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I'm confused about the resampling statistics obtained via the train() and trainControl() functions in R's Caret package. My goal is to perform cross-validation on a machine learning model for a time series by splitting the series into adjacent training/testing sets, ultimately enabling me to tune individual models and compare the different models I create.

I also would like to access the model results for the individual hold out sets (that is, the testing windows during cross validation) - which is what I thought Caret saved in the model$resample object. However, when I look closely at that object, it seems that Caret is saving the in-sample results, possibly from the final model (trained on the entire data set) with predictions corresponding to the indexes of the individual hold-out sets.

My questions are:

  1. Is this (the saving of in-sample rather than hold-out results) the intended behavior of the package?
  2. If so, is there a way to access the hold-out results I am looking for?

Here is an example (apologies for the verbosity):

## Libraries
library(caret);library(quantmod);library(TTR);require(ggplot2);require(reshape)

## Data Acquisition and Wrangling

# download data from yahoo/google
getSymbols("^GSPC", from="2010-01-01")

# create returns series and some indicators
ret <- Delt(Op(GSPC), Cl(GSPC)) #day session return
atr <- ATR(GSPC[, c("GSPC.High", "GSPC.Low", "GSPC.Close")], 14)$atr
rsi <- RSI(Cl(GSPC), n=14, maType="SMA") #relative strength index
cmo <- CMO(Cl(GSPC)) #Chande momentm oscillator
dpo <- DPO(Cl(GSPC)) #de-trended price oscillator

dat <- cbind(ret, Lag(atr), Lag(rsi), Lag(cmo), Lag(dpo))
colnames(dat) <- c("ret", "atr", "rsi", "cmo", "dpo")

dat <- as.data.frame(dat[complete.cases(dat), ]) 

## Set up Time Series Cross Validation Windows

# create indexes for TSCV windows
init = 200 #initial window 
horiz = 20 #prediction horizon 
wdw <- createTimeSlices(1:nrow(dat), initialWindow = init, horizon = horiz, 
                        skip = horiz-1, fixedWindow = TRUE)

trainSlices <- wdw[[1]]
testSlices <- wdw[[2]]

# verify visually correct window setup:
trainSlices[[length(trainSlices)]]
testSlices[[length(testSlices)]]

# custom summary function
absretSummary <- function (data, lev = NULL, model = NULL) {
  positions <- sign(data[, "pred"])
  profits <- positions*data[, "obs"]
  profit <- prod(1+profits)-1
  names(profit) <- 'profit'
  return(profit)
}

# trainControl function
cntrl <- trainControl(savePredictions=FALSE, returnResamp="all", index=trainSlices, indexOut=testSlices, summaryFunction=absretSummary)   

# train gbm
set.seed(503)
gbm.model <- train(x=dat[, -1], y=dat[, 1], method="gbm", trControl=cntrl,  
                   maximize=TRUE, metric="profit", tuneGrid = expand.grid(interaction.depth = c(1,2),
                                                         n.trees = c(50,100),
                                                         shrinkage = c(0.1),
                                                         n.minobsinnode = c(10)))

gbm.model$resample[, 1] # no negative returns! Has to be in-sample!
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I looked extensively into the Caret GitHub repo and couldn't find anything that explained the behavior I described above. So I wrote some code to perform the same analysis without using any of Caret's helper functions. And I got the exact same result. Therefore, the unexpected behavior that I described has a different source than the one I implied in my question, possibly some future-peeking in my slicing and dicing of the time series - although I haven't been able to figure this out yet.

I think this question should be closed and a different one asked, possibly on another exchange.

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  • $\begingroup$ You can close the question yourself. $\endgroup$ – SmallChess Apr 3 '17 at 7:34
  • $\begingroup$ Do I need a certain reputation for that? I don't see the 'close' link referred to in the help documentation. $\endgroup$ – ManChild Apr 3 '17 at 12:06
  • $\begingroup$ Ask on stats.meta.stackexchange.com. I don't know why. $\endgroup$ – SmallChess Apr 3 '17 at 12:09

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