Using lmer I get the following warning:
Warning messages:
1: In optwrap(optimizer, devfun, x@theta, lower = x@lower) :
convergence code 3 from bobyqa: bobyqa -- a trust region step failed to reduce q
This error ois generated after using anova(model1, model2) . I tried to make this reproducible but if I dput the data and try again I the error does not reproduce on the dput data, despite the original and new datarames have the exact same str.
If have tried again in a clean session, and the error reproduces, and again is lost with a dput
I know I am not giving people much to work with here, like i said I would love to reproduce the problem. Cayone shed light on this warning?
(I'm not sure whether this is a comment or an answer, but it's a bit long and might be an answer.)
lme4 uses both environments and reference classes: these are tricky to "serialize", i.e. to translate to a linear stream that can be saved via dput() or save(). (Can you please try save() and see if it works better than dput()?anova() automatically refits the model, which makes some tiny but non-zero changes in the internal structure of the saved model object (we are still trying to track this down).lme4 do not use any calls to the pseudo-random number generator. They are deterministic (but the two points above explain why things might look a bit weird).To allay your concerns with the fit, I would check the fit by computing the gradient and Hessian at the final fit, e.g.
library(lme4)
library(numDeriv)
fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
dd <- update(fm1,devFunOnly=TRUE)
params <- getME(fm1,"theta") ## also need beta for glmer fits
grad(dd,params)
## all values 'small', say < 1e-3
## [1] 0.0002462423 0.0003276917 0.0003415010
eigen(solve(hessian(dd,params)),only.values=TRUE)$values
## all values positive and of similar magnitude
## [1] 0.029051631 0.002757233 0.001182232
We are in the process of implementing similar checks to run automatically within lme4.
That said, I would still love to see your example, if there's a way to reproduce it relatively easily.
PS: in order to be using bobyqa, you must either be using glmer or have used lmerControl to modify the default optimizer choice ... ??
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