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[R-Forge #5660] Interaction between "Caret" package and data.table in R 3.1 gives different column name #476
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Some updates:
First off, @topepo seems to have incorporated a fix for this issue on to the
caretpackage already in v 6.0-29. Much appreciated, thank you.However, the fix doesn't seem to be working. Here's what I get on my system:
library(caret) library(data.table) DT <- data.table(x = rnorm(10), y = rnorm(10)) cv.ctrl <- trainControl(method = 'repeatedcv', number = 5, repeats = 1) fit <- train(y ~ x, data = DT, 'lm', trControl = cv.ctrl) > names(DT) # [1] "x" ".outcome" > sessionInfo() # R version 3.1.1 (2014-07-10) # Platform: x86_64-apple-darwin10.8.0 (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] graphics grDevices datasets stats utils methods base # other attached packages: # [1] data.table_1.9.3 caret_6.0-30 ggplot2_1.0.0 lattice_0.20-29 bit64_0.9-4 # [6] bit_1.1-12 # loaded via a namespace (and not attached): # [1] BradleyTerry2_1.0-5 brglm_0.5-9 car_2.0-20 codetools_0.2-8 # [5] colorspace_1.2-4 compiler_3.1.1 digest_0.6.4 foreach_1.4.2 # [9] grid_3.1.1 gtable_0.1.2 gtools_3.4.1 iterators_1.0.7 # [13] lme4_1.1-7 MASS_7.3-33 Matrix_1.1-4 minqa_1.2.3 # [17] munsell_0.4.2 nlme_3.1-117 nloptr_1.0.0 nnet_7.3-8 # [21] plyr_1.8.1 proto_0.3-10 Rcpp_0.11.2 reshape2_1.4.0.99 # [25] scales_0.2.4 splines_3.1.1 stringr_0.6.2 tools_3.1.1
The issue seems to arise from these lines from
train.formulafunction:res$trainingData <- data isY <- names(res$trainingData) %in% as.character(form[[2]]) if(any(isY)) colnames(res$trainingData)[isY] <- ".outcome"
which should work just fine, except it doesn't on v3.1+. It works just fine with < v3.1. This is because R v3.1+ shallow copies where ever possible as opposed to deep copies and
data.tablewill have to ake care of this. Here's a simple way to reproduce the issue:# R v3.1.1 require(data.table) dt = data.table(x=1:5, y=6:10) ll = vector("list", 2L) names(ll) <- c("a", "b") ll$a = 1L; ll$b = dt idx = c(FALSE, TRUE) colnames(ll$b)[idx] = "bla" names(dt) # [1] "x" "bla" names(ll$b) # [1] "x" "bla"
The function
colnames<-simply callsnames(x) <- valuewhich then calls the appropriatedata.tablemethod that usessetnames. However,xhas only been shallow copied, on which we set names by reference, and hence the issue.Bumping priority. Assigning milestone 1.9.4.
One possible fix for the
caretpackage would be to change this line to:if ("data.table" %in% class(data)) res$trainingData <- copy(data) else res$trainingData <- data
- modified the milestones: ,
on Sep 6, 2014 Updated the SO post: link.
Submitted by: Arun ; Assigned to: Nobody; R-Forge link
As illustrated here on SO.