library(e1071)
library(SparseM)
library(ipred)
library(Matrix)
library(randomForest)
acc <- function(m, test.x, test.y) sum(diag(table(predict(m, test.x), test.y))) / length(test.y)

read.matrix.csr2 <- function(file, fac = TRUE, ncol = NULL)
{
   if (!require(SparseM))     stop("Need `SparseM' package!")
   l <- strsplit(readLines(file(file)), "[ ]+")

   ## y-values
   y <- sapply(l, function(x) x[1])

   ## x-values
   rja <- do.call("rbind", lapply(l, function(x) do.call("rbind", strsplit(x[-1], ":"))))
   ja <- as.integer(rja[,1])
   ia <- cumsum(c(1, sapply(l, length) - 1))

   max.ja <- max(ja)
   dimension <- c(length(l), if (is.null(ncol)) max.ja else max(ncol, 
max.ja))
   x = new("matrix.csr", as.numeric(rja[,2]), ja, as.integer(ia), as.integer(dimension))
   if (length(y))    list(x = x, y = if (fac) as.factor(y) else as.numeric(y))
   else x
}

## data sets

train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-0")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-0")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-1")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-1")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-2")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-2")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-3")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-3")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-4")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-4")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-5")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-5")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-6")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-6")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-7")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-7")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-8")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-8")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-9")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-9")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-10")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-10")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-11")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-11")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-12")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-12")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-13")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-13")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-14")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-14")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-15")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-15")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-16")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-16")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-17")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-17")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-18")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-18")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)
train.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale-19")
test.1 <- read.matrix.csr2("/mnt/89/b89098/svmprob2/jnl/300-500-20/dna/dna.scale.t-19")
myrf<-randomForest(as.matrix(train.1$x), train.1$y, as.matrix(test.1$x), test.1$y)
print(myrf)