[R] lmer error message

Spencer Graves spencer.graves at pdf.com
Sun Jan 8 19:23:21 CET 2006

Hi, Doug:

	  Thanks.  My copy of the 'lmer' documentation does not list the 
'verbose' argument.  Is this something you plan to discontinue or 
modify, or was it recently added to the script but not to the 
documentation I have?

	  Also, I just tried it modifying one of the examples in the 

 > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy,
+              verbose=TRUE)
trace: lmer(Reaction ~ Days + (Days | Subject), sleepstudy, verbose = TRUE)

	  Maybe this example converges so quickly it senses no need for greater 

	  Spencer Graves

R version 2.2.0, 2005-10-06, i386-pc-mingw32

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"

other attached packages:
      lme4   lattice    Matrix
  "0.98-1" "0.12-11"  "0.99-4"

Douglas Bates wrote:

> Also, please try setting
> options(verbose = TRUE)
> immediately before your call to lmer.  This will provide verbose
> output on the progress of the iterations and will probably give an
> indication of where the problem lies.
> On 1/7/06, Spencer Graves <spencer.graves at pdf.com> wrote:
>>          I am not familiar with this particular error message, but I will
>>offer a few suggestions that might help you isolate it.
>>          1.  PLEASE do read the posting guide!
>>"www.R-project.org/posting-guide.html".  The limited information
>>supplied with your question does NOT include data requested of all
>>posts.  The command "sessionInfo()" can proved some of the standard
>>basics that many potential respondants want to know before they consider
>>          2.  Have you tried "traceback()"?  This may or may not help you, but
>>it's quick and worth a try.
>>          3.  Can you provide this list with a very simple, self contained
>>example that produces the error message you mention?
>>          4.  I suggest you list "lmer" by typing the function name and a
>>commmand prompt.  In this case, "lmer" consists solely of a call to
>>"standardGeneric".  The documentation for "standardGeneric" led me to
>>the documentation for "GenericFunctions, which led me to "showMethods".
>>  'showMethods("lmer")' indicated only one method, namely for 'formula =
>>"formula"'.  Then 'dumpMethod("lmer", file="lmer.R",
>>signature="formula")' produced a listing of that function for me in the
>>working directory.  If you have trouble finding the working directory,
>>try 'getwd()'.  I would then modify the function it "lmer.R" to create a
>>new function "lmer.formula".  Then I would try "debug(lmer.formula)".
>>Then I would replace "lmer" by "lmer.formula" in the command that
>>generated the error and execute that modified formula.  This will open a
>>browser and allow you to walk through the function line by line,
>>examining (and changing) anything you want in the environment of that
>>function.  Doing this will, I believe, lead you to exactly the line in
>>the "lmer" code that generated the error message you don't understand.
>>With only a modest amount of luck, you should be able to find in this
>>way what you can do to avoid that error.
>>          Anecdotal evidence suggests that people who use the techniques
>>described in suggestions 1-3 tend to get quicker, more useful replies
>>from this list.  Moreover, in virtually every case that I've tried
>>suggestion 4, I've been able to figure out how to overcome that
>>particular difficulty.  In addition, I've often learned useful things
>>about R that I didn't know befor.
>>          hope this helps.
>>          spencer graves
>>Abderrahim Oulhaj wrote:
>>>Dear All,
>>>I have the following error message when I fitted  lmer to a  binary data with the "AGQ" option:
>>>Error in family$mu.eta(eta) : NAs are not allowed in subscripted assignments
>>>In addition: Warning message:
>>>IRLS iterations for PQL did not converge
>>>Any help?
>>>Thanks in advance,
>>>      [[alternative HTML version deleted]]
>>>R-help at stat.math.ethz.ch mailing list
>>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>>R-help at stat.math.ethz.ch mailing list
>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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