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R Markdown Cookbook（the 1st edition）
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3 Basics
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2021-05-07 20:26:47
Chapter 3 Basics
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7 HTML Output
7.4 Scrollable code blocks (*)
7.2 Center section headings
7.9 Use a custom HTML template (*)
7.12 Use the <details> disclosure element
7.10 Include the content of an existing HTML file (*)
7.5 Fold all code blocks but show some initially
7.15 For hardcore HTML users (*)
7.6 Put content in tabs
7.7 Embed the Rmd source file in the HTML output file
7.13 Sharing HTML output on the web
7.1 Apply custom CSS
7.11 Add a custom browser icon
7.14 Improve accessibility of HTML pages
7.3 Style code blocks and text output
7.8 Embed arbitrary files in the HTML output file
About the Authors
Yihui Xie
Emily Riederer
Christophe Dervieux
11 Chunk Options
11.2 Do not stop on error
11.13 Add attributes to text output blocks (*)
11.10 Reformat R source code
11.3 Multiple graphical output formats for the same plot
11.11 Output text as raw Markdown content (*)
11.4 Cache time-consuming code chunks
11.6 Cache large objects
11.7 Hide code, text output, messages, or plots
11.17 Customize the printing of objects in chunks (*)
11.12 Remove leading hashes in text output
11.16 Step-by-step plots with low-level plotting functions (*)
11.5 Cache a code chunk for multiple output formats
11.9 Collapse text output blocks into source blocks
11.8 Hide everything from a chunk
11.1 Use variables in chunk options
11.15 High-quality graphics (*)
11.18 Option hooks (*)
11.14 Post-process plots (*)
5 Formatting
5.8 Multi-column layout (*)
5.3 Control the width of text output
5.6 Verbatim code chunks
5.7 Line numbers for code blocks (*)
5.2 Indent text
5.1 Font color
5.4 Control the size of plots/images
5.5 Figure alignment
12 Output Hooks (*)
12.2 Add line numbers to source code
12.3 Scrollable text output
12.4 Truncate text output
12.5 Output figures in the HTML5 format
12.1 Redact source code
Preface
How to read this book
Software information and conventions
Structure of the book
Acknowledgments
8 Word
8.1 Custom Word templates
8.2 The two-way workflow between R Markdown and Word
8.3 Style individual elements
1 Installation
1.2 Install LaTeX (TinyTeX) for PDF reports
1.3 Install missing LaTeX packages
1.1 Use a Pandoc version not bundled with the RStudio IDE
9 Multiple Output Formats
9.3 Embed a web page
9.1 LaTeX or HTML output
9.6 Custom blocks (*)
9.4 Multiple figures side by side
9.2 Display HTML widgets
9.5 Write raw content (*)
13 Chunk Hooks (*)
13.1 Crop plots
13.4 Show the chunk header in the output
13.2 Optimize PNG plots
13.5 Embed an interactive 3D plot with rgl
13.3 Report how much time each chunk takes to run
References
6 LaTeX Output
6.3 Add logo to title page
6.12 For hardcore LaTeX users (*)
6.8 Generate a LaTeX fragment
6.7 Render documents containing Unicode characters
6.10 Use a custom Pandoc LaTeX template (*)
6.9 Add custom headers and footers (*)
6.2 Pandoc options for LaTeX output
6.6 LaTeX sub-figures
6.5 Control the placement of figures
6.4 Include additional LaTeX packages
6.1 Add LaTeX code to the preamble
6.11 Write raw LaTeX code
17 Workflow
17.4 Parameterized reports
17.7 Organize an R Markdown project into a research website with workflowr
17.3 Render R Markdown with rmarkdown::render()
17.8 Send emails based on R Markdown
17.6 Collaborate on Rmd documents through Google Drive
17.1 Use RStudio keyboard shortcuts
17.5 Customize the Knit button (*)
17.2 Spell-check R Markdown
4 Document Elements
4.18 Omit a heading in the table of contents
4.16 Escape special characters
4.1 Insert page breaks
4.6 Generate R package citations
4.12 Preserve a large number of line breaks
4.17 Comment out text
4.13 Convert models to equations
4.20 Manipulate Markdown via Pandoc Lua filters (*)
4.4 Unnumbered sections
4.15 Create diagrams
4.3 Access the document metadata in R code
4.7 Cross-referencing within documents
4.19 Put together all code in the appendix (*)
4.2 Set the document title dynamically
4.10 Numbered figure captions
4.5 Bibliographies and citations
4.11 Combine words into a comma-separated phrase
4.8 Update the date automatically
4.9 Multiple authors in a document
4.14 Create an animation from multiple R plots
14 Miscellaneous knitr Tricks
14.9 A more transparent caching mechanism
14.3 Exit knitting early
14.4 Generate a plot and display it elsewhere
14.1 Reuse code chunks
14.7 Use knitr::knit_expand() to generate Rmd source
14.8 Allow duplicate labels in code chunks (*)
14.2 Use an object before it is created (*)
14.6 Save a group of chunk options and reuse them (*)
14.5 Modify a plot in a previous code chunk
3 Basics
3.2 Write Markdown in the RStudio visual editor
3.1 Code chunks and inline R code
3.3 Render an R script to a report
3.4 Convert R Markdown to R script
3.5 R Markdown Notebooks
15 Other Languages
15.5 Visualization with D3
15.2 Run Python code and interact with Python
15.1 Register a custom language engine (*)
15.8 Run Stata code
15.4 Execute Shell scripts
15.3 Execute content conditionally via the asis engine
15.6 Write the chunk content to a file via the cat engine
15.7 Run SAS code
15.9 Create graphics with Asymptote
15.10 Style HTML pages with Sass/SCSS
10 Tables
10.1 The function knitr::kable()
10.3 Other packages for creating tables
10.2 The kableExtra package
2 Conceptual Overview
2.1 What happens when we render?
2.3 What can we change to change the results?
2.2 R Markdown anatomy
16 Managing Projects
16.7 R package vignettes
16.8 R Markdown templates in R packages
16.9 Write books and long-form reports with bookdown
16.6 The working directory for R code chunks
16.3 Read multiple code chunks from an external script (*)
16.5 Keep the plot files
16.1 Source external R scripts
16.2 Read external scripts into a chunk
16.10 Build websites with blogdown
16.4 Child documents (*)
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