Reproducible research

Definition

The goal of reproducible research is to tie specific instructions to data analysis and experimental data so that scholarship can be recreated, better understood and verified.

Source: CRAN Taskview

Literate programming

A new approach to programming, introduced by Donald Knuth
Programme is in natural language, e.g. English
Interspersed with macros that contain machine instructions

Example of LaTEX in text

The purpose of wc is to count lines, words, and/or characters in a list of files. The
number of lines in a file is ......../more explanations/

Here, then, is an overview of the file wc.c that is defined by the noweb program wc.nw:

<<*>>=
    <<Header files to include>>
    <<Definitions>>
    <<Global variables>>
    <<Functions>>
    <<The main program>>
    @

We must include the standard I/O definitions, since we want to send formatted output
to stdout and stderr.

<<Header files to include>>=
    #include <stdio.h>
    @

From LaTex to Notebooks

First there was LaTex

Then knitr emerged, followed by rmarkdown

Jupyter Notebooks followed a different evolutionary path

Markdown vs Notebooks

knitr and rmardown	Notebooks
Runs in IDE	Runs in web browser
R embedded in markdown	Markdown and R both embedded as cells
Static	Interactive
Better for reporting	Better for exploration, prototyping

You can use both systems for creating automated reporting:

With knitr use knit() and family
With notebooks use nbconvert on the command line