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R Markdown: The Definitive Guide [Pehme köide]

, , (RStudio, Inc. Boston, MA, USA)
  • Formaat: Paperback / softback, 304 pages, kõrgus x laius: 234x156 mm, kaal: 1140 g
  • Sari: Chapman & Hall/CRC The R Series
  • Ilmumisaeg: 17-Jul-2018
  • Kirjastus: CRC Press
  • ISBN-10: 1138359335
  • ISBN-13: 9781138359338
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  • Formaat: Paperback / softback, 304 pages, kõrgus x laius: 234x156 mm, kaal: 1140 g
  • Sari: Chapman & Hall/CRC The R Series
  • Ilmumisaeg: 17-Jul-2018
  • Kirjastus: CRC Press
  • ISBN-10: 1138359335
  • ISBN-13: 9781138359338
Teised raamatud teemal:
R Markdown: The Definitive Guide is the first official book authored by the core R Markdown developers that provides a comprehensive and accurate reference to the R Markdown ecosystem. With R Markdown, you can easily create reproducible data analysis reports, presentations, dashboards, interactive applications, books, dissertations, websites, and journal articles, while enjoying the simplicity of Markdown and the great power of R and other languages. In this book, you will learnBasics: Syntax of Markdown and R code chunks, how to generate figures and tables, and how to use other computing languages Built-in output formats of R Markdown: PDF/HTML/Word/RTF/Markdown documents and ioslides/Slidy/Beamer/PowerPoint presentations Extensions and applications: Dashboards, Tufte handouts, xaringan/reveal.js presentations, websites, books, journal articles, and interactive tutorials Advanced topics: Parameterized reports, HTML widgets, document templates, custom output formats, and Shiny documents. Yihui Xie is a software engineer at RStudio. He has authored and co-authored several R packages, including knitr, rmarkdown, bookdown, blogdown, shiny, xaringan, and animation. He has published three other books, Dynamic Documents with R and knitr, bookdown: Authoring Books and Technical Documents with R Markdown, and blogdown: Creating Websites with R Markdown.J.J. Allaire is the founder of RStudio and the creator of the RStudio IDE. He is an author of several packages in the R Markdown ecosystem including rmarkdown, flexdashboard, learnr, and radix.Garrett Grolemund is the co-author of R for Data Science and author of Hands-On Programming with R. He wrote the lubridate R package and works for RStudio as an advocate who trains engineers to do data science with R and the Tidyverse.

Arvustused

"The manuscript offers a detailed documentation of the R Markdown document format and its related packages for R (e.g. knitr, rmarkdown, flexdashboard, shiny). These packages form an important ecosystem for reproducible research using R and are widely used across academia and the private sector. All the authors have been key contributors to developing the core R Markdown packages and are knowledgable about the inner workings of these functions and all the available options to customize published documentsThe target audience for this manuscript would be experienced R users who frequently use R Markdown to generate publications for a variety of mediums (articles, books, information dashboards, interactive web applications, etc.)While this book is strongly related to the authors previous book (Dynamic Documents with R and knitr), a wider range of readers should find this new manuscript useful for its focus on the broad range of output formats generated by R Markdown and how to customize those outputs." ~Benjamin Soltoff, Department of Computational Social Science, University of Chicago

"A main strength of the software described herein is that it facilitates reproducible documents incorporating analyses and figures. The first topics covered in chapters 6-13 include handout and presentation formats that could be used effectively for teaching or presenting statistical results. The other topics focus on larger scale documents such as complex websites, books, and academic journal articles. From academic teaching and research to industry and other settings, the material covered by this book allows statisticians and data scientists to disseminate results in a highly effective manner." ~David Whitney, Department of Biostatistics, University of Washington

"This book will be a valuable reference for students, academics, and professionals using R that is to say, any one in a wide (and growing) variety of fields focused on practical data analysis including statistics, machine learning, the social sciences, etc. There is increasing awareness that nearly any occasion calling for analysis code also calls for some amount of corresponding documentation, explanation, and/or interpretation. Rapid improvement in tools for R markdown has made integrating code and text less and less of a chore, and therefore more and more common even among users new to R. R markdown is a popular choice now for a range of formats including blog posts, user manuals, books, dissertations, and undergraduate homework assignments. I personally use R markdown for nearly all of my website content, presentations, research papers, and to generate reports for the clients of my statistical consulting business. Because of its many applications, however, the ecosystem of R markdown tools has become unwieldy, and many tutorials reference outdated techniques or unnecessary workarounds. A definitive guide has been long needed." ~Rose Hartman, UnderstandingData

