On a broad question that I haven't been able to find for R:
I'm trying to add a counter at the beginning of a loop. 
So that when I run the loop sim = 1000:
if(hours$week1 > 1 and hours$week1 < 48) add 1 to the counter 
ifelse add 0
I have came across counter tutorials that print a sentence to let you know where you are (if something goes wrong): e.g
For (i in 1:1000) {
    if (i%%100==0) print(paste("No work", i)) 
}
But the purpose of my counter is to generate a value output, measuring how many of the 1000 runs in the loop fall inside a specified range.
You basically had it. You just need to a) initialize the counter before the loop, b) use & instead of and in your if condition, c) actually add 1 to the counter. Since adding 0 is the same as doing nothing, you don't have to worry about the "else".
counter = 0
for (blah in your_loop_definition) {
    ... loop code ...
    if(hours$week1 > 1 & hours$week1 < 48) {
        counter = counter + 1
    }
    ... more loop code ...
}
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