Is normalization an acceptable alternative to rarefaction? Nope. (CC190)

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

Given the controversy around rarefaction an alternative that has been proposed is to use relative abundance data or normalization. In this Code Club, Pat uses R to compare pairwise distances from a null community model calculated using rarefaction, relative abundances, and normalization using the SRS algorithm with vegdist and avgdist functions from the vegan R package. He’ll show how to synthesize and visualize the data using tools from dplyr, ggplot2, and other tidyverse packages.

Code

You can browse the state of the repository at the

• beginning of the episode
• end of the episode