R Markdown: The Definitive Guide

339 Pages·2018·4.64 MB·English

by  Yihui Xie

R Markdown
The Definitive Guide
Chapman & Hall/CRC
The R Series
Series Editors
John M. Chambers, Department of Statistics Stanford University Stanford,
California, USA
Torsten Hothorn, Division of Biostatistics University of Zurich Switzerland
Duncan Temple Lang, Department of Statistics University of California,
Davis, California, USA
Hadley Wickham, RStudio, Boston, Massachusetts, USA
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For more information about this series, please visit:
https://www.crcpress.com/go/the-r-series
R Markdown
The Definitive Guide
Yihui Xie
J. J. Allaire
Garrett Grolemund
CRC Press
Taylor & Francis Group
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To Jung Jae-sung (1982 – 2018),
aremarkablyhard-workingbadmintonplayerwitharemarkably
simpleplayingstyle

Contents
ListofTables xvii
ListofFigures xix
Preface xxiii
AbouttheAuthors xxxiii
I GetStarted 1
1 Installation 3
2 Basics 5
2.1 Exampleapplications . . . . . . . . . . . . . . . . . . . . . 9
2.1.1 Airbnb’sknowledgerepository . . . . . . . . . . . . 9
2.1.2 HomeworkassignmentsonRPubs . . . . . . . . . . 10
2.1.3 Personalizedmail . . . . . . . . . . . . . . . . . . . 10
2.1.4 2017EmployerHealthBenefitsSurvey. . . . . . . . 11
2.1.5 Journalarticles . . . . . . . . . . . . . . . . . . . . . 12
2.1.6 Dashboardsateelloo . . . . . . . . . . . . . . . . . 12
2.1.7 Books. . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.1.8 Websites . . . . . . . . . . . . . . . . . . . . . . . . 13
2.2 CompileanRMarkdowndocument . . . . . . . . . . . . . 14
2.3 Cheatsheets . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.4 Outputformats . . . . . . . . . . . . . . . . . . . . . . . . 16
2.5 Markdownsyntax . . . . . . . . . . . . . . . . . . . . . . . 19
2.5.1 Inlineformatting . . . . . . . . . . . . . . . . . . . 19
2.5.2 Block-levelelements . . . . . . . . . . . . . . . . . 20
2.5.3 Mathexpressions . . . . . . . . . . . . . . . . . . . 23
2.6 RcodechunksandinlineRcode . . . . . . . . . . . . . . . 24
2.6.1 Figures . . . . . . . . . . . . . . . . . . . . . . . . . 27
2.6.2 Tables . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.7 Otherlanguageengines . . . . . . . . . . . . . . . . . . . . 30
vii
viii Contents
2.7.1 Python . . . . . . . . . . . . . . . . . . . . . . . . . 32
2.7.2 Shellscripts . . . . . . . . . . . . . . . . . . . . . . 34
2.7.3 SQL . . . . . . . . . . . . . . . . . . . . . . . . . . 35
2.7.4 Rcpp . . . . . . . . . . . . . . . . . . . . . . . . . . 37
2.7.5 Stan . . . . . . . . . . . . . . . . . . . . . . . . . . 39
2.7.6 JavaScriptandCSS . . . . . . . . . . . . . . . . . . 39
2.7.7 Julia . . . . . . . . . . . . . . . . . . . . . . . . . . 40
2.7.8 CandFortran . . . . . . . . . . . . . . . . . . . . . 40
2.8 Interactivedocuments . . . . . . . . . . . . . . . . . . . . . 41
2.8.1 HTMLwidgets . . . . . . . . . . . . . . . . . . . . 41
2.8.2 Shinydocuments . . . . . . . . . . . . . . . . . . . 42
II OutputFormats 47
3 Documents 49
3.1 HTMLdocument . . . . . . . . . . . . . . . . . . . . . . . 49
3.1.1 Tableofcontents . . . . . . . . . . . . . . . . . . . . 50
3.1.2 Sectionnumbering . . . . . . . . . . . . . . . . . . 51
3.1.3 Tabbedsections . . . . . . . . . . . . . . . . . . . . 51
3.1.4 Appearanceandstyle . . . . . . . . . . . . . . . . . 52
3.1.5 Figureoptions . . . . . . . . . . . . . . . . . . . . . 54
3.1.6 Dataframeprinting . . . . . . . . . . . . . . . . . . 55
