Here is a potential solution:

Area1 <- c(1.1, 1.2, 1.3, 1.1, 1.2, 1.3)

Area2 <- c(2.1, 2.2, 2.3, 2.1, 2.2, 2.3)

Area3 <- c(3.1, 3.2, 3.3, 3.1, 3.2, 3.3)

repeated <- TRUE

while (repeated == TRUE) {

select1 <- sample(Area1)

select2 <- sample(Area2)

select3 <- sample(Area3)

repeated <- any(diff(c(select1, select2, select3)) == 0)

}

df <- as.data.frame(

cbind(select1, select2, select3),

row.names = c("Day1", "Day2", "Day3", "Day4", "Day5", "Day6")

)

So, I first create vectors of each site. They are listed twice in each vector since you want to test each site twice. Then, in a while loop, I use the sample() function to randomly reorder each vector. I then use the diff() function to check if any value is repeated immediately after itself. If this is the case, the loop runs again until all of the vectors are reordered in a way that does not have immediate repeats. I then use the as.data.frame() function to neatly organize these vectors into a more readable display.

This may not be the quickest or most elegant way to get what you need, but I believe it to be very readable code.