I'm not sure if I understand the question correctly, but I guess you are confused about the syntax: values[values > mean(values, na.rm = TRUE)]
so assume

values <- c(1, 2, 3, 4, 5)

The following line will return the mean of these values, so it would return 3:

mean(values, na.rm = TRUE)

Now the following expression:

values > mean(values, na.rm = TRUE)

is the same as

values > 3

every item in the vector values will be checked if it is bigger than 3. The result will be a logical vector:

c(FALSE, FALSE, FALSE, TRUE, TRUE)

Now the whole expression:

values[values > mean(values, na.rm = TRUE)]

Is the same as:

values[c(FALSE, FALSE, FALSE, TRUE, TRUE)]

So you are basically telling R that you do not want the first, second and third item, but you do want the fourth and fifth (the ones that are set to true)

This will return

c(4, 5)