R Markdown Cookbook (Paperback, 1)

Installation Use a Pandoc version not bundled with the RStudio IDE Install LaTeX (TinyTeX) for PDF reports Install missing LaTeX packages 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? 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 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 (*) 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 (*) 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 (*) 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 <details> 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 Appendix A knitr’s Chunk and Package Options