"This book is so far the most comprehensive reference for the R Markdown format and its associated extensions and tools. On a high level, Part I and II (Chapter 1-4) of this book cover the basic use of the R Markdown document and the knitr and rmarkdown packages, which are helpful for new users to quickly get started. Part III (Chapter 5-13) introduces a lot of new developments and powerful tools for R Markdown, including creating presentations, authoring books, building websites, writing journal articles, etc. In my personal point of view this is the most attractive part of this book, as it opens a new world for users who have only used R Markdown to create ordinary documents." ~Yixuan Qui, Department of Statistics, Purdue University

"This book represents a valuable contribution to the target field due to its exploration of a wide range of features in the markdown language. If other books on this topic exist, this one has the advantage that the authors have already made significant contributions to the markdown language in the R platform and certainly have a comprehensive understanding of the topicI recommend this book for publication because the topic is sophisticated and complex, and the interested audience will certainly be satisfied with the clarity of presentation and the depth that the authors reach in their exploratory examples" ~Jon Katz, data analyst "The manuscript offers a detailed documentation of the R Markdown document format and its related packages for R (e.g. knitr, rmarkdown, flexdashboard, shiny). These packages form an important ecosystem for reproducible research using R and are widely used across academia and the private sector. All the authors have been key contributors to developing the core R Markdown packages and are knowledgable about the inner workings of these functions and all the available options to customize published documentsThe target audience for this manuscript would be experienced R users who frequently use R Markdown to generate publications for a variety of mediums (articles, books, information dashboards, interactive web applications, etc.)While this book is strongly related to the authors previous book (Dynamic Documents with R and knitr), a wider range of readers should find this new manuscript useful for its focus on the broad range of output formats generated by R Markdown and how to customize those outputs." ~Benjamin Soltoff, Department of Computational Social Science, University of Chicago

"A main strength of the software described herein is that it facilitates reproducible documents incorporating analyses and figures. The first topics covered in chapters 6-13 include handout and presentation formats that could be used effectively for teaching or presenting statistical results. The other topics focus on larger scale documents such as complex websites, books, and academic journal articles. From academic teaching and research to industry and other settings, the material covered by this book allows statisticians and data scientists to disseminate results in a highly effective manner." ~David Whitney, Department of Biostatistics, University of Washington

"This book will be a valuable reference for students, academics, and professionals using R that is to say, any one in a wide (and growing) variety of fields focused on practical data analysis including statistics, machine learning, the social sciences, etc. There is increasing awareness that nearly any occasion calling for analysis code also calls for some amount of corresponding documentation, explanation, and/or interpretation. Rapid improvement in tools for R markdown has made integrating code and text less and less of a chore, and therefore more and more common even among users new to R. R markdown is a popular choice now for a range of formats including blog posts, user manuals, books, dissertations, and undergraduate homework assignments. I personally use R markdown for nearly all of my website content, presentations, research papers, and to generate reports for the clients of my statistical consulting business. Because of its many applications, however, the ecosystem of R markdown tools has become unwieldy, and many tutorials reference outdated techniques or unnecessary workarounds. A definitive guide has been long needed." ~Rose Hartman, UnderstandingData

"This book is so far the most comprehensive reference for the R Markdown format and its associated extensions and tools. On a high level, Part I and II (Chapter 1-4) of this book cover the basic use of the R Markdown document and the knitr and rmarkdown packages, which are helpful for new users to quickly get started. Part III (Chapter 5-13) introduces a lot of new developments and powerful tools for R Markdown, including creating presentations, authoring books, building websites, writing journal articles, etc. In my personal point of view this is the most attractive part of this book, as it opens a new world for users who have only used R Markdown to create ordinary documents." ~Yixuan Qui, Department of Statistics, Purdue University

"This book represents a valuable contribution to the target field due to its exploration of a wide range of features in the markdown language. If other books on this topic exist, this one has the advantage that the authors have already made significant contributions to the markdown language in the R platform and certainly have a comprehensive understanding of the topicI recommend this book for publication because the topic is sophisticated and complex, and the interested audience will certainly be satisfied with the clarity of presentation and the depth that the authors reach in their exploratory examples" ~Jon Katz, data analyst

