[R-sig-ME] [FORGED] Re: Error from glmmTMB() --- no joy.

[Ben Bolker]

 Yeah, I realized today that I was wrong about this fixing the problem.
I'm not stuck yet/want to work on this, but I will pursue it in the
context of a glmmTMB issue.

  (I like everyone else am a little busier than usual these days ...)

 Ben

On 2020-03-19 8:17 p.m., Rolf Turner wrote:
> 
> On 19/03/20 3:52 pm, Ben Bolker wrote:
> 
> <SNIP>
> 
>> I made a small change that appears to allow the
>> original model to run correctly.  If you want to try it out, and have
>> development tools (compilers etc.) and the remotes package installed,
>>
>> remotes::install_github("glmmTMB/glmmTMB/glmmTMB using cloglog_fix")
>>
>>    should install the patched version (I think).
>>
>> This will presumably be merged with the master branch sometime soon but
>> I want to add some tests etc.
> 
> I've finally got around to trying out your patch.  No problems with the
> install_github() process, but after doing the install I executed:
> 
>> library(glmmTMB)
>> fmla <- cbind(Dead, Alive) ~ (Trt + 0)/Dose + (Dose | Rep)
>> X    <- dget("X.txt")
>> fit  <- glmmTMB(fmla, data = X, family = betabinomial(link = "cloglog"),
>>                dispformula = ~1
> and got:
> 
>> Error in (function (start, objective, gradient = NULL, hessian =
>> NULL,  :   NA/NaN gradient evaluation
>> In addition: Warning messages:
>> 1: In (function (start, objective, gradient = NULL, hessian = NULL,  :
>>   NA/NaN function evaluation
>> 2: In (function (start, objective, gradient = NULL, hessian = NULL,  :
>>   NA/NaN function evaluation
>> 3: In (function (start, objective, gradient = NULL, hessian = NULL,  :
>>   NA/NaN function evaluation
>> 4: In (function (start, objective, gradient = NULL, hessian = NULL,  :
>>   NA/NaN function evaluation
>> 5: In (function (start, objective, gradient = NULL, hessian = NULL,  :
>>   NA/NaN function evaluation
>> Timing stopped at: 0.572 0 0.572
> 
> So my Sadim touch persists in its effect.
> 
> cheers,
> 
> Rolf
> 
> P. S. With the logit link I got warnings
> 
>> 1: In (function (start, objective, gradient = NULL, hessian = NULL,  :
>>   NA/NaN function evaluation
>> 2: In fitTMB(TMBStruc) :
>>   Model convergence problem; non-positive-definite Hessian matrix. See
>> vignette('troubleshooting')
> 
> but no errors as such.
> 
> R.
>