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A 90-minute introduction to R Markdown for Medicine
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R Markdown for Medicine: From Data to Manuscript

This repo contains materials for the R Markdown for Medicine workshop, to be offered at the R/Medicine 2019 conference.


Join us for a 90-minute workshop that will take you on a tour of how to get from data to manuscript using R Markdown. Starting with a mock medical dataset, we'll use R Markdown to combine prose, R code, and figures and tables created with R code into a nicely formatted and reproducible final manuscript.

The workshop will be 90 minutes and taught on, and will focus on three topics:

  1. R Markdown basics

  2. Adding graphics

  3. Adding tables

R Markdown basics

You'll start with a mock medical dataset, and jump right into an R Markdown project. You'll knit a report to analyze and visualize the data. Along the way, you'll learn about key concepts like YAML, pandoc, markdown, knitr, output options, and output formats- and how you can use all of them in your medical research.

Adding graphics

You'll take an R Markdown report, and learn how to add graphics to your knitted report. You'll learn ggplot2 basics around plots and layering, knitr code chunk options to improve graphics presentation, and packages for sewing together multiple plots into a multipanel figure.

Adding tables

You will learn how to knit a "Table 1" using medical data into an R Markdown document, and how to customize a table to report common summary statistics for studies with multiple arms.

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