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Literature programming and RMarkdown

Introduction to Data Science (BIOL7800)

https://introdatasci.dlilab.com/

Daijiang Li

LSU

2021/09/15

1 / 6

Literature programming

Let us change our traditional attitude to the construction of programs: Instead of imagining that our main task is to instruct a computer what to do, let us concentrate rather on explaining to humans what we want the computer to do.

--- Donald E. Knuth, Literate Programming, 1984

Literature programming weaves text (e.g., documentation, explanation, comments, etc.) in between machine executable code.

Need to compile it to get a final report, not What You See Is What You Get (WYSIWYG, e.g., MS Word)

2 / 6

R Markdown (https://rmarkdown.rstudio.com/)

A powerful tool for combining analysis (in R, Python, Julia, or other programming languages) and reporting into the same document

rmarkdown workflow

YAML

---
title: "Untitled"
author: "Daijiang Li"
date: "8/17/2021"
output: html_document
---
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Rmarkdown reference

4 / 6

Open RStudio for demonstration

https://github.com/daijiang/phyr_ms

5 / 6

Reference books

R Markdown: The Definitive Guide

R Markdown Cookbook

6 / 6

Literature programming

Let us change our traditional attitude to the construction of programs: Instead of imagining that our main task is to instruct a computer what to do, let us concentrate rather on explaining to humans what we want the computer to do.

--- Donald E. Knuth, Literate Programming, 1984

Literature programming weaves text (e.g., documentation, explanation, comments, etc.) in between machine executable code.

Need to compile it to get a final report, not What You See Is What You Get (WYSIWYG, e.g., MS Word)

2 / 6
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