Markdown

In this tutorial, I’ll share my top 10 tips for getting started with Academic:

Tip 1

Tip 2

Most of my colleagues will know that I am interested in open science and using R to do reproducible analyses. As 2018 comes to an end, I figured I’d write a post about some of the great tools that support my day-to-day work. This will be centered around R and RStudio and the fantastic extensions that exist today. This post assumes you already know how to do statistical analyses in R but want to extend its capabilities.

Writing manuscripts in R

You don’t have to use expensive, clunky, software like Word to get your writing done, but it is unfortunately still the standard in my part of academia. It does not seem to be going away any time soon so my strategy right now is to adapt.

I myself have used the papaja package since it can create Word-documents with proper formatting (most of my co-authors use Word and most journals in my field want submissions as Word-files). There is also the rticles package which has templates for many journals.

Free reference management with Zotero

No academic text is complete without references and researchers at most institutions have access to paid options like EndNote, but Zotero is a free option that can handle all of the basic tasks like adding references to Word documents. The killer feature of Zotero is that I can easily insert references into ®markdown documents using the simple citation keys generated by the better bibtex plugin. There’s even a mini app called zotpick which lets you search for the reference and insert into your document, but I usually just look at the citekey in Zotero and insert: [@reference2000]. When you knit the document in RStudio, you’ll get properly formatted references and a bibliography at the end of your document!

Hosting a website using Blogdown

This website is built from RStudio by using a package and addin called blogdown. I know absolutely nothing about how to create websites (HTML, CSS, etc) but still managed to create a personal website that looks professional in just a few hours. Everything is completely free! The only thing that you (optionally) pay for is the name; I pay $10 each year to keep the oskarflygare.com address.

Writing a book, e-book or thesis using Bookdown1

Just as in blogdown, you don’t need to learn anything beyond basic markdown syntax in order to compile longer-form documents like a book or thesis. There is even a Karolinska Institutet template available!

Version control with Git and GitHub


  1. Looks similar to blogdown? Both packages have the same author, Yihui Xie, who has extended the uses of RStudio more than anyone else. ^