R help - May 2007 - predict.nls - gives error but only on some nls objects

Dear list,
I have encountered a problem with predict.nls (Windows XP, R.2.5.0), but I am
not sure if it is a bug...
 
On the nls man page, an example is:
 
DNase1 <- subset(DNase, Run == 1)
fm2DNase1 <- nls(density ~ 1/(1 + exp((xmid - log(conc))/scal)),
                 data = DNase1,
                 start = list(xmid = 0, scal = 1))
                 alg = "plinear", trace = TRUE)

Now consider prediction:
 
> predict(fm2DNase1)
 [1] 0.001424337 0.001424337 0.028883648 0.028883648 .....
> predict(fm2DNase1,newdata=fm2DNase1)
Error in if (sum(wrong) == 1) stop(gettextf("variable '%s' was
fitted with class \"%s\" but class \"%s\" was
supplied",  :
        missing value where TRUE/FALSE needed
 
What causes the trouble is the call to .checkMFClasses(cl, newdata) in
predict.nls.
 
 
Incidently, on the predict.nls page the example works:
 
> fm <- nls(demand ~ SSasympOrig(Time, A, lrc), data = BOD)
> predict(fm)              
[1]  7.887449 12.524977 15.251673 16.854870 17.797490
18.677580
> predict(fm,newdata=BOD)              
[1]  7.887449 12.524977 15.251673 16.854870 17.797490 18.677580
attr(,"gradient")
             A      lrc
[1,] 0.4120369 5.977499
[2,] 0.6542994 7.029098
....
 
Is there a bug, or am I overlooking something??
 
Regards
Søren
 

	[[alternative HTML version deleted]]

Why do you think feeding a model fit (fm2DNase1) is suitable 'newdata'?.
>From the help page
  newdata: A named list or data frame in which to look for variables
           with which to predict.  If 'newdata' is missing the fitted
           values at the original data points are returned.

It is the unsuitable 'newdata' that is causing the error.


On Thu, 31 May 2007, S?ren H?jsgaard wrote:
> Dear list,
> I have encountered a problem with predict.nls (Windows XP, R.2.5.0), but I
am not sure if it is a bug...
>
> On the nls man page, an example is:
>
> DNase1 <- subset(DNase, Run == 1)
> fm2DNase1 <- nls(density ~ 1/(1 + exp((xmid - log(conc))/scal)),
>                 data = DNase1,
>                 start = list(xmid = 0, scal = 1))
>                 alg = "plinear", trace = TRUE)
>
> Now consider prediction:
>
>> predict(fm2DNase1)
> [1] 0.001424337 0.001424337 0.028883648 0.028883648 .....
>
>> predict(fm2DNase1,newdata=fm2DNase1)
> Error in if (sum(wrong) == 1) stop(gettextf("variable '%s' was
fitted with class \"%s\" but class \"%s\" was
supplied",  :
>        missing value where TRUE/FALSE needed
>
> What causes the trouble is the call to .checkMFClasses(cl, newdata) in
predict.nls.
>
>
> Incidently, on the predict.nls page the example works:
>
>> fm <- nls(demand ~ SSasympOrig(Time, A, lrc), data = BOD)
>> predict(fm)
> [1]  7.887449 12.524977 15.251673 16.854870 17.797490 18.677580
>> predict(fm,newdata=BOD)
> [1]  7.887449 12.524977 15.251673 16.854870 17.797490 18.677580
> attr(,"gradient")
>             A      lrc
> [1,] 0.4120369 5.977499
> [2,] 0.6542994 7.029098
> ....
>
> Is there a bug, or am I overlooking something??
>
> Regards
> S?ren
>
>
> 	[[alternative HTML version deleted]]
>
>
-- 
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