Rmarkdown Html

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In this tutorial, we will cover the R knitr package that is used to convertR Markdown into a rendered document (HTML, PDF, etc).

By default R Markdown produces standalone HTML files with no external dependencies, using data: URIs to incorporate the contents of linked scripts, stylesheets, images, and videos. This means you can share or publish the file just like you share Office documents or PDFs. Rstudio and R users in general can benefit from Rmarkdown for producing reproducible reports. R Markdown is an easy-to-write plain text format for creating dynamic documents and reports. 7.9 Use a custom HTML template (.) R Markdown Cookbook This book showcases short, practical examples of lesser-known tips and tricks to helps users get the most out of these tools. After reading this book, you will understand how R Markdown documents are transformed from plain text and how you may customize nearly every step of this processing.

Learning Objectives

At the end of this activity, you will:

  • Be able to produce (‘knit’) an HTML file from a R Markdown file.
  • Know how to modify chunk options to change the output in your HTML file.

Things You’ll Need To Complete This Tutorial

You will need the most current version of R and, preferably, RStudio loaded onyour computer to complete this tutorial.

Install R Packages

  • knitr:install.packages('knitr')
  • rmarkdown:install.packages('rmarkdown')

Share & Publish Results Directly from Your Code!

The knitr package allow us to:

  • Publish & share preliminary results with collaborators.
  • Create professional reports that document our workflow and results directlyfrom our code, reducing the risk of accidental copy and paste or transcription errors.
  • Document our workflow to facilitate reproducibility.
  • Efficiently change code outputs (figures, files) given changes in the data, methods, etc.

Publish from Rmd files with knitr

To complete this tutorial you need:

  1. The R knitr package to complete this tutorial. If you need help installing packages, visit the R packages tutorial.
  2. An R Markdown document that contains a YAML header, code chunks and markdownsegments. If you don't have an .Rmd file, visit the R Markdown tutorial to create one.

When To Knit: Knitting is a useful exercisethroughout your scientific workflow. It allows you to see what your outputslook like and also to test that your code runs without errors.The time required to knit depends on the length and complexity of the scriptand the size of your data.

How to Knit

To knit in RStudio, click the knit pull down button. You want to use the
knit HTML for this lesson.

When you click the Knit HTML button, a window will open in your console titled R Markdown. Thispane shows the knitting progress. The output (HTML in this case) file willautomatically be saved in the current working directory. If there is an errorin the code, an error message will appear with a line number in the R Consoleto help you diagnose the problem.

Data Tip: You can run knitr from the command promptusing: render(“input.Rmd”, “all”).

Activity: Knit Script

Knit the .Rmd file that you built inthe last tutorial.What does it look like?

View the Output

When knitting is complete, the new HTML file produced will automatically open.

Notice that information from the YAML header (title, author, date) is printedat the top of the HTML document. Then the HTML shows the text, code, andresults of the code that you included in the RMD document.


Data Institute Participants: Complete Week 2 Assignment

  • Read this week’s assignment closely.
  • Be sure to carefully check your knitr output to make sure it is rendering theway you think it should!
  • When you are complete, submit your .Rmd and .html files to the NEON Institute participants GitHub repository (NEONScience/DI-NEON-participants).
  • The files will have automatically saved to your R working directory, you will need to transfer the files to the /participants/pre-institute3-rmd/ directory and submitted via a pull request.

Table of Contents

You can add a table of contents using the toc option and specify the depth of headers that it applies to using the toc_depth option. For example:

If the table of contents depth isn’t explicitly specified then it defaults to 3 (meaning that all level 1, 2, and 3 headers will be included in the table of contents).

Floating TOC

You can specify the toc_float option to float the table of contents to the left of the main document content. The floating table of contents will always be visible even when the document is scrolled. For example:

You may optionally specify a list of options for the toc_float parameter which control it’s behavior. Options include:

  • collapsed (defaults to TRUE) controls whether the table of contents appers with only the top-level (e.g. H2) headers. When collapsed the table of contents is automatically expanded inline when necessary.

  • smooth_scroll (defaults to TRUE) controls whether page scrolls are animated when table of contents items are navigated to via mouse clicks.

For example:


Support for floating table of contents is only available in very recent versions of the rmarkdown package. You can install the most current version as follows:

Section Numbering

R Markdown Html

You can add section numbering to headers using the number_sections option:

Note that if you do choose to use the number_sections option you will likely also want to use # (H1) headers in your document as ## (H2) headers will include a decimal point.