Using R to compare empirical and exact rarefaction values (CC199)
Channel: Riffomonas Project
Date: 28/03/2022

In this Code Club, I'll use R to show you how to use an empirical approach to rarefaction with tools from the tidyverse packages. We'll look at the effect of different numbers of iterations on the precision of the rarefied richness values relative to the exact rarefactoin value. You can find my blog post for this episode at https://www.riffomonas.org/code_club/2022-03-28-rarefaction-empirical. The data were generated in our Kozich et al. 2013 paper (http://doi.org/10.1128/AEM.01043-13) using samples from the Schloss et al. 2012 paper (http://doi.org/10.4161/gmic.21008).

#rarefation #math #R #Rstudio #Rstats

Want more practice on the concepts covered in Code Club? You can sign up for my weekly newsletter at https://shop.riffomonas.org/youtube to get practice problems, tips, and insights.

If you're interested in taking an upcoming 3 day R workshop be sure to check out our schedule at https://riffomonas.org/workshops/

You can also find complete tutorials for learning R with the tidyverse using...
Microbial ecology data: https://www.riffomonas.org/minimalR/
General data: https://www.riffomonas.org/generalR/

0:00 Comparing empirical and exact rarefaction values
3:19 Completing a single subsampling
5:48 Rarefying data
7:47 Visualizing difference between empirical and exact results
13:01 Investigating the impact of the number of iterations