lmer error message

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lmer error message

Abderrahim Oulhaj
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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Re: lmer error message

Spencer Graves
          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]]
>
> ______________________________________________
> [hidden email] mailing list
> 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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Re: lmer error message

Douglas Bates
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 <[hidden email]> 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]]
> >
> > ______________________________________________
> > [hidden email] mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

______________________________________________
[hidden email] mailing list
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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Re: lmer error message

Spencer Graves
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 <[hidden email]> 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]]
>>>
>>>______________________________________________
>>>[hidden email] mailing list
>>>https://stat.ethz.ch/mailman/listinfo/r-help
>>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>>
>>______________________________________________
>>[hidden email] mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

______________________________________________
[hidden email] mailing list
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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Re: lmer error message

Brian Ripley
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 <[hidden email]> 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]]
>>>>
>>>> ______________________________________________
>>>> [hidden email] mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>>>
>>> ______________________________________________
>>> [hidden email] mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

--
Brian D. Ripley,                  [hidden email]
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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