R Markdown Cookbook (Chapman & Hall/CRC The R Series)

Cover
Half Title
Title Page
Copyright Page
Dedication
Table of Contents
List of Tables
List of Figures
Preface
About the Authors
1 Installation
	1.1 Use a Pandoc version not bundled with the RStudio IDE
	1.2 Install LaTeX (TinyTeX) for PDF reports
	1.3 Install missing LaTeX packages
2 Conceptual Overview
	2.1 What happens when we render?
	2.2 R Markdown anatomy
		2.2.1 YAML metadata
		2.2.2 Narrative
		2.2.3 Code chunks
		2.2.4 Document body
	2.3 What can we change to change the results?
3 Basics
	3.1 Code chunks and inline R code
	3.2 Write Markdown in the RStudio visual editor
	3.3 Render an R script to a report
	3.4 Convert R Markdown to R script
	3.5 R Markdown Notebooks
4 Document Elements
	4.1 Insert page breaks
	4.2 Set the document title dynamically
	4.3 Access the document metadata in R code
	4.4 Unnumbered sections
	4.5 Bibliographies and citations
		4.5.1 Changing citation style
		4.5.2 Add an item to a bibliography without using it
		4.5.3 Add all items to the bibliography
		4.5.4 Include appendix after bibliography (*)
	4.6 Generate R package citations
	4.7 Cross-referencing within documents
	4.8 Update the date automatically
	4.9 Multiple authors in a document
	4.10 Numbered figure captions
	4.11 Combine words into a comma-separated phrase
	4.12 Preserve a large number of line breaks
	4.13 Convert models to equations
	4.14 Create an animation from multiple R plots
	4.15 Create diagrams
		4.15.1 Basic diagrams
		4.15.2 Adding parameters to plots
		4.15.3 Other packages for making diagrams
	4.16 Escape special characters
	4.17 Comment out text
	4.18 Omit a heading in the table of contents
	4.19 Put together all code in the appendix (*)
	4.20 Manipulate Markdown via Pandoc Lua filters (*)
5 Formatting
	5.1 Fontcolor
		5.1.1 Using an R function to write raw HTML or LaTeX code
		5.1.2 Using a Pandoc Lua filter (*)
	5.2 Indent text
	5.3 Control the width of text output
	5.4 Control the size of plots/images
	5.5 Figure alignment
	5.6 Verbatim code chunks
		5.6.1 Show a verbatim inline expression
	5.7 Line numbers for code blocks (*)
	5.8 Multi-column layout (*)
6 LaTeX Output
	6.1 Add LaTeX code to the preamble
	6.2 Pandoc options for LaTeX output
	6.3 Add logo to title page
	6.4 Include additional LaTeX packages
		6.4.1 Loading LaTeX packages
		6.4.2 Example packages
	6.5 Control the placement of figures
		6.5.1 Floating environments
		6.5.2 Prevent figures from floating
		6.5.3 Force floats forward
		6.5.4 Adjust LaTeX placement rules (*)
	6.6 LaTeX sub-figures
	6.7 Render documents containing Unicode characters
	6.8 Generate a LaTeX fragment
	6.9 Add custom headers and footers (*)
	6.10 Use a custom Pandoc LaTeX template (*)
	6.11 Write raw LaTeX code
	6.12 For hardcore LaTeX users (*)
7 HTML Output
	7.1 Apply custom CSS
	7.2 Center section headings
	7.3 Style code blocks and text output
	7.4 Scrollable code blocks (*)
	7.5 Fold all code blocks but show some initially
	7.6 Put content in tabs
	7.7 Embed the Rmd source file in the HTML output file
	7.8 Embed arbitrary files in the HTML output file
	7.9 Use a custom HTML template (*)
	7.10 Include the content of an existing HTML file (*)
	7.11 Add a custom browser icon
	7.12 Use the 
 disclosure element
	7.13 Sharing HTML output on the web
		7.13.1 R-specific services
		7.13.2 Static website services
	7.14 Improve accessibility of HTML pages
	7.15 For hardcore HTML users (*)
8 Word
	8.1 Custom Word templates
	8.2 The two-way workflow between R Markdown and Word
	8.3 Style individual elements
9 Multiple Output Formats
	9.1 LaTeX or HTML output
	9.2 Display HTML widgets
	9.3 Embed a web page
	9.4 Multiple figures side by side
	9.5 Write raw content (*)
	9.6 Custom blocks (*)
		9.6.1 Syntax
		9.6.2 Adding a shaded box
		9.6.3 Including icons
10 Tables
	10.1 The function knitr::kable()
		10.1.1 Supported table formats
		10.1.2 Change column names
		10.1.3 Specify column alignment
		10.1.4 Add a table caption
		10.1.5 Format numeric columns
