Introduction to Markdown in R

Introduction to Markdown in R#

Course description#

Reproducibility is a core feature of successful research software development and data science projects. Fully reproducable workflows can be created by integrating data with code and outputs using a special type of text language called “Markdown”. This course will introduce you to the Markdown langauge and conceptualise the benefits towards ensuring reproducibility in coding-based research activities. You will also gain hands-on experience of creating reproducible Markdown documents using R: a popular coding environment used in research software development and data science projects.

Course objectives#

By the end of this workshop you will be able to:

  1. Describe what Markdown is and why it is useful

  2. Recognise the main components of a Markdown document

  3. Use basic Markdown syntax

  4. Generate Markdown documents using R/RStudio

Pre-requisite knowledge#

You are not expected to be familiar with either the Markdown language or creating Markdown documents in R prior to attending this workshop. You are also not required to be an advanced user of R. However, a basic working knowledge of R programming is beneficial. As such, you are encouraged to work through our Introduction to R course content (either by attending the course or via independent self-study) prior to attending this particular workshop.

Sign-up#

To check for upcoming course dates and to register, please visit the Workshop Schedule and Sign-up page available here.

Installation guide#

All CfRR courses require attendees to use their own computer/laptop to follow workshop activities and take effective notes. The software required for this course is the same as the Introduction to R course, with the guide available here.

Self study materials#

This course will be delivered via a mixture of slides and programming tutorials. All materials for this course can be found and downloaded from the course landing page here.

Developers#

The developer of this course is Craig Willis.

License info#

Instructional Material

The instructional material in this course is copyright © 2025 University of Exeter and is made available under the Creative Commons Attribution 4.0 International licence (https://creativecommons.org/licenses/by/4.0/). Instructional material consists of material that is contained within the “individual_modules/Introduction_to_Markdown_in_R” directory, and images folders in this directory, with the exception of code snippets and example programs found in files within these folders. Such code snippets and example programs are considered software for the purposes of this licence.

Software

Except where otherwise noted, software provided in this repository is made available under the MIT licence (https://opensource.org/licenses/MIT).

Copyright © 2025 University of Exeter

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

The software in this repository is adapted from software that is covered by the following copyright and permission notice:

Copyright © 2025 Software Carpentry

Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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