How to get over writers block when analyzing data: Using pseudocode when coding with R (CC041)
Channel: Riffomonas Project
Date: 2020-10-22

In this screencast tutorial, Pat Schloss shows how you can outline your data analysis plan using pseudocode to help organize your thoughts and create a roadmap. The pseudocode also provides a great scaffold for documenting your code. We'll see how to use pseudocode as we attempt to generate a plot showing the specificity of ASVs within each taxonomic rank. This episode is part of a larger arc of episodes investigating the sensitivity and specificity of amplicon sequence variants (ASVs), also known as exact sequence variants (ESVs). ASVs are growing in popularity for analyzing microbial communities using 16S rRNA gene sequences. Pat demonstrates these concepts by live coding at the command line interface using RStudio, GitHub Flow, and make.

0:00 Introduction
2:41 Today's issue
4:23 Introducing pseudocode
10:31 Filling in R code
22:31 Interpreting results
25:57 Creating the Make rule to build markdown file
28:03 Conclusion

The accompanying blog post contains the exercises and solutions can be found at http://www.riffomonas.org/code_club/2020-10-22-pseudocode