[R-sig-ME] allFit fails after removing object with starting values for model parameters from workspace

[Gerrit Eichner]

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 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
---------------------------------------------------------------------


  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
 >>>>