R Markdown provides a powerful formatting syntax for diverse types of content generation in R, a programming language highly regarded for statistical computing and data analysis.
Markdown itself is straightforward, designed to be as readable as possible, and R Markdown extends this by allowing the integration of R code into the text.
This means that one may include code chunks within their document that can be evaluated and have their results automatically included in the output.
The formatting of an R Markdown document is highly customizable. It can accommodate everything from markdown syntax, section headers, and LaTeX equations to complex figure options and footnotes.
An R Markdown document starts with a YAML header that specifies the document type, title, output options, and other metadata, followed by the body where the content resides.
Users can manipulate the styling and presentation of the document via Pandoc’s markdown, a versatile tool that R Markdown relies on to convert documents into various formats.
Special features that make R Markdown an indispensable tool for data analysis include syntax highlighting, which makes code easier to read, and the ability to embed inline code along with its output.
This means that analyses described in the text can be substantiated by live results from the executed code, providing a dynamic and robust report.
Knitr is an essential package that processes the document, running the embedded R code and inserting results into the text.
Headings and subheadings can be created using markdown syntax to structure the document efficiently, and users can even incorporate math equations in their reports, all leading to the creation of a sophisticated HTML output or PDF document amongst other formats.
Basic Markdown Elements in R
R Markdown allows users to combine narrative text with code in a single document, facilitating dynamic report generation.
This section introduces fundamental markdown syntax to format text, create lists, add headers, incorporate links, images, and integrate code in R Markdown documents.
Text Formatting
In R Markdown, one can apply emphasis by wrapping text in single asterisks or underscores, like *italic* or _italic_.
For bold text, use double asterisks or underscores: **bold** or __bold__.
Combine both to create bold italic text: ***bold italic***.
Superscript is achieved with caret signs, for example, super^script^. To strike through text, use two tildes: ~~strikethrough~~.
A manual line break is inserted with two spaces followed by an enter key.
Lists and Bullet Points
- Unordered lists are created using asterisks, plus signs, or hyphens:
* item 1+ item 2- item 3
- To create sub-items, indent the bullet point by two spaces or a tab.
- Ordered lists are created with numbers followed by periods:
1. First item2. Second item
- Adding a backslash before a period prevents the number from being interpreted as a list item.
Headers and Sections
Headers in R Markdown are designated with hash symbols (#):
# Header 1for top-level headers (H1)## Header 2for second-level headers (H2)### Header 3for third-level headers (H3)
A horizontal rule—for visual section separation—is produced with three or more hyphens, asterisks, or underscores: ---, ***, or ___.
Adding Links and Images
- Links are included using square brackets for text followed by parentheses for the URL:
[link](http://example.com). - Images use a similar syntax, prefixed with an exclamation point:
.
Both links and images can include optional titles within the parentheses after the URL: [link](http://example.com "Title").
Code Integration
- Plain code blocks are wrapped in triple backticks with optional language identifier:
print("Hello World") - R code chunks are created with triple backticks followed by
{r}:```{r} summary(cars) - Inline code is delimited with single backticks:
A `code` example. - Page breaks are created using the LaTeX command
\newpagewithin R Markdown.
Advanced R Markdown Features
R Markdown provides a suite of advanced features that allow for more sophisticated documents. These include customization of document output through YAML headers, advanced table formatting, cross-referencing, and support for complex mathematical equations.
YAML Headers and Output Formats
The YAML header in an R Markdown document specifies how the document should be rendered. It controls the output format be it HTML, PDF, or Word, among others.
Users can set various output options including html_document, pdf_document, or word_document.
Advanced settings within the YAML headers can further customize the appearance and functionality of the output. For instance, they can specify a table of contents, adjust toc_depth, or add a floating toc_float.
output:
html_document:
toc: true
toc_float:
collapsed: false
smooth_scroll: true
toc_depth: 2
Additionally, HTML-specific features such as custom CSS styles can be included in the YAML to enhance the visual format of the html_output.
Tables and Cross-referencing
R Markdown supports advanced table features using packages like knitr and kableExtra.
These features allow users to create well-formatted tables that can also be cross-referenced within the text.
The kable function from knitr creates LaTeX or HTML tables, while kableExtra offers further customizations such as striped rows, resizing, and text formatting.
Cross-referencing within R Markdown documents is facilitated by the bookdown package.
Users can assign labels to tables, figures, and other elements using the syntax (ref:label) and then reference them with @ref(label), ensuring that references are dynamically updated.
knitr::kable(head(mtcars), caption = "A subset of the mtcars dataset.")
Math and Equations
R Markdown natively supports LaTeX for writing mathematical notation.
Equations can be embedded inline using the $...$ syntax, or as blocks using $$...$$ for more complex latex_equations.
For users who are not familiar with LaTeX, cheat sheets are available to help with the syntax.
Here is an inline equation: $A = \pi r^{2}$.
And here is a block equation:
$$
E = mc^2
$$
RStudio, a popular integrated development environment for R, provides helpful features for writing and previewing LaTeX equations within R Markdown documents.
This robust support for LaTeX greatly enhances the ability to communicate scientific and technical content effectively.
