Remove explicit loading of knitr

**knitr** is not needed by the reader to follow the paper or use **neotoma** so we shouldn't explicitly load it in the code chunks. Previously this would have broken the `Makefile` but now that `knitr::kabel()` is not used to render tables and we use `knitr::opts_chunk$set()` (i.e. explicitly reference the knitr namespace) we should be OK.

To fully round this out, the `Makefile` *should* be changed to load `library("knitr")` explicitly when calling `Rscript`, but I'll leave that for others to handle if they want.