Content adapted from Candace Savonen.

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.

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.

Provide sufficient detail so that you can understand what you did.

Use set.seed() : sets the starting state for the random number generator (RNG) in R.

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 psuedo 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.

Before:

After knit:

Go to Help > Cheat Sheets > R Markdown Cheat Sheet (which will download it)

Or checkout Help > Cheat Sheets > R Markdown Reference Guide

Or checkout the 🏠 Class Website!

sessionInfo()

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

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

These are just some quick tips, for more information:

• Reproducibility in Cancer Informatics course
• Advanced Reproducibility in Cancer Informatics course
• The RMarkdown book
• Jenny Bryan’s organizational strategies.
• Write efficient R code for science.

To help make your work more reproducible:

• Use R Markdown
• Clean your environment regularly
• Check the knit of your R Markdown regularly
• Tell your future self and others what you did!
• Print session info!

🏠 Class Website
💻 Lab
🗒 Day 2 Cheatsheet
🗒 RStudio Cheatsheet

Image by Gerd Altmann from Pixabay