R Markdown Cookbook

著者名：Xie, Yihui/Dervieux, Christophe/Riederer, Emily

Chapman and Hall/CRC（2020/10/21発売）

• 言語：ENG
• ISBN：9780367563820
• eISBN：9781000290882

Description

This new book written by the developers of R Markdown is an essential reference that will help users learn and make full use of the software.

Those new to R Markdown will appreciate the short, practical examples that address the most common issues users encounter. Frequent users will also benefit from the wide ranging tips and tricks that expose ‘hidden’ features, support customization and demonstrate the many new and varied applications of the software.

After reading this book users will learn how to:

• Enhance your R Markdown content with diagrams, citations, and dynamically generated text
• Streamline your workflow with child documents, code chunk references, and caching
• Control the formatting and layout with Pandoc markdown syntax or by writing custom HTML and LaTeX templates
• Utilize chunk options and hooks to fine-tune how your code is processed
• Switch between different language engineers to seamlessly incorporate python, D3, and more into your analysis

Table of Contents

1. Installation

Use a Pandoc version not bundled with the RStudio IDE

Install LaTeX (TinyTeX) for PDF reports

Install missing LaTeX packages

2. Conceptual Overview

What happens when we render?

R Markdown anatomy

YAML metadata

Narrative

Code chunks

Document body

What can we change to change the results?

3. Basics

Code chunks and inline R code

Write Markdown in the RStudio visual editor

Render an R script to a report

Convert R Markdown to R script

R Markdown Notebooks

4. Document Elements

Insert page breaks

Set the document title dynamically

Access the document metadata in R code

Unnumbered sections

Bibliographies and citations

Changing citation style

Add an item to bibliography without using it

Add all items to bibliography

Include appendix after bibliography (*)

Generate R package citations

Cross-referencing within documents

Update the date automatically

Multiple authors in a document

Numbered figure captions

Combine words into a comma-separated phrase

Preserve a large number of linebreaks

Convert models to equations

Create an animation from multiple R plots

Create diagrams

Basic diagrams

Adding parameters to plots

Other packages for making diagrams

Escape special characters

Comment out text

Omit a heading in the table of contents

Put together all code in the appendix (*)

Manipulate Markdown via Pandoc Lua filters (*)

5. Formatting

Font color

Using an R function to write raw HTML or LaTeX code

Using a Pandoc Lua filter (*)

Indent text

Control the width of text output

Control the size of plots/images

Figure alignment

Verbatim code chunks

Show a verbatim inline expression

Line numbers for code blocks (*)

Multi-column layout (*)

6. LaTeX Output

Add LaTeX code to the preamble

Pandoc options for LaTeX output

Add logo to title page

Include additional LaTeX packages

Loading LaTeX packages

Example packages

Control the placement of figures

Floating environments

Prevent figures from floating

Force floats forwards

Adjust LaTeX placement rules (*)

LaTeX sub-figures

Render documents containing Unicode characters

Generate a LaTeX fragment

Add custom headers and footers (*)

Use a custom Pandoc LaTeX template (*)

Write raw LaTeX code

For hardcore LaTeX users (*)

7. HTML Output

Apply custom CSS

Center section headings

Style code blocks and text output

Scrollable code blocks (*)

Fold all code blocks but show some initially

Put content in tabs

Embed the Rmd source file in the HTML output file

Embed arbitrary files in the HTML output file

Use a custom HTML template (*)

Include the content of an existing HTML file (*)

Add a custom browser icon

Use the

disclosure element

Sharing HTML output on the web

R-specific services

Static website services

Improve accessibility of HTML pages

For hardcore HTML users (*)

Word

Custom Word templates

The two-way workflow between R Markdown and Word

Style individual elements

Multiple Output Formats

LaTeX or HTML output

Display HTML widgets

Embed a web page

Multiple figures side-by-side

Write raw content (*)

Custom blocks (*)

Syntax

Adding a shaded box

Including icons

Tables

The function knitr::kable()

Supported table formats

Change column names

Specify column alignment

Add a table caption

Format numeric columns

Display missing values

Escape special characters

Multiple tables side by side

Generate multiple tables from a for-loop (*)

Customize LaTeX tables (*)

Customize HTML tables (*)

The kableExtra package

Set the font size

Style specific rows/columns

Group rows/columns

Scaling down wide tables in LaTeX

Other packages for creating tables

Chunk Options

Use variables in chunk options

Do not stop on error

Multiple graphical output formats for the same plot

Cache time-consuming code chunks

Cache a code chunk for multiple output formats

Cache large objects

Hide code, text output, messages, or plots

Hide everything from a chunk

Collapse text output blocks into source blocks

Reformat R source code

Output text as raw Markdown content (*)

Remove leading hashes in text output

Add attributes to text output blocks (*)

Post-process plots (*)

High-quality graphics (*)

Step-by-step plots with low-level plotting functions (*)

Customize the printing of objects in chunks (*)

Option hooks (*)

Output Hooks (*)

Redact source code

Add line numbers to source code

Scrollable text output

Truncate text output

Output figures in the HTML format

Chunk Hooks (*)

Crop plots

Optimize PNG plots

Report how much time each chunk takes to run

Show the chunk header in the output

Embed an interactive D plot with rgl

Miscellaneous knitr Tricks

Reuse code chunks

Embed one chunk in another chunk (*)

Use the same chunk label in another chunk

Use reference labels (*)

Use an object before it is created (*)

Exit knitting early

Generate a plot and display it elsewhere

Modify a plot in a previous code chunk

Save a group of chunk options and reuse them (*)

Use knitr::knit_expand() to generate Rmd source

Allow duplicate labels in code chunks (*)

A more transparent caching mechanism

Invalidate the cache by changing code in the expression

Invalidate the cache by changes in global variables

Keep multiple copies of the cache

Comparison with knitr’s caching

Other Languages

Register a custom language engine (*)

Run Python code and interact with Python

Execute content conditionally via the asis engine

Execute Shell scripts

Visualization with D

Write the chunk content to a file via the cat engine

Write to a CSS file

Include LaTeX code in the preamble

Write YAML data to a file and also display it

Run SAS code

Run Stata code

Create graphics with Asymptote

Generate data in R and read it in Asymptote

Style HTML pages with Sass/SCSS

Managing Projects

Source external R scripts

Read external scripts into a chunk

Read multiple code chunks from an external script (*)

Child documents (*)

Keep the plot files

The working directory for R code chunks

R package vignettes

R Markdown templates in R packages

Template use-cases

Template set-up

Write books and long-form reports with bookdown

Build websites with blogdown

Workflow

          Use RStudio keyboard shortcuts

          Spell check R Markdown

          Render R Markdown with rmarkdown::render()

          Parameterized reports

          Customize the Knit button (*)

          Collaborate on Rmd documents through Google Drive

          Organize an R Markdown project into a research website with workflowr

          Send Emails based on R Markdown