> On Jun 26, 2016, at 1:03 PM, Lars Bishop <lars...@gmail.com> wrote:
>
> Thanks, David. Sorry, do you mean this?
>
> 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, setNames(data.frame(X_new),c("X1","X2","X3") ), type =
> "probs")
>
> Error in predict.multinom(fit, setNames(data.frame(X_new), c("X1", "X2", :
> NAs are not
> allowed in subscripted assignments
> In addition:
> Warning message:
> 'newdata' had
> 200 rows but variables found have 300 rows
Apparently I mixed some of your original code with some of my newer code that
created dataframes. Using `str(fit)` we see that the model object does
recognize that the argument named "X" is a matrix although it also considers
the 'coefnames' to be: chr [1:4] "(Intercept)" "X1" "X2" "X3"
The $ terms :Classes 'terms', 'formula' language y ~ X
.. ..- attr(*, "variables")= language list(y, X)
.. ..- attr(*, "factors")= int [1:2, 1] 0 1
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:2] "y" "X"
.. .. .. ..$ : chr "X"
.. ..- attr(*, "term.labels")= chr "X"
.. ..- attr(*, "order")= int 1
.. ..- attr(*, "intercept")= int 1
.. ..- attr(*, "response")= int 1
.. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
.. ..- attr(*, "predvars")= language list(y, X)
.. ..- attr(*, "dataClasses")= Named chr [1:2] "nmatrix.3" "nmatrix.3"
.. .. ..- attr(*, "names")= chr [1:2] "y" "X"
$ weights : num [1:300, 1] 1 1 1 1 1 1 1 1 1 1 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:300] "1" "2" "3" "4" ...
.. ..$ : NULL
$ deviance : num 653
$ rank : int 2
$ lab : chr [1:3] "ysim1" "ysim2" "ysim3"
$ coefnames : chr [1:4] "(Intercept)" "X1" "X2" "X3"
$ vcoefnames : chr [1:4] "(Intercept)" "X1" "X2" "X3"
I haven't found a newdata argument that It may be that is is so difficult to
match the various assignments that predict.multinom cannot be convinced that a
new argument has all the correct attributes. This is the code that is used:
else {
newdata <- as.data.frame(newdata)
rn <- row.names(newdata)
Terms <- delete.response(object$terms)
m <- model.frame(Terms, newdata, na.action = na.omit,
xlev = object$xlevels)
if (!is.null(cl <- attr(Terms, "dataClasses")))
.checkMFClasses(cl, m)
keep <- match(row.names(m), rn)
X <- model.matrix(Terms, m, contrasts = object$contrasts)
Y1 <- predict.nnet(object, X)
Y <- matrix(NA, nrow(newdata), ncol(Y1), dimnames = list(rn,
colnames(Y1)))
Y[keep, ] <- Y1
}
I failed with both these:
> str( setNames(as.data.frame(X_new),c("X1","X2","X3") ) )
'data.frame': 200 obs. of 3 variables:
$ X1: num 2.021 0.285 1.478 1.385 1.126 ...
$ X2: num 1.66 2.06 1.97 1.99 1.42 ...
$ X3: num 1.977 0.555 2.863 2.694 2.831 ...
> str( data.matrix( setNames(as.data.frame(X_new),c("X1","X2","X3") ) ) )
num [1:200, 1:3] 2.021 0.285 1.478 1.385 1.126 ...
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr [1:3] "X1" "X2" "X3"
>
> On Sun, Jun 26, 2016 at 3:46 PM, David Winsemius <dwinsem...@comcast.net>
> wrote:
>
> > On Jun 26, 2016, at 12:39 PM, Lars Bishop <lars...@gmail.com> wrote:
> >
> > Many thanks David. That works. Looks then this error will always occur in
> > predict.multinom whenever the data argument is missing in the mutlinom fit,
> > but the data argument is optional as per documentation.
>
> I don't agree with that analysis. The problem occurs because of a mismatch of
> names in the new data argument. With your original code this runs without
> error:
>
> pred <- predict(fit, setNames(data.frame(X_new),c("X1","X2","X3") ), type =
> "probs")
>
> --
> David.
> >
> > Best,
> > Lars.
> >
> > On Sun, Jun 26, 2016 at 3:14 PM, David Winsemius <dwinsem...@comcast.net>
> > wrote:
> >
> > > On Jun 26, 2016, at 11:32 AM, Lars Bishop <lars...@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.4...@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 <lars...@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@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@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
> >
> >
>
> David Winsemius
> Alameda, CA, USA
>
>
David Winsemius
Alameda, CA, USA
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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