[R] lmer error message

Sun Jan 8 20:10:11 CET 2006

Spencer:

It is an option, not an argument, and sets the default for the lmerControl 
arguments msVerbose and EMverbose (see ?lmer)

> options(verbose=TRUE)
> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
   EM iterations
   0 1768.412 ( 3.75000  106.875  0.00000:    3.21    0.174    0.663)
   1 1749.892 ( 2.67539  62.5305 -5.17591:    2.36    0.176    0.479)
...
   0      1743.63: 0.918936 0.0531527 -0.304877
...

On Sun, 8 Jan 2006, Spencer Graves wrote:

> 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
> documentation:
>
> > 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
> verbosity.
>
> 	  Thanks,
> 	  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
>>> replying.
>>>
>>>          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,
>>>>
>>>> Abderrahim
>>>>
>>>>
>>>>      [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
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>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>>>
>>> ______________________________________________
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>>> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
> ______________________________________________
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>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
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