I know that R works most efficiently with vectors and looping should be avoided. I am having a hard time teaching myself to actually write code this way. I would like some ideas
To answer your question about why the loop of 10000 took much longer than your loop of 1000:
I think the primary suspect is the concatenations that are happening every loop. As the data gets longer R is probably copying every element of the vector into a new vector that is one longer. Copying a small (500 elements on average) data set 1000 times is fast. Copying a larger (5000 elements on average) data set 10000 times is slower.