[R] lmer error message
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sun Jan 8 20:10:11 CET 2006
It is an option, not an argument, and sets the default for the lmerControl
arguments msVerbose and EMverbose (see ?lmer)
> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
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
> > 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:
>  "methods" "stats" "graphics" "grDevices" "utils" "datasets"
>  "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
> R-help at stat.math.ethz.ch mailing list
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Brian D. Ripley, ripley at 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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