[R] How can you find the optimal number of values to randomly sample to optimize random forest classification without trial and error?

Jack Arnestad jackarnestad at gmail.com
Sat Dec 2 19:43:06 CET 2017

I have data set up like the following:

control1 <- sample(1:75, 3947398, replace=TRUE)
control2 <- sample(1:75, 28793, replace=TRUE)
control3 <- sample(1:100, 392733, replace=TRUE)
control4 <- sample(1:75, 858383, replace=TRUE)
patient1 <- sample(1:100, 28048, replace=TRUE)
patient2 <- sample(1:50, 80400, replace=TRUE)
patient3 <- sample(1:100, 48239, replace=TRUE)
control <- list(control1, control2, control3, control4)
patient <- list(patient1, patient2, patient3)

To classify these samples as either control or patient, I want make
frequency distributions of presence of each of the 100 variables being
considered. To do this, I randomly sample "s" values from each sample and
generate a frequency vector of length 100. This is how I would do it:

control_s <- list()
patient_s <- list()for (i in 1:length(control))
        control_s[[i]] <- sample(control[[i]], s)for (i in 1:length(patient))
        patient_s[[i]] <- sample(patient[[i]], s)

Once I do this, I generate the frequency vector of length 100 as follows:

controlfreq <- list()for (i in 1:length(control_s)){
controlfreq[[i]] <-
        control_s[[i]], levels = 1:100
patientfreq <- list()for (i in 1:length(patient_s)){
patientfreq[[i]] <-
        patient_s[[i]], levels = 1:100
controlfreq <- t(as.data.frame(controlfreq))
controltrainingset <- transform(controlfreq, status = "control")
patientfreq <- t(as.data.frame(patientfreq))
patienttrainingset <- transform(patientfreq, status = "patient")

dataset <- rbind(controltrainingset, patienttrainingset)

This is the final data frame being used in the classification algorithm. My
goal of this post is to figure out how to identify the optimal "s" value so
that the highest ROC is achieved. I am using "rf" from the caret package to
do classification.

fitControl <-trainControl(method = "LOOCV", classProbs = T, savePredictions = T)
model <- train(status ~ ., data = dataset, method = "rf", trControl =

How can I automate it to start "s" at 5000, change it to another value, and
based on the change in ROC, keep changing "s" to work towards the best
possible "s" value?


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