allFit fails after removing object with starting values for model parameters from workspace
Hi, Ben, in fact, it does work in the latest development version. I apparently missed to try that one; sorry for bothering and. Thank you very much once more for your efforts! Best regards -- Gerrit --------------------------------------------------------------------- Dr. Gerrit Eichner Mathematical Institute, Room 212 gerrit.eichner at math.uni-giessen.de Justus-Liebig-University Giessen Tel: +49-(0)641-99-32104 Arndtstr. 2, 35392 Giessen, Germany http://www.uni-giessen.de/eichner --------------------------------------------------------------------- This works for me in the latest *development* version of lme4 (probably fixed since around the end of August). Does devel version work for you? Maybe getting to be time for a new release (it's been 6 months: here's what's changed ... https://github.com/lme4/lme4/blob/master/inst/NEWS.Rd )
On 2019-10-07 1:12 p.m., Gerrit Eichner wrote:
> Dear Ben and other lmer-experts,
>
> if I extend my setting a little bit, a new/similar problem appears.
> For some reasons I would like to change the control structures and
> "hardwire" that as in:
>
> lmerCtrl <- lmerControl(optCtrl = list(xtol_abs = 1e-9,
> ftol_abs = 1e-9))
>
> theta <- c(1, 0.01, 0.2)
> fm <- eval(bquote(
> lmer(Reaction ~ Days + (Days | Subject), data = sleepstudy,
> start = .(theta),
> control = .(lmerCtrl)) # THIS IS NEW.
> ))
>
>
> Then allFit "goes on strike" again, now complaining about unused
> arguments:
>
> allFit(fm, verbose = FALSE)
> Error in (function (optimizer = "nloptwrap", restart_edge = TRUE,
> boundary.tol = 1e-05, :
> unused arguments (checkControl = list("ignore", "stop", "ignore",
> "stop", "stop", "message+drop.cols", "warning", "stop"), checkConv =
> list(list("warning", 0.002, NULL), list("message", 1e-04),
> list("warning", 1e-06)))
>
>
> Any ideas how to circumvent this?
>
> Best regards -- Gerrit
>
> ---------------------------------------------------------------------
> Dr. Gerrit Eichner Mathematical Institute, Room 212
> gerrit.eichner using math.uni-giessen.de Justus-Liebig-University
Giessen
> Tel: +49-(0)641-99-32104 Arndtstr. 2, 35392 Giessen, Germany
> http://www.uni-giessen.de/eichner
> ---------------------------------------------------------------------
>
> Am 08.08.2019 um 15:41 schrieb Gerrit Eichner:
>> Thx a lot, Ben, for the fast reply which clearly explains the
>> cause of my problem. I've just found a solution which works for
>> me (and which is not as simple as "don't delete theta" ;-) ):
>> I "hardwire" theta's value into the function call:
>>
>> theta <- c(1, 0.01, 0.2)
>> fm <- eval(bquote(
>> lmer(Reaction ~ Days + (Days | Subject), data = sleepstudy,
>> start = .(theta))
>> ))
>>
>> rm(theta)
>> allFit(fm, verbose = FALSE)
>>
>>
>> Works like a "charm", at least in my current workflow. :-)
>>
>> Thanks once more -- Gerrit
>>
>> ---------------------------------------------------------------------
>> Dr. Gerrit Eichner Mathematical Institute, Room 212
>> gerrit.eichner using math.uni-giessen.de Justus-Liebig-University
Giessen
>> Tel: +49-(0)641-99-32104 Arndtstr. 2, 35392 Giessen, Germany
>> http://www.uni-giessen.de/eichner
>> ---------------------------------------------------------------------
>>
>> Am 08.08.2019 um 15:26 schrieb Ben Bolker:
>>>
>>> This is not surprising, as allFit() uses update(), which tries to
>>> re-evaluate the function ... at the very least allFit needs a
>>> documentation update with that hint ... (I also notice at a glance that
>>> the allFit docs seem to be incomplete anyway).
>>>
>>> If you say more about your workflow we might be able to find a
way to
>>> help. (If your workflow is this simple then the answer would be "well
>>> then don't delete theta" ...)
>>>
>>> cheers
>>> Ben Bolker
>>>
>>>
>>> On 2019-08-08 9:06 a.m., Gerrit Eichner wrote:
>>>> Dear lmer-experts, >>>> >>>> if I refit a fitted model with all available optimizers AFTER >>>> removing the object which contains the starting values for the >>>> parameters of the model as in >>>> >>>> theta <- c(1, 0.01, 0.2) >>>> fm <- lmer(Reaction ~ Days + (Days | Subject), data = sleepstudy, >>>> start = theta) >>>> rm(theta) >>>> allFit(fm, verbose = FALSE) >>>> >>>> none of the optimizers succeeds: >>>> >>>> original model: >>>> Reaction ~ Days + (Days | Subject) >>>> optimizers (7): bobyqa, Nelder_Mead, nlminbwrap, nmkbw, >>>> optimx.L-BFGS-B, >>>> nloptwrap.NLOPT_LN_N... >>>> 7 optimizer(s) failed >>>> differences in negative log-likelihoods: >>>> max= -Inf ; std dev= NA >>>> Warning messages: >>>> 1: In min(nllvec) : no non-missing arguments to min; returning Inf >>>> 2: In max(nllvec - min(nllvec)) : >>>> no non-missing arguments to max; returning -Inf >>>> >>>> >>>> If I don't remove theta from my workspace everything works fine. >>>> Is there a workaround for this - from my perspective - unwanted >>>> behaviour? (I have situations where allFit is used in a different >>>> environment from the one wherein the model was fit, e.g., after >>>> fitting the model the object which contains the fit is saved and >>>> later loaded in another R-session to be processed by allFit.) >>>> I could, of course, save theta everytime as well ... Any ideas? >>>> >>>> Best regards -- Gerrit >>>>