In the previous tutorials we’ve learned about the R Markdown format and how to create a report using R Markdown in RStudio. In this tutorial, we will render or knit an R Markdown document to a web friendly, html format using the Rknitr package. knitr can be used to convert R Markdown files to many different formats including: html, pdf, GitHub markdown (.md) and more.

Learning Objectives

At the end of this lesson, you will:

R Markdown Tables

• The first official book authored by the core R Markdown developers that provides a comprehensive and accurate reference to the R Markdown ecosystem. With R Markdown, you can easily create reproducible data analysis reports, presentations, dashboards, interactive applications, books, dissertations, websites, and journal articles, while enjoying the simplicity of Markdown and the great power of.
• Rich Markdown editor StackEdit’s Markdown syntax highlighting is unique. The refined text formatting of the editor helps you visualize the final rendering of your files.

• Be able to produce (knit) an html file from an R Markdown file.
• Know how to modify chuck options to change what is rendered and not rendered on the output html file.

What You Need

You will need the most current version of R and, preferably, RStudio loaded on your computer to complete this tutorial. You will also need an R Markdown document that contains a YAML header, code chunks and markdown segments.

Install R Packages

Secure Markdown Formatter. It free and easy to use and formatter and Markdown Beautifier also Support Markdown File and URL. Knitr is the R package that we use to convert an R Markdown document into another, more user friendly format like.html or.pdf. The knitr package allows us to. Publish & share preliminary results with collaborators. Create professional reports that document our workflow and results directly from our code, reducing the risk of accidental copy and paste or transcription errors.

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

What is Knitr?

knitr is the R package that we use to convert an R Markdown document into another, more user friendly format like .html or .pdf.

The knitr package allows us to:

• Publish & share preliminary results with collaborators.
• Create professional reports that document our workflow and results directly from 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.

The knitr package was designed to be a transparent engine for dynamic report generation with R – Yihui Xi – knitr package creator

When To Knit: Knitting is a useful exercise throughout your scientific workflow. It allows you to see what your outputs look like and also to test that your code runs without errors. The time required to knit depends on the length and complexity of the script and 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 option for this lesson.

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

Data tip: You can run knitr from the command prompt using: render(“input.Rmd”, “all”).

R Markdown Online Compiler

View the Output

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

Notice that information from the YAML header (title, author, date) is printed at the top of the HTML document. Then the html shows the text, code, and results of the code that you included in the Rmd document.

R Markdown To Pdf Online

Challenge Activity

Add the code below to your .Rmd document. Then knit to .html format.

When you knit your .Rmd file to pdf, the plot you produce should look like the one below. Not so pretty, eh? Don’t worry - we will learn more about plotting in a later tutorial!

Where is the File?

R Markdown Online Game

In the steps above, we downloaded a file. However, where did that file go on your computer? Let’s find it before we go any further.

R Markdown List

Is the boulder-precip.csv file there?