List of Tables xvii
List of Figures xix
Preface xxiii
About the Authors xxxiii
I Get Started 1(46)
1 Installation
3(2)
2 Basics
5(42)
2.1 Example applications
9(5)
2.1.1 Airbnb's knowledge repository
9(1)
2.1.2 Homework assignments on RPubs
10(1)
2.1.3 Personalized mail
10(1)
2.1.4 2017 Employer Health Benefits Survey
11(1)
2.1.5 Journal articles
12(1)
2.1.6 Dashboards at eelloo
12(1)
2.1.7 Books
12(1)
2.1.8 Websites
13(1)
2.2 Compile an R Markdown document
14(2)
2.3 Cheat sheets
16(1)
2.4 Output formats
16(3)
2.5 Markdown syntax
19(5)
2.5.1 Inline formatting
19(1)
2.5.2 Block-level elements
20(3)
2.5.3 Math expressions
23(1)
2.6 R code chunks and inline R code
24(6)
2.6.1 Figures
27(2)
2.6.2 Tables
29(1)
2.7 Other language engines
30(11)
2.7.1 Python
32(2)
2.7.2 Shell scripts
34(1)
2.7.3 SQL
35(2)
2.7.4 Rcpp
37(2)
2.7.5 Stan
39(1)
2.7.6 JavaScript and CSS
39(1)
2.7.7 Julia
40(1)
2.7.8 C and Fortran
40(1)
2.8 Interactive documents
41(8)
2.8.1 HTML widgets
41(1)
2.8.2 Shiny documents
42(5)
II Output Formats 47(68)
3 Documents
49(44)
3.1 HTML document
49(14)
3.1.1 Table of contents
50(1)
3.1.2 Section numbering
51(1)
3.1.3 Tabbed sections
51(1)
3.1.4 Appearance and style
52(2)
3.1.5 Figure options
54(1)
3.1.6 Data frame printing
55(1)
3.1.7 Code folding
56(1)
3.1.8 MathJax equations
57(1)
3.1.9 Document dependencies
58(1)
3.1.10 Advanced customization
59(3)
3.1.11 Shared options
62(1)
3.1.12 HTML fragments
62(1)
3.2 Notebook
63(15)
3.2.1 Using Notebooks
63(9)
3.2.2 Saving and sharing
72(1)
3.2.3 Notebook format
73(5)
3.3 PDF document
78(7)
3.3.1 Table of contents
79(1)
3.3.2 Figure options
80(1)
3.3.3 Data frame printing
80(1)
3.3.4 Syntax highlighting
81(1)
3.3.5 LaTeX options
81(1)
3.3.6 LaTeX packages for citations
82(1)
3.3.7 Advanced customization
83(1)
3.3.8 Other features
84(1)
3.4 Word document
85(1)
3.4.1 Other features
85(1)
3.5 OpenDocument Text document
86(1)
3.5.1 Other features
86(1)
3.6 Rich Text Format document
87(1)
3.6.1 Other features
87(1)
3.7 Markdown document
88(2)
3.7.1 Markdown variants
88(1)
3.7.2 Other features
89(1)
3.8 R package vignette
90(3)
4 Presentations
93(22)
4.1 ioslides presentation
93(9)
4.1.1 Display modes
95(1)
4.1.2 Incremental bullets
95(1)
4.1.3 Visual appearance
96(2)
4.1.4 Code highlighting
98(1)
4.1.5 Adding a logo
98(1)
4.1.6 Tables
99(1)
4.1.7 Advanced layout
100(1)
4.1.8 Text color
100(1)
4.1.9 Presenter mode
101(1)
4.1.10 Printing and PDF output
101(1)
4.1.11 Custom templates
101(1)
4.1.12 Other features
102(1)
4.2 Slidy presentation
102(4)
4.2.1 Display modes
104(1)
4.2.2 Text size
104(1)
4.2.3 Footer elements
105(1)
4.2.4 Other features
105(1)
4.3 Beamer presentation
106(3)
4.3.1 Themes
107(1)
4.3.2 Slide level
108(1)
4.3.3 Other features
109(1)
4.4 PowerPoint presentation
109(8)
4.4.1 Custom templates
112(1)
4.4.2 Other features
113(2)
III Extensions 115(122)
5 Dashboards
117(20)
5.1 Layout
118(6)
5.1.1 Row-based layouts
120(1)
5.1.2 Attributes on sections
120(1)
5.1.3 Multiple pages
121(2)
5.1.4 Story boards
123(1)
5.2 Components
124(7)
5.2.1 Value boxes
125(1)
5.2.2 Gauges
