R Markdown enables data scientists to create reproducible reports that blend code, its output, and prose commentary.
In many situations, it might be necessary to hide certain outputs when knitting documents to HTML or PDF.
This can help in making the final report more readable or in focusing on commentary and interpretation rather than raw output.
Hiding output in R Markdown can be especially useful when dealing with large datasets or when intermediate steps are required for data processing that need not be shown to the end user.
This ensures that the final document highlights important results and insights without cluttering pages with unnecessary code or voluminous output.
The flexibility of R Markdown provides several methods to suppress output, ranging from simple options within individual code chunks to more complex document-wide settings.
Understanding these options aids in tailoring reports to the desired audience, whether the priority is clear presentation, conciseness, or emphasis on interpreted results.
Basics of R Markdown
R Markdown provides an authoring framework for data science. One can integrate prose, code, and output into a single document.
R Markdown documents are fully reproducible and support a wide variety of static and dynamic output formats.
Understanding R Markdown
R Markdown is a file format combining executable R code chunks with the easy syntax of Markdown. It allows for dynamic report generation within an R environment, enabling the user to weave together narrative text and code to produce elegantly formatted output.
The knitr package is the engine behind R Markdown that knits the text and code to produce the final document.
Chunk Options and Customization
Every R Markdown document contains code chunks that can be customized using chunk options—attributes that control various aspects such as whether code should be evaluated or whether output should be included in the final document.
The echo option can be set to FALSE to hide code but show results, whereas results='hide' will not display the output.
Utilizing opts_chunk$set(), one can define default chunk options at the start of a document using a setup chunk, compelling all chunks to inherit these options unless specified otherwise.
| Chunk Option | Default | Description |
|---|---|---|
| echo | TRUE | Determines if code is displayed in the output |
| results | TRUE | Controls if outputs are included in the output |
| fig.height | 7 | Sets the default height for figures |
Output Formats and YAML Header
The output format of an R Markdown document is specified in the YAML header at the top of the document.
This header can include fields like output: html_document or output: pdf_document which tells knitr to compile the document into HTML or PDF formats respectively.
Additional options can be specified to customize the output further, such as the document’s title or the inclusion of a table of contents.
Packages loaded in the YAML header or in a setup chunk can extend the functionality of R Markdown, such as rmarkdown and bookdown, or enhance the appearance of the document.
YAML Header Example:
---
title: "Sample Document"
output: html_document
---
Advanced R Markdown Features
R Markdown allows for sophisticated data presentation and customization of document styling through a variety of features.
Users can integrate R code directly within the text or hide complex code from the output, offering a seamless integration of code execution and narrative.
Data Presentation and Visualization
When creating documents with R Markdown, one can present data effectively using tables and plots.
The knitr::kable function formats data frames and matrices into simple, elegant HTML or PDF tables.
For a higher degree of customization, kableExtra can be utilized to add features such as striped rows, resizing, and fonts.
# Example R code to generate a table using kable
library(knitr)
kable(head(mtcars), caption = "A Table of Motor Trend Car Road Tests")
For visualization, packages like ggplot2 allow the creation of high-quality graphics.
Data administrators commonly use R code chunks in R Markdown to craft plots that are automatically included in the final document.
R Markdown Extensions and Custom Styling
Advanced R Markdown documents may include custom styling and HTML output.
With the use of R Markdown extensions, the appearance and behavior of the output can be significantly enhanced.
The rmarkdown package along with HTML widgets facilitates the inclusion of interactive elements directly into the report.
Further customization is achievable with Cascading Style Sheets (CSS) and JavaScript for web-based HTML output. These tools allow one to tailor the reader’s experience beyond the default settings.
Users might specify results='hide' to omit specific R code chunks from rendering, thus maintaining the focus on the narrative and results.
By mastering these advanced features, one can transform R Markdown from a simple reporting tool into a powerful platform for data analysis and communication.
