why I've been using base plot

Nobody cares what I think, of course. The grammar of graphics is The Way, and ggplot2 is my preferred method of visualization. I never even really tried to make my own graphs with base plot until some point last fall (so: after 5 years of R) - I mean, I’m at Iowa State, after all. I don’t hang out with our Graphics Group as much as I should but that’s how I think about plotting. There are a few things at work here:

1. Sometimes it’s hard to do something in ggplot2 and it’s nice to have something else in your back pocket - that’s what happened this fall.
2. If you’re working with somebody, they might not want to use ggplot2 so you’d better be able to cope.
3. It’s good to be able to deliver code without having to worry about installing or loading a library. Sure, you can use something like if(!require('ggplot2')) install.packages('ggplot2') but added flexibility is never a bad thing.