Using R to compare empirical and exact rarefaction values (CC199)

March 24, 2022 • PD Schloss • 1 min read • •

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).

Code

You can browse the state of the repository at the

• beginning of the episode
• end of the episode