Thanks, David. That is very interesting, because ?multinom says that the value is:
"A nnet object with additional components: ..." Of course I could have checked methods(predict), but I just took the Help file at its word. Should it not be revised to say explicitly: "An object of class 'multinom', which is a nnet object ... " ?? 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 12:14 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 > ______________________________________________ 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.