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

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/.... 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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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 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