1
How to organise your project directories
1.1
Directory layout
1.1.1
The general disaster
1.1.2
A niceR solution
1.1.3
Treat data as read only
1.1.4
Treat generated output as disposable
1.1.5
Separate function definition and application
1.2
Setting up a project in RStudio
2
Version control
2.1
Why use version control?
2.1.1
You are already using version control
2.1.2
Version control is not a back up
2.2
Basic git configuration
2.2.1
Keeping your email private
2.2.2
Line Endings
2.2.3
Configure your text editor
2.2.4
Other editors
2.3
Git basics
2.3.1
What goes in my repository?
2.3.2
The commit cycle
2.3.3
Creating a repository
2.3.4
The add-commit cycle
2.3.5
History
2.3.6
Looking at the history
2.4
Branching
2.4.1
What do branches look like?
2.4.2
Workflows that use branches
2.4.3
Listing branches
2.4.4
Creating branches
2.4.5
How branches grow
2.4.6
Merging branches back together
2.4.7
Merging when branches have diverged
2.4.8
Branches and old versions
2.4.9
Concluding remarks
2.5
Further reading material
3
Lecture slides
4
Resources for pracs
5
Acknowledgements
Organised, transparent and reproducible science using R, git, and drake
3
Lecture slides
Day 1: Open Science
Day 2: Reproducibility