lme4 troubles

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On 14-12-16 05:49 PM, Andrew C. Shaver wrote:
> Hi Ben!
>
> I hope this note finds you well.

  [I'm fine, but cc'ing to r-sig-mixed-models at r-project.org]
>
> I hate to trouble you, but I've having some troubles with the lme4
> package that I'm hoping you might be able to help me quick
> resolve.
>
> Using an earlier version of the package, I was running the
> following type of model without problem:
>
> output <- glmer(Y ~ X + Z + (1 | Province) + (1 | Year), data =
> data, family = "binomial", verbose = TRUE, control =
> list(maxIter=1000))
>
> I've since upgraded, and attempting to run this model now results
> in the following message:
>
> Error: PIRLS step failed In addition: Warning message: In
> checkArgs("glmer", sparseX, ...) : extra argument(s) ?control?,
> ?verbose? disregarded

  What version of lme4 are you now using (results of sessionInfo(),
or packageVersion("lme4") ?)

  Is there any chance you can provide a reproducible example?
Using one of the built-in examples from lme4 with the latest
(development) version of lme4 (although I think it should be identical
for these purposes to the CRAN version of lme4, 1.1-7):

library("lme4")
gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
                   data = cbpp, family = binomial,
                  verbose=TRUE, control=list(maxIter=1000))

gives

Warning in glmer(cbind(incidence, size - incidence) ~ period + (1 |
herd),  :
  Use control=glmerControl(..) instead of passing a list of class ?list?
Error in (function (optimizer = c("bobyqa", "Nelder_Mead"),
restart_edge = FALSE,  :
  unused argument (maxIter = 1000)

If I use

gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
                   data = cbpp, family = binomial,
                  verbose=TRUE,
                 control=glmerControl(optCtrl=list(maxfun=20000)))

it works (I don't get the specified error) -- but of course it would
be likely to work with this well-behaved example.

> If I run something like: output <- glmer(Y ~ X + Z + (1 | Province)
> + (1 | Year), data = data, family = "binomial"), i get: "Error:
> pwrssUpdate did not converge in 30 iterations". And if I attempt
> to increase the number of iterations by including
> "control=glmerControl(optCtrl=list(maxfun=20000)", I get:
>
> Error in checkArgs("glmer", sparseX, ...) : could not find
> function "glmerControl"

  That's surprising.

  FWIW the max number of PIRLS iterations is hard-coded in the current
version of lme4, although you can adjust the tolerance (tolPwrss).
However, usually when this goes wrong there's some other problem
that has to/can be fixed in another way.  Again, a reproducible example
would be really useful ...

> I am also no longer able to load the "blme" package. Before the
> update, had no problems running, for instance, bglmer(). Now, when
> I attempt to load the package, I get the following messages:
>
> Error : class "mer" is not exported by 'namespace:lme4' Error:
> package/namespace load failed for ?blme?

  I'm a little surprised/confused by this one.
  Make sure you're running a clean R session and (re)install lme4
and blme from scratch?

> Any hints on how to get back to running the model??
>
> Thank you very much in advance!
>
> Very best,
>
> Andrew

> --- Andrew Shaver PhD Candidate Woodrow Wilson School Princeton
> University scholar.princeton.edu/ashaver ---
>
>

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