Is normalization an acceptable alternative to rarefaction? Nope. (CC190)
Channel: Riffomonas Project
Date: 2022-02-24

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.

You can find my blog post for this episode at https://www.riffomonas.org/code_club/2022-02-24-normalization. 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).

#SRS #vegdist #avgdist #ggplot2 #R #Rstudio #Rstats

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0:00 Is normalization an acceptable alternative to rarefaction?
5:01 Review of using null community model
6:34 Calculating distances based on relative abundances
11:56 A simple method of normalizing data
14:26 The SRS approach to normalizing data
17:21 Calculating distances based on SRS normalized data