Content adapted from Candace Savonen.
What’s Reproducibility
Reproducibility vs Repeatability vs Replicability
Why Reproducibility is important…
We can’t get to replicability without reproducibility
It’s worth the wait
Reproducibility can also be for your future self!
The process
R Markdown
R Markdown lets you test your work
R Markdown allows you to more clearly show what you did
R Markdown makes it easier to update code and see results
Clean your environment
Regularly cleaning your environment and trying your code again, can help ensure that your code is running as expected.
Occasionally we might forget to save a step of our code in our R Markdown file that we ran only in the console. This will help us figure that out.
Check if your file knits regularly
Regularly checking if your file knits will help you spot a missing step or error earlier when you have less code to try to identify where your code might have gone wrong.
Image by Allison Horst.
Tell your future self and others what you did!
Provide sufficient detail so that you can understand what you did and why.
# Taking a random sample of 100 individuals from the population # WITHOUT replacement samp_pop <- sample(100, replace = FALSE) # Then split them into two groups of 50 # a[x:xx] is the syntax for indexing a vector samp_pop1 <- samp_pop[1:50] samp_pop2 <- samp_pop[51:100]
Need random numbers to stay consistent?
Use set.seed(): sets the starting state for the random number generator.
set.seed(123) sample(10)
[1] 3 10 2 8 6 9 1 7 5 4
set.seed(123) sample(10)
[1] 3 10 2 8 6 9 1 7 5 4
set.seed(456) sample(10)
[1] 5 3 6 10 4 9 1 2 8 7
Note that these are only pseudo random and the values are created doing calculations based on the given seed. Thus the same “random” values will be reproduced by everyone using the same seed with set.seed.
R Markdown syntax
Before: 
After knit: 
R Markdown syntax
Go to the RStudio toolbar: Help > Cheat Sheets > R Markdown Cheat Sheet (which will download it)
Or Help > Cheat Sheets > R Markdown Reference Guide
Additional references
Or check out the 🏠 Class Website! The Resources page has links to additional helpful cheat sheets.
Versions matter
Session info can help
GUT CHECK
Why is reproducibility so important?
A. It helps to ensure that your code is working consistently and it helps others understand what you did
B. It ensures that your code is correct
GUT CHECK
What is NOT a practice to improve the reproducibility of our work?
A. Using R Markdown files to describe what your code is doing
B. Using scripts instead of R Markdown files
C. Testing your code with R Markdown files or the run previous button
D. Regularly cleaning the environment
More resources
These are just some quick tips, for more information:
Summary
To help make your work more reproducible:
- Use RMarkdown
- Clean your environment regularly
- Check the knit of your RMarkdown regularly
- Tell your future self and others what you did!
- Print session info!
Resources & Lab
💻 Lab
Image by Gerd Altmann from Pixabay