# Bug with RStudio + doMC + caret combination
#
# (1) Problem when calling PenalizedLDA
#
# With registerDoMC the libraries called within train() do not get loaded
#
# PenalizedLDA : penalizedLDA and flsa do not get loaded
# LDA : MASS does not get loaded
# nb: klaR does not get loaded
#
# (The libraries are loaded in createModel.R and predictionFunction.R)
#
# This results in an error when calling train
#   Error in names(resamples) <- gsub("^\\.", "", names(resamples)) :
#   attempt to set an attribute on NULL
# registerDoSEQ does not have this problem
# This problem is unique to RStudio, the default R shell does not have this
# problem


rm(list=ls(all = TRUE))
library(caret)
library(doMC)

registerDoMC()
#registerDoSEQ()


data(mdrr)
nearZeroVar_classwise <- function(X,y) (unique(unlist(dlply(data.frame(X=X, y=y),.(y),function(Z) nearZeroVar(Z[,1:NCOL(X)])))))
X <- mdrrDescr
y <- mdrrClass
X <- X[,-nearZeroVar_classwise(X,y)]
X <- X[,-findCorrelation(cor(X), cutoff=0.75)]


# library(klaR)
# detach("package:klaR")
ptm <- proc.time()
(fit <- train(X, y, method="nb", trControl=trainControl(method="boot", number=5)))
print(proc.time() - ptm)


# library(penalizedLDA)
# library(flsa)
# detach("package:penalizedLDA")
# detach("package:flsa")
ptm <- proc.time()
(fit <- train(X, y, method="lda", trControl=trainControl(method="boot", number=5)))
print(proc.time() - ptm)

# library(MASS)
# detach("package:MASS")
ptm <- proc.time()
(fit <- train(X, y, method="PenalizedLDA", trControl=trainControl(method="boot", number=5)))
print(proc.time() - ptm)