Rmarkdown for Reproducible...

Rmarkdown for Reproducible Research

Andrew Caines | Linguistics, Cambridge | apc38

27 November 2015

Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 1 / 9

What is R Markdown?

source file / output file paradigm (cp LaTeX, HTML, markdown)

plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2

What is R Markdown?

source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by R

markdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2

What is R Markdown?

source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)

R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2

What is R Markdown?

source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunks

uses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2

What is R Markdown?

source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion program

can produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2

What is R Markdown?

source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documents

maintained by R Studio, now R Markdown v2

What is R Markdown?

source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2

What is R Markdown?

simple syntax: shallow learning curve

human-readable: emphasis on communication and clarity, ratherthan technique and complexitytransparent formatting: wysiwygembedded computation: share with collaborators, reviewers,colleagues, students, critics

What is R Markdown?

simple syntax: shallow learning curvehuman-readable: emphasis on communication and clarity, ratherthan technique and complexity

transparent formatting: wysiwygembedded computation: share with collaborators, reviewers,colleagues, students, critics

What is R Markdown?

simple syntax: shallow learning curvehuman-readable: emphasis on communication and clarity, ratherthan technique and complexitytransparent formatting: wysiwyg

embedded computation: share with collaborators, reviewers,colleagues, students, critics

What is R Markdown?

simple syntax: shallow learning curvehuman-readable: emphasis on communication and clarity, ratherthan technique and complexitytransparent formatting: wysiwygembedded computation: share with collaborators, reviewers,colleagues, students, critics

What is R Markdown?

. . . integrating source code, statistical output, and text in RMarkdown is a model of reproducibility.

Such transparency facilitates comprehension, defensibility, andfurther research or testing.

R Markdown helps to bring the vision for reproducibility instatistical analysis articulated by Gentleman & Temple Lang[2004] to reality.

Baumer & Udwin 2015, ‘R Markdown’, WIRES: ComputationalStatistics

How to use R Markdown

installationinstall.packages('rmarkdown')

library(rmarkdown)

How to use R Markdown

installationinstall.packages('rmarkdown')library(rmarkdown)

How to use R Markdownsimple syntax, human-readable, transparent formatting

How to use R Markdownembedded computation

R Markdown and Reproducibility

User experience?

disappointing :-/Computational linguistics >(open) Linguisticsculture of Shared Tasks, for exampleCurrent project: proprietary data + 4p paper + no shared code +authors moved onMartijn Wieling’s statistics course: Rmd, HTML

User experience?disappointing :-/

Computational linguistics >(open) Linguisticsculture of Shared Tasks, for exampleCurrent project: proprietary data + 4p paper + no shared code +authors moved onMartijn Wieling’s statistics course: Rmd, HTML

User experience?disappointing :-/Computational linguistics >(open) Linguistics

culture of Shared Tasks, for exampleCurrent project: proprietary data + 4p paper + no shared code +authors moved onMartijn Wieling’s statistics course: Rmd, HTML

User experience?disappointing :-/Computational linguistics >(open) Linguisticsculture of Shared Tasks, for example

Current project: proprietary data + 4p paper + no shared code +authors moved onMartijn Wieling’s statistics course: Rmd, HTML

User experience?disappointing :-/Computational linguistics >(open) Linguisticsculture of Shared Tasks, for exampleCurrent project: proprietary data + 4p paper + no shared code +authors moved on

Martijn Wieling’s statistics course: Rmd, HTML

User experience?disappointing :-/Computational linguistics >(open) Linguisticsculture of Shared Tasks, for exampleCurrent project: proprietary data + 4p paper + no shared code +authors moved onMartijn Wieling’s statistics course: Rmd, HTML

useful linksRStudio: R MarkdownUdwin & Baumer arXiv.org paper (= WIRES paper)Shiny & R Markdownmy GitHub ‘replication’ repo

contact meapc38my website[@cainesap](https://twitter.com/cainesap)

Rmarkdown for Reproducible...

Documents

Eduardo Guamán Introducción a R Markdown · R Markdown es un formato que permite una fácil creación de documentos, presentaciones dinámicas e informes de R. R Markdown admite

markdown-memo example document - Ryan Reecerreece.github.io/sw/markdown-memo/example.pdf · DRAFT:November1,2017. Pleasedonotcitewithoutpermission.EXAMPLE-DOC-000 markdown-memo example

Reproducible Research With Rmarkdown

A Markdown Interpreter for TeX - TeXdoc Onlinetexdoc.net/texmf-dist/doc/generic/markdown/markdown.pdf10if not modules then modules = { } end 11modules['markdown'] = metadata 1.1 Feedback

R Markdown - Journalism Courses Knight Center · 2020. 8. 5. · R Markdown Andrew Ba Tran Contents WhatisMarkdown? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Take it easy with markdown

DITA and Markdown - oxygenxml.comDITA and Markdown What is Lightweight DITA? LwDITA is a proposed standard for expressing simplified DITA documents in XML, HTML5, and Markdown. The

R Markdown Cheat Sheet - RStudio – Open source and · PDF file · 2017-02-14evaluate code chunks in ... word_document Microso# Word (.docx) odt_document OpenDocument Text ... rmarkdown-cheatsheet-2.0

MARKDOWN SYNTAX

4R MARKDOWN OPTIMISATION · your primary concern, the best markdown will balance retail price reduction against sales increase. To maximise inventory consumption, your markdown should

Oracle® Retail Markdown Optimization · The Oracle Retail Markdown Optimization User’s Guide is intended for Markdown Optimization users. It covers user tasks and application functionality

IS YOUR MARKDOWN OPTIMIZATION STRATEGY · 2020. 4. 22. · markdown budgets likely to be significantly higher this year, markdown decisions will be a major focal point for 2020. Regardless

Literate Programming in R Markdown

Oracle Retail Markdown Optimization - Data sheet | Oracle · Oracle Retail Markdown Optimization With Oracle Retail Markdown Optimization, it is easy to improve lifecycle pricing

Rmarkdown-Intro-Workshop - GitHub...R Markdown: The Definitive Guide Preface How to read this book Structure of the book Softh'are information and conventions Acknowledgments About

R Markdown Cheat Sheet - Hello FriendR Markdown Cheat Sheet ... Several functions format R data into tables data

Markdown Slides [EN]

MARKDOWN OPTIMIZATION - 4R Systems4rsystems.com/wp-content/uploads/2017/06/Markdown-Optimization-Brochure.pdfA key element in markdown optimization is determining how your products

A Markdown Interpreter for TeX - University of Washingtonctan.math.washington.edu/.../generic/markdown/markdown.pdf · 2020. 3. 21. · 10if not modules then modules = { } end 11modules['markdown']

Markdown By Example · Simpletext 2 Simpletext Since Markdown is supposed to make reading and writingfileseasywithoutstrippingtheauthorofthe abilitytocreatewellformattedoutput,aMarkdown