Re: [R] lme convergence

From: Spencer Graves <spencer.graves_at_pdf.com>
Date: Sat 01 Jul 2006 - 03:28:19 EST

          Harold is correct. The help page for 'Orthodont' includes the following example:

 > formula(Orthodont)
distance ~ age | Subject

          If 'random' is not specified, 'lme' sets random = formula(data). If that's NULL, the 'lme' help page says it "Defaults to a formula consisting of the right hand side of 'fixed'." This will generally return an error, indicated by the following example:

 > tstDF <- data.frame(gp=rep(1:2, 2), y=1:4)  > lme(y~1, tstDF)
Error in getGroups.data.frame(dataMix, groups) :

        Invalid formula for groups
 > lme(y~1, tstDF, random=~1)
Error in getGroups.data.frame(dataMix, groups) :

        Invalid formula for groups
 >

	  Hope this helps.
	  Spencer

Doran, Harold wrote:

> In the old version of lme, one could construct a grouped data object and
> this would alleviate the need to specify the random portion of the
> model. So, Spencer's call is equivalent to 
> 
> fm1 <- lme(distance ~ age, random= ~age| Subject, data = Orthodont)
> 
> This condition does not hold under lmer, however.
> 

>> -----Original Message-----
>> From: r-help-bounces@stat.math.ethz.ch
>> [mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of
>> Michael Jerosch-Herold
>> Sent: Friday, June 30, 2006 12:37 PM
>> To: spencer.graves@pdf.com
>> Cc: r-help@stat.math.ethz.ch
>> Subject: Re: [R] lme convergence
>>
>> It looks like in the call to lme
>>
>> fm1 <- lme(distance ~ age, data = Orthodont,
>> + control=lmeControl(msMaxIter=1))
>>
>> you did not specify any random effects. Why not try:
>>
>> fm1 <- lme(distance ~ age, random= ~1| groupID, data = Orthodont,
>> + control=lmeControl(msMaxIter=1))
>>
>> where groupID is some factor that can be used to stratify the data.
>>
>> Also, the "Othodont" data set is used in Pinheiro & Bates
>> book, and you may want to consult that book to see the models
>> they use in connection with that data set. For the Orthodont
>> data set the groupID would most likely be the subject ID
>> ("Subject" variable).
>>
>> So a possible model would be:
>>
>>> fm1 <- lme(distance ~ age, random= ~1|Subject, data=Orthodont)
>>> summary(fm1)
>> Linear mixed-effects model fit by REML
>> Data: Orthodont
>> AIC BIC logLik
>> 455.0025 465.6563 -223.5013
>>
>> Random effects:
>> Formula: ~1 | Subject
>> (Intercept) Residual
>> StdDev: 2.114724 1.431592
>>
>> Fixed effects: distance ~ age
>> Value Std.Error DF t-value p-value
>> (Intercept) 16.761111 0.8023952 80 20.88885 0
>> age 0.660185 0.0616059 80 10.71626 0
>> Correlation:
>> (Intr)
>> age -0.845
>>
>> Standardized Within-Group Residuals:
>> Min Q1 Med Q3 Max
>> -3.66453932 -0.53507984 -0.01289591 0.48742859 3.72178465
>>
>> Number of Observations: 108
>> Number of Groups: 27
>>
>> So this runs fine.
>>
>> As, I said this data set and its analysis is discussed
>> extensively in Pinheiro and Bates book
>>
>> Michael Jerosch-Herold
>>
>>
>>>>> "Spencer Graves" <spencer.graves@pdf.com> 06/29/06 7:08 PM >>>
>> Does anyone know how to obtain the 'returnObject'
>> from an 'lme' run that fails to converge? An argument of
>> this name is described on the 'lmeControl' help page as, "a
>> logical value indicating whether the fitted object should be
>> returned when the maximum number of iterations is reached
>> without convergence of the algorithm. Default is 'FALSE'."
>>
>> Unfortunately, I've so far been unable to get it to
>> work, as witnessed by the following modification of an
>> example from the '?lme'
>> help page:
>>
>> > library(nlme)
>> > fm1 <- lme(distance ~ age, data = Orthodont,
>> + control=lmeControl(msMaxIter=1))
>> Error in lme.formula(distance ~ age, data = Orthodont,
>> control = lmeControl(msMaxIter = 1)) :
>> iteration limit reached without convergence (9) > fm1
>> Error: object "fm1" not found
>> > fm1 <- lme(distance ~ age, data = Orthodont,
>> + control=lmeControl(msMaxIter=1,
>> + returnObject=TRUE))
>> Error in lme.formula(distance ~ age, data = Orthodont,
>> control = lmeControl(msMaxIter = 1, :
>> iteration limit reached without convergence (9) > fm1
>> Error: object "fm1" not found
>>
>> I might be able to fix the problem myself, working
>> through the 'lme'
>> code line by line, e.g., using 'debug'. However, I'm not
>> ready to do that just now.
>>
>> Best Wishes,
>> Spencer Graves
>>
>> Ravi Varadhan wrote:
>>> Use "try" to capture error messages without breaking the loop.
>>> ?try
>>>
>>>
>> ----------------------------------------------------------------------
>>> ----
>>> Ravi Varadhan, Ph.D.
>>> Assistant Professor, The Center on Aging and Health Division of
>>> Geriatric Medicine and Gerontology Johns Hopkins University
>>> Ph: (410) 502-2619
>>> Fax: (410) 614-9625
>>> Email: rvaradhan@jhmi.edu
>>> Webpage:
>>> http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
>>>
>> ----------------------------------------------------------------------
>>> ----
>>>
>>>> -----Original Message-----
>>>> From: r-help-bounces@stat.math.ethz.ch [mailto:r-help-
>>>> bounces@stat.math.ethz.ch] On Behalf Of Pryseley Assam
>>>> Sent: Wednesday, June 28, 2006 12:18 PM
>>>> To: R-Users
>>>> Subject: [R] lme convergence
>>>>
>>>> Dear R-Users,
>>>>
>>>> Is it possible to get the covariance matrix from an lme
>> model that
>>>> did not converge ?
>>>>
>>>> I am doing a simulation which entails fitting linear
>> mixed models,
>>>> using a "for loop".
>>>> Within each loop, i generate a new data set and analyze
>> it using a
>>>> mixed model. The loop stops When the "lme function" does not
>>>> converge for a simulated dataset. I want to inquire if there is a
>>>> method to suppress the error message from the lme
>> function, or better
>>>> still, a way of going about this issue of the loop ending
>> once the lme function does not converge.
>>>> Thanks in advance,
>>>> Pryseley
>>>>
>>>>
>>>> ---------------------------------
>>>>
>>>>
>>>> [[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 Received on Sat Jul 01 03:56:13 2006

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