[R] my error with augPred

[Spencer Graves]

      Thank you for providing such a complete, self contained example.  
I found that 'predict.nlme' does not like a factor in the 'fixed' 
argument as you used it, "fixed=list(Asym~x1, R0+lrc~1)".  To see this, 
I added 'x1.' as a numeric version of the factor 'x1' and reran it 
successfully: 

fm2.<-update(fm1, fixed=list(Asym~x1., R0+lrc~1), start=c(103,0,-8.5,-3))
aP2. <- augPred(fm2.)
plot(aP2.)

      Unfortunately, it looks like this work-around won't help you with 
your original problem, because there, the counterpart to 'x1' is an 
ordered factor with more than 2 levels. 

      The error message refers to 'predict.nlme'.  I know no reason why 
'predict.nlme' shouldn't work with a factor with more than 2 levels in 
this context.  If it were my problem and it was sufficiently important, 
I would make a local copy of 'predict.nlme' as follows: 

      predict.nlme <- getAnywhere("predict.nlme")

      Then I'd use 'debug(nlme:::predict.nlme)' to walk through the 
problem example line by line until I figured out what I had to change to 
make this work. 

      I hesitate to use the "B" word, but I think it might be 
appropriate to file a bug report on this;  perhaps someone else will do 
that.  

      I'm sorry I couldn't solve your original problem.  With luck, 
someone else will convert this example into a fix to the code. 
      Spencer Graves
     
Petr Pikal wrote:
> Hallo
>
> thank you for your response. I am not sure but maybe fixed effects 
> cannot be set to be influenced by a factor to be able to use augPred.
>
> lob<-Loblolly[Loblolly$Seed!=321,]
> set.seed(1)
> lob<-data.frame(lob, x1=sample(letters[1:3], replace=T)) # add a 
> #factor
> lob<-groupedData(height~age|Seed, data=lob)
> fm1 <- nlme(height ~ SSasymp(age, Asym, R0, lrc),
>             data = lob,
>             fixed = Asym + R0 + lrc ~ 1,
>             random = Asym ~ 1,
>             start = c(Asym = 103, R0 = -8.5, lrc = -3.3))
>
> fm2<-update(fm1, fixed=list(Asym~x1, R0+lrc~1), start=c(103,0,-8.5,-3))
>                                              ^^^^^^^
> and
>
> plot(augPred(fm2))
>
> Throws an error.
> So it is not possible to use augPred with such constructions.
>
> Best regards.
> Petr Pikal
>
> On 2 Sep 2006 at 17:58, Spencer Graves wrote:
>
> Date sent:      	Sat, 02 Sep 2006 17:58:05 -0700
> From:           	Spencer Graves <spencer.graves at pdf.com>
> To:             	Petr Pikal <petr.pikal at precheza.cz>
> Copies to:      	r-help at stat.math.ethz.ch
> Subject:        	Re: [R] my error with augPred
>
>   
>> <comments in line> 
>>
>> Petr Pikal wrote:
>>     
>>> Dear all
>>>
>>> I try to refine my nlme models and with partial success. The model
>>> is refined and fitted (using Pinheiro/Bates book as a tutorial) but
>>> when I try to plot
>>>
>>> plot(augPred(fit4))
>>>
>>> I obtain
>>> Error in predict.nlme(object, value[1:(nrow(value)/nL), , drop =
>>> FALSE],  : 
>>>         Levels (0,3.5],(3.5,5],(5,7],(7,Inf] not allowed for 
>>> vykon.fac
>>>   
>>>
>>> Is it due to the fact that I have unbalanced design with not all
>>> levels of vykon.fac present in all levels of other explanatory
>>> factor variable?
>>>   
>>>       
>> I don't know, but I'm skeptical. 
>>     
>>> I try to repeat 8.19 fig which is OK until I try:
>>>
>>> fit4 <- update(fit2, fixed = list(A+B~1,xmid~vykon.fac, scal~1), 
>>> start = c(57, 100, 700, rep(0,3), 13))
>>>
>>> I know I should provide an example but maybe somebody will be clever
>>> enough to point me to an explanation without it.
>>>   
>>>       
>> I'm not. 
>>
>> To answer these questions without an example from you, I'd have to
>> make up my own example and try to see if I could replicate the error
>> messages you report, and I'm not sufficiently concerned about this
>> right now to do that. 
>>
>> Have you tried taking an example from the book and deleting certain
>> rows from the data to see if you can force it to reproduce your error?
>>
>>
>> Alternatively, have you tried using 'debug' to trace through the code
>> line by line until you learn enough of what it's doing to answer your
>> question? 
>>
>> Spencer Graves
>>     
>>> nlme version 3.1-75
>>> SSfpl model
>>> R 2.4.0dev (but is the same in 2.3.1), W2000.
>>>
>>> Thank you
>>> Best regards.
>>>
>>> Petr PikalPetr Pikal
>>> petr.pikal at precheza.cz
>>>
>>> ______________________________________________
>>> R-help at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html and provide commented,
>>> minimal, self-contained, reproducible code.
>>>
>>>       
>> ______________________________________________
>> R-help at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html and provide commented,
>> minimal, self-contained, reproducible code.
>>     
>
> Petr Pikal
> petr.pikal at precheza.cz
>
>