Interactive notebooks such as RMarkdown or Jupyter-notebooks are an excellent way to perform exploratory data-analysis. Not only you can keep all the code together but also write annotations and notes in Markdown project --- all of which together serves like a summary document. I have had great success using them not only for research for also for doing homeworks.
One of my current classes, however, had a very specific requirement: all the accompanying code should appear at the end of the document. Generally, the analysis in the notebooks is done in "inline" style, where you write code and see the results in the same place.
However, I found a great trick in knitr to put all the code at the end.
Bla bla ...
x = rnorm(100,10,5)
y = rnorm(100,10,5)
plot(x,y)
Code chunk:
Neat! Altough, it will be great if there was a single configuration that does
all of that automagically. Perhaps, I need to look at the source code of
knitr...
Happy hacking!