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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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