China 
Africa 
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Reproducible projects with RStudio and R markdown
Published in Rafael A. Irizarry, Introduction to Data Science, 2019
R markdown is a format for literate programming documents. It is based on markdown, a markup language that is widely used to generate html pages. You can learn more about markdown here: https://www.markdowntutorial.com. Literate programming weaves instructions, documentation, and detailed comments in between machine executable code, producing a document that describes the program that is best for human understanding (Knuth 1984). Unlike a word processor, such as Microsoft Word, where what you see is what you get, with R markdown, you need to compile the document into the final report. The R markdown document looks different than the final product. This seems like a disadvantage at first, but it is not because, for example, instead of producing plots and inserting them one by one into the word processing document, the plots are automatically added.
Reproducible research: a minority opinion
Published in Journal of Experimental & Theoretical Artificial Intelligence, 2018
With many open source packages, it is now much easier to tie the writing of a paper to the computational tools that carry out experiments. Literate programming has blocks of code embedded within the text of a paper (Knuth, 1988). This code can be executed to run an experiment and put the graphical output directly into the paper. This has a number of advantages: updating of a paper is quick and easy; and the code is better documented by connecting it directly to its broader purpose. Clearly it does improve the ease of sharing code. However, the sort of mandated sharing that Reproducible Research proposes is just a small part of that. So, I see little support for the two being intimately tied, as some claim (Schulte, Davison Dye, & Dominik, 2012).