126(2)
5.2.3 Text annotations
128(2)
5.2.4 Navigation bar
130(1)
5.3 Shiny
131(6)
5.3.1 Getting started
132(1)
5.3.2 A Shiny dashboard example
132(3)
5.3.3 Input sidebar
135(1)
5.3.4 Learning more
135(2)
6 Tufte Handouts
137(10)
6.1 Headings
138(1)
6.2 Figures
139(2)
6.2.1 Margin figures
139(1)
6.2.2 Arbitrary margin content
139(1)
6.2.3 Full-width figures
140(1)
6.2.4 Main column figures
141(1)
6.3 Sidenotes
141(1)
6.4 References
142(1)
6.5 Tables
143(1)
6.6 Block quotes
143(1)
6.7 Responsiveness
144(1)
6.8 Sans-serif fonts and epigraphs
145(1)
6.9 Customize CSS styles
145(2)
7 xaringan Presentations
147(18)
7.1 Get started
148(1)
7.2 Keyboard shortcuts
149(1)
7.3 Slide formatting
150(7)
7.3.1 Slides and properties
150(2)
7.3.2 The title slide
152(1)
7.3.3 Content classes
153(1)
7.3.4 Incremental slides
154(1)
7.3.5 Presenter notes
155(1)
7.3.6 yolo: true
156(1)
7.4 Build and preview slides
157(1)
7.5 CSS and themes
158(1)
7.6 Some tips
159(6)
7.6.1 Autoplay slides
159(1)
7.6.2 Countdown timer
160(1)
7.6.3 Highlight code lines
160(1)
7.6.4 Working offline
161(1)
7.6.5 Macros
162(1)
7.6.6 Disadvantages
163(2)
8 reveal.js Presentations
165(10)
8.1 Display modes
166(1)
8.2 Appearance and style
167(1)
8.2.1 Smaller text
167(1)
8.3 Slide transitions
168(1)
8.4 Slide backgrounds
169(1)
8.5 2-D presenations
169(1)
8.6 Custom CSS
170(1)
8.6.1 Slide IDs and classes
170(1)
8.6.2 Styling text spans
171(1)
8.7 reveal.js options
171(1)
8.8 reveal.js plugins
172(1)
8.9 Other features
173(2)
9 Community Formats
175(6)
9.1 Lightweight Pretty HTML Documents
175(2)
9.1.1 Usage
176(1)
9.1.2 Package vignettes
176(1)
9.2 The rmdformats package
177(2)
9.3 Shower presentations
179(2)
10 Websites
181(20)
10.1 Get started
182(1)
10.2 The directory structure
183(1)
10.3 Deployment
184(1)
10.4 Other site generators
185(1)
10.5 rmarkdown's site generator
185(16)
10.5.1 A simple example
186(1)
10.5.2 Site authoring
187(3)
10.5.3 Common elements
190(3)
10.5.4 Site navigation
193(2)
10.5.5 HTML generation
195(1)
10.5.6 Site configuration
196(1)
10.5.7 Publishing websites
197(1)
10.5.8 Additional examples
197(1)
10.5.9 Custom site generators
198(3)
11 HTML Documentation for R Packages
201(4)
11.1 Get started
201(1)
11.2 Components
202(3)
11.2.1 Home page
203(1)
11.2.2 Function reference
203(1)
11.2.3 Articles
204(1)
11.2.4 News
204(1)
11.2.5 Navigation bar
204(1)
12 Books
205(14)
12.1 Get started
206(1)
12.2 Project structure
207(2)
12.2.1 Index file
208(1)
12.2.2 Rmd files
208(1)
12.2.3 _bookdown.yml
209(1)
12.2.4 _output.yml
209(1)
12.3 Markdown extensions
209(4)
12.3.1 Number and reference equations
210(1)
12.3.2 Theorems and proofs
210(1)
12.3.3 Special headers
211(1)
12.3.4 Text references
211(1)
12.3.5 Cross referencing
212(1)
12.4 Output Formats
213(2)
12.4.1 HTML
213(1)
12.4.2 LaTeX/PDF
214(1)
12.4.3 E-books
214(1)
12.4.4 A single document
214(1)
12.5 Editing
215(1)
12.5.1 Build the book
215(1)
12.5.2 Preview a chapter
216(1)
12.5.3 Serve the book
216(1)
12.5.4 RStudio addins
216(1)
12.6 Publishing
216(3)
12.6.1 RStudio Connect
217(1)
12.6.2 Other services