		10.1.6 Display missing values
		10.1.7 Escape special characters
		10.1.8 Multiple tables side by side
		10.1.9 Generate multiple tables from a for-loop (*)
		10.1.10 Customize LaTeX tables (*)
		10.1.11 Customize HTML tables (*)
	10.2 The kableExtra package
		10.2.1 Set the font size
		10.2.2 Style specific rows/columns
		10.2.3 Group rows/columns
		10.2.4 Scaling down wide tables in LaTeX
	10.3 Other packages for creating tables
11 Chunk Options
	11.1 Use variables in chunk options
	11.2 Do not stop on error
	11.3 Multiple graphical output formats for the same plot
	11.4 Cache time-consuming code chunks
	11.5 Cache a code chunk for multiple output formats
	11.6 Cache large objects
	11.7 Hide code, text output, messages, or plots
	11.8 Hide everything from a chunk
	11.9 Collapse text output blocks into source blocks
	11.10 Reformat R source code
	11.11 Output text as raw Markdown content (*)
	11.12 Remove leading hashes in text output
	11.13 Add attributes to text output blocks (*)
	11.14 Post-process plots (*)
	11.15 High-quality graphics (*)
	11.16 Step-by-step plots with low-level plotting functions (*)
	11.17 Customize the printing of objects in chunks (*)
	11.18 Option hooks (*)
12 Output Hooks (*)
	12.1 Redact source code
	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
13 Chunk Hooks
	13.1 Crop plots
	13.2 Optimize PNG plots
	13.3 Report how much time each chunk takes to run
	13.4 Show the chunk header in the output
	13.5 Embed an interactive 3D plot with rgl
14 Miscellaneous knitr Tricks
	14.1 Reuse code chunks
		14.1.1 Embed one chunk in another chunk (*)
		14.1.2 Use the same chunk label in another chunk
		14.1.3 Use reference labels (*)
	14.2 Use an object before it is created (*)
	14.3 Exit knitting early
	14.4 Generate a plot and display it elsewhere
	14.5 Modify a plot in a previous code chunk
	14.6 Save a group of chunk options and reuse them (*)
	14.7 Use knitr::knit_expand () to generate Rmd source
	14.8 Allow duplicate labels in code chunks (*)
	14.9 A more transparent caching mechanism
		14.9.1 Invalidate the cache by changing code in the expression
		14.9.2 Invalidate the cache by changes in global variables
		14.9.3 Keep multiple copies of the cache
		14.9.4 Comparison with knitr’s caching
15 Other Languages
	15.1 Register a custom language engine (*)
	15.2 Run Python code and interact with Python
	15.3 Execute content conditionally via the asis engine
	15.4 Execute Shell scripts
	15.5 Visualization with D3
	15.6 Write the chunk content to a file via the cat engine
		15.6.1 Write to a CSS file
		15.6.2 Include LaTeX code in the preamble
		15.6.3 Write YAML data to a file and also display it
	15.7 Run SAS code
	15.8 Run Stata code
	15.9 Create graphics with Asymptote
		15.9.1 Generate data in Rand read it in Asymptote
	15.10 Style HTML pages with Sass/SCSS
16 Managing Projects
	16.1 Source external R scripts
	16.2 Read external scripts into a chunk
	16.3 Read multiple code chunks from an external script (*)
	16.4 Child documents (*)
	16.5 Keep the plot files
	16.6 The working directory for R code chunks
	16.7 R package vignettes
	16.8 R Markdown templates in R packages
		16.8.1 Template use-cases
		16.8.2 Template setup
	16.9 Write books and long-form reports with bookdown
	16.10 Build websites with blogdown
17 Workflow
	17.1 Use RStudio keyboard shortcuts
	17.2 Spell-check R Markdown
	17.3 Render R Markdown with rmarkdown::render ()
	17.4 Parameterized reports
	17.5 Customize the Knit button (*)
	17.6 Collaborate on Rmd documents through Google Drive
	17.7 Organize an R Markdown project into a research website with workflowr
	17.8 Send emails based on R Markdown
Appendix
	A knitr’s Chunk and Package Options
		A.1 Chunk options
			A.1.1 Code evaluation
			A.1.2 Text output
			A.1.3 Code decoration
			A.1.4 Cache
			A.1.5 Plots
			A.1.6 Animation
			A.1.7 Code chunk
			A.1.8 Child documents
			A.1.9 Language engines
			A.1.10 Option templates
			A.1.11 Extracting source code
			A.1.12 Other chunk options
		A.2 Package options
Bibliography
Index