Re: [R] problem with predict.gam in package gam
On Wed, 2011-09-14 at 18:06 -0500, Drew Tyre wrote: I am trying to reproduce plots in Chapter 3 of Zuur et al Mixed Effects models and extensions in Ecology. For pedagogical reasons, they make a series of plots with gam(...) in package gam. I encounter errors that trace back to the predict.gam method. Below is a repeatable example using one of the example datasets: The code works for me with: sessionInfo() R version 2.13.1 Patched (2011-07-08 r56332) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines grid stats graphics grDevices utils datasets [8] methods base other attached packages: [1] gam_1.04 analogue_0.7-4 princurve_1.1-10 MASS_7.3-13 [5] lattice_0.19-23 vegan_1.17-12 loaded via a namespace (and not attached): [1] tools_2.13.1 G library(gam) data(kyphosis) test = gam(Kyphosis ~ s(Age,4) + Number, family = binomial, data=kyphosis) predict(test) # works predict(test,se.fit=TRUE) # fails #Error in dim(data) - dim : attempt to set an attribute on NULL # after debugging, it wants a model frame ... test = gam(Kyphosis ~ s(Age,4) + Number, family = binomial, data=kyphosis, model=TRUE) predict(test,se.fit=TRUE) # fails, but with a different error # Error in terms.default(object, data = data) : # no terms component nor attribute I am using R 2.13.1 on a PC inside RStudio. I realize I can do this in package mgcv, but just curious as to whether this is something known and fixable? Thanks -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list 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.
Re: [R] problem with predict.gam in package gam
Thank you! It also works on a second computer here with the details below, so something must be messed up on the other machine. sessionInfo() R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] gam_1.04.1 loaded via a namespace (and not attached): [1] blme_0.01-3grid_2.13.1lattice_0.19-30lme4_0.999375-41 [5] Matrix_0.9996875-3 nlme_3.1-101 stats4_2.13.1 tcltk_2.13.1 [9] tools_2.13.1 On Thu, Sep 15, 2011 at 9:44 AM, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Wed, 2011-09-14 at 18:06 -0500, Drew Tyre wrote: I am trying to reproduce plots in Chapter 3 of Zuur et al Mixed Effects models and extensions in Ecology. For pedagogical reasons, they make a series of plots with gam(...) in package gam. I encounter errors that trace back to the predict.gam method. Below is a repeatable example using one of the example datasets: The code works for me with: sessionInfo() R version 2.13.1 Patched (2011-07-08 r56332) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines grid stats graphics grDevices utils datasets [8] methods base other attached packages: [1] gam_1.04 analogue_0.7-4 princurve_1.1-10 MASS_7.3-13 [5] lattice_0.19-23 vegan_1.17-12 loaded via a namespace (and not attached): [1] tools_2.13.1 G library(gam) data(kyphosis) test = gam(Kyphosis ~ s(Age,4) + Number, family = binomial, data=kyphosis) predict(test) # works predict(test,se.fit=TRUE) # fails #Error in dim(data) - dim : attempt to set an attribute on NULL # after debugging, it wants a model frame ... test = gam(Kyphosis ~ s(Age,4) + Number, family = binomial, data=kyphosis, model=TRUE) predict(test,se.fit=TRUE) # fails, but with a different error # Error in terms.default(object, data = data) : # no terms component nor attribute I am using R 2.13.1 on a PC inside RStudio. I realize I can do this in package mgcv, but just curious as to whether this is something known and fixable? Thanks -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% -- Drew Tyre School of Natural Resources University of Nebraska-Lincoln 416 Hardin Hall, East Campus 3310 Holdrege Street Lincoln, NE 68583-0974 phone: +1 402 472 4054 fax: +1 402 472 2946 email: aty...@unl.edu http://snr.unl.edu/tyre http://aminpractice.blogspot.com http://www.flickr.com/photos/atiretoo __ R-help@r-project.org mailing list 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.
[R] problem with predict.gam in package gam
I am trying to reproduce plots in Chapter 3 of Zuur et al Mixed Effects models and extensions in Ecology. For pedagogical reasons, they make a series of plots with gam(...) in package gam. I encounter errors that trace back to the predict.gam method. Below is a repeatable example using one of the example datasets: library(gam) data(kyphosis) test = gam(Kyphosis ~ s(Age,4) + Number, family = binomial, data=kyphosis) predict(test) # works predict(test,se.fit=TRUE) # fails #Error in dim(data) - dim : attempt to set an attribute on NULL # after debugging, it wants a model frame ... test = gam(Kyphosis ~ s(Age,4) + Number, family = binomial, data=kyphosis, model=TRUE) predict(test,se.fit=TRUE) # fails, but with a different error # Error in terms.default(object, data = data) : # no terms component nor attribute I am using R 2.13.1 on a PC inside RStudio. I realize I can do this in package mgcv, but just curious as to whether this is something known and fixable? Thanks -- Drew Tyre School of Natural Resources University of Nebraska-Lincoln 416 Hardin Hall, East Campus 3310 Holdrege Street Lincoln, NE 68583-0974 phone: +1 402 472 4054 fax: +1 402 472 2946 email: aty...@unl.edu http://snr.unl.edu/tyre http://aminpractice.blogspot.com http://www.flickr.com/photos/atiretoo __ R-help@r-project.org mailing list 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.
