[R] Help please with error from nnet::multinom

[David Winsemius]

> On Jun 26, 2016, at 11:32 AM, Lars Bishop <lars52r at gmail.com> wrote:
> 
> Thanks Bert.
> 
> But I it doesn't complain when predict is used on X instead of X_new
> (using nnet_7.3-12), which is even more puzzling to me:
> 
> pred <- predict(fit, X, type = "probs")

Indeed: There is a predict.multinom function and it does have 'probs' as an acceptable argument to type:

I got success (or at least an absence of an error message) with:

#----------
 X <- data.frame(matrix( 3 * runif(length(ysim)), nrow = 300, ncol = 3))
 X_new <- data.frame(matrix( 3 * runif(length(ysim)), nrow = 200, ncol = 3))
 str(X)

'data.frame':	300 obs. of  3 variables:
 $ X1: num  0.797 1.116 1.719 2.725 0.605 ...
 $ X2: num  0.797 1.116 1.719 2.725 0.605 ...
 $ X3: num  0.797 1.116 1.719 2.725 0.605 ...

 fit <- multinom(y ~ ., data=X, trace = FALSE)
 pred <- predict(fit, setNames(X_new, names(X)), type = "probs")

> head(pred)
      ysim1     ysim2     ysim3
1 0.3519378 0.3517418 0.2963204
2 0.3135513 0.3138573 0.3725915
3 0.3603779 0.3600461 0.2795759
4 0.3572297 0.3569498 0.2858206
5 0.3481512 0.3480128 0.3038360
6 0.3813310 0.3806118 0.2380572

#------------


> head(pred)
> ysim1     ysim2     ysim3
> 1 0.3059421 0.3063284 0.3877295
> 2 0.3200219 0.3202551 0.3597230
> 3 0.3452414 0.3451460 0.3096125
> 4 0.3827077 0.3819603 0.2353320
> 5 0.2973288 0.2977994 0.4048718
> 6 0.3817027 0.3809759 0.2373214
> 
> Thanks again,
> Lars.
> 
> 
> On Sun, Jun 26, 2016 at 1:05 PM, Bert Gunter <bgunter.4567 at gmail.com> wrote:
> 
>> Well, for one thing, there is no "probs" method for predict.nnet, at
>> least in my version: nnet_7.3-12
>> 
>> Cheers,
>> Bert
>> 
>> 
>> Bert Gunter
>> 
>> "The trouble with having an open mind is that people keep coming along
>> and sticking things into it."
>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>> 
>> 
>> On Sun, Jun 26, 2016 at 9:27 AM, Lars Bishop <lars52r at gmail.com> wrote:
>>> Hello,
>>> 
>>> I'd appreciate your help in spotting the reason for the error and warning
>>> messages below.
>>> 
>>> library(nnet)
>>> set.seed(1)
>>> ysim <- gl(3, 100)
>>> y <- model.matrix(~ysim -1)
>>> X <- matrix( 3 * runif(length(ysim)), nrow = 300, ncol = 3)
>>> X_new <- matrix( 3 * runif(length(ysim)), nrow = 200, ncol = 3)
>>> 
>>> fit <- multinom(y ~ X, trace = FALSE)
>>> pred <- predict(fit, X_new, type = "probs")
>>> 
>>> Error in predict.multinom(fit, X_new, type = "probs") :
>>>  NAs are not allowed in subscripted assignments
>>> In addition: Warning message:
>>>  'newdata' had 200 rows but variables found have 300 rows
>>> 
>>> Thanks,
>>> Lars.
>>> 
>>>        [[alternative HTML version deleted]]
>>> 
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> 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.
>> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.

David Winsemius
Alameda, CA, USA