Generate Pdf From Markdown

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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

Script to recursively generate PDF files from markdown files in the current directory and its subfolders using 'pandoc'. A comparison of the survey results between the year 2019 and 2020 generated as an R Markdown pdf (Click on the picture above to see the entire PDF document) Styling an R Markdown documents. Styling the document may be a little trickier than dealing with R itself. R Markdown doesn’t provide too many styling options out of the box.

At the end of this lesson, you will:

  • 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.
  1. Visual Studio Code User and Workspace Settings. Select File Preferences UserSettings or Workspace Settings. Find markdown-pdf settings in the Default Settings. Copy markdown-pdf. settings. Paste to the settings.json, and change the value.
  2. The command scans for all the markdown files and passes them as arguments to pandoc. And this wraps up how I wrote my book in markdown! I’m so thankful to Adam Wathan for sharing his code with me. I don’t know how I would have been able to create the PDF that I wanted without it. It’s in that spirit that I wrote this article.

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.

Convert

Install R Packages

Markdown
  • 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:

Markdown To Pdf Vscode

  • 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

Generate Pdf From Markdown Online

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”).

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.

Github

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!

Generate Pdf From Markdown File

Where is the File?

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.

Is the boulder-precip.csv file there?

Add images to R Markdown Code chunks

Using Markdown is a great way to store documentation in source control. You can check in your documentation along with your issue code, and websites like GitLab and GitHub will automatically convert it to HTML.

But not everyone wants to browse your source control website to view documentation. Sometimes documentation needs to be distributed to team members or bosses. In that case you could keep a word document or text file, but word docs are binaries and are not ideal for version control, and text files just don't look great to distribute.

Generate pdf from markdown excel

So use Markdown for everything. Keep your documentation in Markdown, convert it to a PDF using Pandoc, and automate the process using Powershell. I'll also show you how to easily add a date stamp to all of your PDFs. And at the very end there's a quick way to cheat if you're using Visual Studio Code.

Install Pandoc

Install Pandoc by downloading from https://pandoc.org/ or by using chocolatey.

Chocolatey makes it easy:
choco install pandoc

Or you can run the windows installer on the pandoc downloads page.

Install Miktex

Next you need to install Miktex. Miktex will allow you to include macros and scripts in your markdown that is processed by Pandoc. In our case we're using it to substitute the date and time in our documentation.

Install MiKTex from https://miktex.org/download

Markdown To Pdf Npm

Follow the instructions at http://www.texts.io/support/0002/. Make sure to select 'Install missing packages on the fly'.

Restart your computer after installing MiKTex. The first time you run Pandoc at the command line it may take a little longer because it's downloading and installing updates. Make sure that you run from an Administrator prompt the first time.

Adding Timestamps to your Documents

Use the {{currentdate}} token at any spot that you want the current date inserted.

Use Powershell to convert Markdown Files to PDFs

We're using a lua script to insert the date. Create a text file called currentdate.lua and insert the script below.

The double dashes are comments. The return statement says that when the string {{currentdate}} is found that it should be replaced by the date using the format %m/%d/%Y %I:%M %p. You can change the {{currentdate}} token to whatever you like, and the date format can also be whatever you like.

Convert Markdown to PDF

Here's how to create a PDF from markdown at the command line.

pandoc documentation.md --pdf-engine=xelatex -o documentation.pdf --lua-filter=currentdate.lua

The lua filter is what substitutes the current date for {{currentdate}}

We can use Powershell to create PDFs for every file in a directory:

From there you can work the Powershell into a Post-Build event or execute it manually any time your documentation changes.

A Cheat that Cuts to the Chase

If you're using Visual Studio Code you can install an extension called Markdown Converter that will convert Markdown to PDF. It supports other substitutions such as {{author}}. But doing it with Pandoc is more fun and flexible. You can now write your own lua scripts following the format above.

Further Reading