Nicole, after we spoke, I was having trouble using the pandoc wrapper within the knitr() package in R Studio -- R Studio wasn't seeing that pandoc was installed. Normally, that's not a problem, since I usually use pandoc from the bash shell. But in this case, it annoyed me. So just in case you ever do start using R Studio, here's the answer, at least for Unix-y systems like Linux and OSX: In a terminal, do echo PATH=$PATH > ~/.Renviron ~/.Renviron is a file that RStudio will look for on startup, following . By putting a line in ~/.Renviron with the current $PATH environment variable (which may include stuff that's installed in weird places, like Pandoc), RStudio will see that updated variable. This can be checked within R Studio with `Sys.getenv("PATH")` I'm sending this to you both in case it comes up in the future with anyone else you see struggling with it.