven't already ...
> 
> On Mon, Feb 12, 2018 at 3:04 AM, Diego Pavon
> <diego.pavonjordan at gmail.com> wrote:
>> Dear list
>> 
>> I am trying to run this model
>> 
>> M1.zi <- glmmTMB(Abundance ~ Temp_std + NEness_std + WithinNatura +
>> Winter_std
>>                 + WithinNatura * Winter_std + NEness_std * Winter_std +
>> Temp_std * WithinNatura
>>                 + WithinNatura * Winter_std  * NEness_std
>>                 + (1|fWinter/site) + (1|species),
>>                 family = poisson,
>>                 ziformula = ~ 1,
>>                 data = AllSpecies)
>> 
>> but after a couple of days (I have 3.5 million data points), I finally got
>> an error:
>> 
>> Error in optimHess(par.fixed, obj$fn, obj$gr) :
>>  gradient in optim evaluated to length 1 not 14
>> In addition: There were 11 warnings (use warnings() to see them)
>> 
>> 
>> Then I tried to add the CONTROL argument following
>> https://cran.r-project.org/web/packages/glmmTMB/glmmTMB.pdf:
>> 
>> M1.zi <- glmmTMB(Abundance ~ Temp_std + NEness_std + WithinNatura +
>> Winter_std
>>                 + WithinNatura * Winter_std + NEness_std * Winter_std +
>> Temp_std * WithinNatura
>>                 + WithinNatura * Winter_std  * NEness_std
>>                 + (1|fWinter/site) + (1|species),
>>                 family = poisson,
>>                 control = glmmTMBControl(optCtrl = list(iter.max = 1000,
>> eval.max = 1000), profile = TRUE, collect = FALSE),
>>                 ziformula = ~ 1,
>>                 data = AllSpecies)
>> 
>> 
>> For some reason, I get this error message:
>> 
>> Error in glmmTMB(Abundance ~ Temp_std + NEness_std + WithinNatura +
>> Winter_std +  :
>>  unused argument (control = glmmTMBControl(optCtrl = list(iter.max = 1000,
>> eval.max = 1000), profile = TRUE, collect = FALSE))
>> 
>> 
>> Does anyone have an idea how to specify the control arguments? I suspect
>> this is some small thing I am missing but I can't see it anymore...
>> 
>> Thank you very much for your time and help.
>> 
>> Best
>> 
>> Diego
>> 
>> 
>> 
>> --
>> *Diego Pavón Jordán*
>> 
>> *Finnish Museum of Natural History*
>> *PO BOX 17 *
>> 
>> *Helsinki. Finland*
>> 
>> *0445061210https://www.researchgate.net/profile/Diego_Pavon-jordan
>> <https://www.researchgate.net/profile/Diego_Pavon-jordan>*
>> 
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>> 
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