Replace comments in Examples 2 and 3 with more narrative text in the main manuscript

[gavinsimpson]

Examples 2 and 3 have extensive chunks of R code with comments rendered as code chunks. A more natural way to do this would be to mix small R chunks within sentences or paragraphs of text, with the text replacing the comment text in a more narrative form.

If we break this chunks of code up in a style more reminiscent of typical R vignettes I feel those sections of the paper will read more easily.

[SimonGoring]

I'm okay with this. My original intention was to allow someone to copy the whole chunk at once, rather than copying multiple small chunks.

[karthik]

We can easily extract the code out of the Rmd and write to a R script after we're done.

[gavinsimpson]

What @karthik said. We should probably do a tangle (or whatever knitr calls it) so users have an R script to work from.