3.1.7 Codefolding . . . . . . . . . . . . . . . . . . . . . . 56
3.1.8 MathJaxequations. . . . . . . . . . . . . . . . . . . 57
3.1.9 Documentdependencies . . . . . . . . . . . . . . . 58
3.1.10 Advancedcustomization . . . . . . . . . . . . . . . 59
3.1.11 Sharedoptions . . . . . . . . . . . . . . . . . . . . . 62
3.1.12 HTMLfragments . . . . . . . . . . . . . . . . . . . 62
3.2 Notebook . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
3.2.1 UsingNotebooks . . . . . . . . . . . . . . . . . . . 63
3.2.2 Savingandsharing . . . . . . . . . . . . . . . . . . 72
3.2.3 Notebookformat . . . . . . . . . . . . . . . . . . . 73
3.3 PDFdocument . . . . . . . . . . . . . . . . . . . . . . . . . 78
3.3.1 Tableofcontents . . . . . . . . . . . . . . . . . . . . 79
3.3.2 Figureoptions . . . . . . . . . . . . . . . . . . . . . 80
3.3.3 Dataframeprinting . . . . . . . . . . . . . . . . . . 80
3.3.4 Syntaxhighlighting . . . . . . . . . . . . . . . . . . 81
3.3.5 LaTeXoptions . . . . . . . . . . . . . . . . . . . . . 81
3.3.6 LaTeXpackagesforcitations . . . . . . . . . . . . . 82
3.3.7 Advancedcustomization . . . . . . . . . . . . . . . 83
Contents ix
3.3.8 Otherfeatures . . . . . . . . . . . . . . . . . . . . . 84
3.4 Worddocument . . . . . . . . . . . . . . . . . . . . . . . . 85
3.4.1 Otherfeatures . . . . . . . . . . . . . . . . . . . . . 85
3.5 OpenDocumentTextdocument . . . . . . . . . . . . . . . . 86
3.5.1 Otherfeatures . . . . . . . . . . . . . . . . . . . . . 86
3.6 RichTextFormatdocument . . . . . . . . . . . . . . . . . . 87
3.6.1 Otherfeatures . . . . . . . . . . . . . . . . . . . . . 87
3.7 Markdowndocument . . . . . . . . . . . . . . . . . . . . . 88
3.7.1 Markdownvariants . . . . . . . . . . . . . . . . . . 88
3.7.2 Otherfeatures . . . . . . . . . . . . . . . . . . . . . 89
3.8 Rpackagevignette . . . . . . . . . . . . . . . . . . . . . . 90
4 Presentations 93
4.1 ioslidespresentation . . . . . . . . . . . . . . . . . . . . . . 93
4.1.1 Displaymodes . . . . . . . . . . . . . . . . . . . . . 95
4.1.2 Incrementalbullets . . . . . . . . . . . . . . . . . . 95
4.1.3 Visualappearance . . . . . . . . . . . . . . . . . . . 96
4.1.4 Codehighlighting . . . . . . . . . . . . . . . . . . . 98
4.1.5 Addingalogo . . . . . . . . . . . . . . . . . . . . . 98
4.1.6 Tables . . . . . . . . . . . . . . . . . . . . . . . . . 99
4.1.7 Advancedlayout . . . . . . . . . . . . . . . . . . . 100
4.1.8 Textcolor . . . . . . . . . . . . . . . . . . . . . . . 100
4.1.9 Presentermode . . . . . . . . . . . . . . . . . . . . 101
4.1.10 PrintingandPDFoutput . . . . . . . . . . . . . . . 101
4.1.11 Customtemplates . . . . . . . . . . . . . . . . . . . 101
4.1.12 Otherfeatures . . . . . . . . . . . . . . . . . . . . . 102
4.2 Slidypresentation . . . . . . . . . . . . . . . . . . . . . . . 102
4.2.1 Displaymodes . . . . . . . . . . . . . . . . . . . . . 104
4.2.2 Textsize . . . . . . . . . . . . . . . . . . . . . . . . 104
4.2.3 Footerelements . . . . . . . . . . . . . . . . . . . . 105
4.2.4 Otherfeatures . . . . . . . . . . . . . . . . . . . . . 105
4.3 Beamerpresentation . . . . . . . . . . . . . . . . . . . . . . 106
4.3.1 Themes . . . . . . . . . . . . . . . . . . . . . . . . . 107
4.3.2 Slidelevel . . . . . . . . . . . . . . . . . . . . . . . 108
4.3.3 Otherfeatures . . . . . . . . . . . . . . . . . . . . . 109
4.4 PowerPointpresentation . . . . . . . . . . . . . . . . . . . 109
4.4.1 Customtemplates . . . . . . . . . . . . . . . . . . . 112
4.4.2 Otherfeatures . . . . . . . . . . . . . . . . . . . . . 113
III Extensions 115