217(1)
12.6.3 Publishers
217(2)
13 Journals
219(8)
13.1 Get started
219(3)
13.2 rticles templates
222(1)
13.3 Using a template
222(2)
13.4 LaTeX content
224(1)
13.5 Linking with bookdown
224(1)
13.6 Contributing templates
225(2)
14 Interactive Tutorials
227(10)
14.1 Get started
227(2)
14.2 Tutorial types
229(1)
14.3 Exercises
230(3)
14.3.1 Solutions
230(1)
14.3.2 Hints
231(2)
14.4 Quiz questions
233(1)
14.5 Videos
234(1)
14.6 Shiny components
235(1)
14.7 Navigation and progress tracking
235(2)
IV Other Topics 237(62)
15 Parameterized reports
239(8)
15.1 Declaring parameters
239(1)
15.2 Using parameters
240(1)
15.3 Knitting with parameters
241(3)
15.3.1 The Knit button
241(1)
15.3.2 Knit with custom parameters
241(1)
15.3.3 The interactive user interface
242(2)
15.4 Publishing
244(3)
16 HTML Widgets
247(26)
16.1 Overview
247(1)
16.2 A widget example (sigma.js)
248(8)
16.2.1 File layout
249(1)
16.2.2 Dependencies
250(1)
16.2.3 R binding
250(2)
16.2.4 JavaScript binding
252(3)
16.2.5 Demo
255(1)
16.3 Creating your own widgets
256(2)
16.3.1 Requirements
256(1)
16.3.2 Scaffolding
257(1)
16.3.3 Other packages
258(1)
16.4 Widget sizing
258(6)
16.4.1 Specifying a sizing policy
259(1)
16.4.2 JavaScript resize method
260(4)
16.5 Advanced topics
264(9)
16.5.1 Data transformation
264(5)
16.5.2 Passing JavaScript functions
269(1)
16.5.3 Custom widget HTML
270(1)
16.5.4 Create a widget without an R package
271(2)
17 Document Templates
273(6)
17.1 Template structure
274(2)
17.2 Supporting files
276(1)
17.3 Custom Pandoc templates
277(1)
17.4 Sharing your templates
278(1)
18 Creating New Formats
279(4)
18.1 Deriving from built-in formats
279(1)
18.2 Fully custom formats
280(2)
18.3 Using a new format
282(1)
19 Shiny Documents
283(16)
19.1 Getting started
283(4)
19.2 Deployment
287(2)
19.2.1 ShinyApps.io
287(1)
19.2.2 Shiny Server/RStudio Connect
288(1)
19.3 Embedded Shiny apps
289(1)
19.3.1 Inline applications
289(1)
19.3.2 External applications
290(1)
19.4 Shiny widgets
290(3)
19.4.1 The shinyApp() function
290(1)
19.4.2 Example: k-Means clustering
291(2)
19.4.3 Widget size and layout
293(1)
19.5 Multiple pages
293(1)
19.6 Delayed rendering
294(1)
19.7 Output arguments for render functions
294(5)
19.7.1 A caveat
297(2)
Bibliography 299(4)
Index 303
Yihui Xie is a software engineer at RStudio. He has authored and co-authored several R packages, including knitr, rmarkdown, bookdown, blogdown, shiny, xaringan, and animation. He has published three other books, Dynamic Documents with R and knitr, bookdown: Authoring Books and Technical Documents with R Markdown, and blogdown: Creating Websites with R Markdown.

J.J. Allaire is the founder of RStudio and the creator of the RStudio IDE. He is an author of several packages in the R Markdown ecosystem including rmarkdown, flexdashboard, learnr, and radix.

Garrett Grolemund is the co-author of R for Data Science and author of Hands-On Programming with R. He wrote the lubridate R package and works for RStudio as an advocate who trains engineers to do data science with R and the Tidyverse.