Re: [R] lmer error message

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Mon 09 Jan 2006 - 06:10:11 EST

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@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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>>>
>>> ______________________________________________
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>
> ______________________________________________
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>

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Mon Jan 09 06:19:44 2006

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