Rarefying ecological distances with R: Should you? (CC189)

Rarefaction of ecological distances and alpha diversity metrics has become controversial in the microbial ecology field. In this Code Club, Pat will use R to look at issues that surround the controversy. Pat will generate a null community distribution model and then assess the impact of rarefaction using the 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).

#vegdist #avgdist #vegan #ggplot2 #R #Rstudio #Rstats

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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 What happens if you rarefy your data? If you don't?
4:13 Generating a null community model
11:56 Calculating distances with and without rarefaction
13:35 Comparing distance calculation approaches
17:17 Assessing sensitivity to difference in sampling depth