How to rarefy community data in R with vegan and the tidyverse (CC200)

The vegan R package has a lot of useful functions for doing community ecology analysis including rarefaction with the rarefy, rrarefy, drarefy, and rarecurve functions. In this episode, I'll show how to get data into the right format to run these functions and how to get the output into the tidyverse. 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).

#rarefation #math #R #Rstudio #Rstats

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Microbial ecology data: https://www.riffomonas.org/minimalR/
General data: https://www.riffomonas.org/generalR/

0:00 Using vegan to rarefy richness values
5:45 vegan's rarefy function
11:22 vegan's rrarefy function
12:35 vegan's drarefy function
15:25 vegan's rarecurve function