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

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 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.

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 markdown segments. If you don't have an .Rmd file, visit the R Markdown tutorial to create one.

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. 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.

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 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.