The following block of code fails, for no reason I can discern.
library(caret)
data(iris)
TrainData <- iris[,1:4]
TrainClasses <- factor(ifelse(iris[,5]=='versicolor','versicolor','other'))
model1 <- train(TrainData,TrainClasses,method='glmnet')
With the following error:
Error in { : task 1 failed - "'n' must be a positive integer >= 'x'"
If I sub in a different model, such as glm it runs fine. If I uses 3 classes, TrainClasses <- iris[,5], it also works fine.
What about 2 classes is uniquely causing the glmnet method to fail?
This is R version 2.14.0, caret version 5.09-006, on windows. The same error happens on my mac and on linux.
I'm not able to give you an answer about why you are getting an error (since the code runs fine on my machine) but I will suggest you following the advice in the R-hel Posting Guide and include more details about your versions and set up.:
> model1
150 samples
4 predictors
2 classes: 'other', 'versicolor'
No pre-processing
Resampling: Bootstrap (25 reps)
Summary of sample sizes: 150, 150, 150, 150, 150, 150, ...
Resampling results across tuning parameters:
alpha lambda Accuracy Kappa Accuracy SD Kappa SD
0.1 0.1 0.698 0.19 0.0419 0.0891
0.1 0.462 0.675 0.0311 0.0399 0.0719
# >>> snipped the rest of a page of code
I have a fairly full session and yours will surely have been different. There can be conflicts that arise because of functions having been masked by other packages that were loaded later in a session. There were quite a few warnings when I loaded "caret" just now.
> sessionInfo()
R version 2.14.0 Patched (2011-11-13 r57650)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] tools stats4 grid splines stats graphics grDevices utils
[9] datasets methods base
other attached packages:
[1] glmnet_1.7.1 Matrix_1.0-1 e1071_1.6 class_7.3-3
[5] caret_5.09-012 foreach_1.3.2 codetools_0.2-8 iterators_1.0.5
[9] cluster_1.14.1 mlogit_0.2-1 maxLik_1.0-2 miscTools_0.6-10
[13] lmtest_0.9-29 statmod_1.4.13 Formula_1.0-1 mvbutils_2.5.101
[17] data.table_1.7.1 party_0.9-99995 vcd_1.2-12 colorspace_1.1-0
[21] strucchange_1.4-6 sandwich_2.2-8 coin_1.0-20 modeltools_0.2-18
[25] lubridate_0.2.5 quantreg_4.71 SparseM_0.89 raster_1.9-41
[29] MASS_7.3-16 ks_1.8.4 misc3d_0.8-1 rgl_0.92.798
[33] mvtnorm_0.9-9991 KernSmooth_2.23-7 sp_0.9-91 latticeExtra_0.6-19
[37] RColorBrewer_1.0-5 zoo_1.7-6 ggplot2_0.8.9 proto_0.3-9.2
[41] reshape_0.8.4 plyr_1.6 rms_3.3-2 Hmisc_3.9-0
[45] survival_2.36-10 sos_1.3-1 brew_1.0-6 lattice_0.20-0
loaded via a namespace (and not attached):
[1] compiler_2.14.0 digest_0.5.1 stringr_0.5