[R] nnet behaves as documented (was nnet behaving oddly)

[Prof Brian Ripley]

On 20 Oct 2003, Rajarshi Guha wrote:

> Hi,
>   I was trying to use the nnet library and am not sure of whats going
> on. I am calling the nnet function as:
> 
>  n <- nnet(x,y,size=3,subset=sets[[1]], maxit=200)
> 
> Where x is a 272x4 matrix of observations (examples) and y is a 272x1
> matrix of target values. However when I look at nnet$residuals they are
> off by two orders of magnitude (compared to the output from neural
> network code that I already have). Looking at nnet$fitted.values shows
> all the values to be 1 (whereas my target values range from 0 to 150).
> 
> Am I making an obvious mistake in the way I'm calling the function? Is
> the fact that n$fitted.values is all 1's indicating that the NN is doing
> a classification? If so how can I make it do quantitation?

Yes, so please do read the help page accurately.

> The man page mentions that if the response is a factor then it defaults
> to quantitation. However my y matrix just contain numbers - so it
> should'nt be doing classification.

That's incorrect reading of the help page, which actually says

     If the response in 'formula' is a factor, an appropriate
     classification network is constructed; this has one output and
     entropy fit if the number of levels is two, and a number of
     outputs equal to the number of classes and a softmax output stage
     for more levels.  If the response is not a factor, it is passed on
     unchanged to 'nnet.default'.

and you did not give a formula.

As someone else said recently. those who write the manuals don't expect to 
either read them for you nor re-write them here, so please show more 
consideration for their work.

-- 
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