Is richness estimation an alternative to rarefaction? Trying breakaway and Chao1 (CC201)
Channel: Riffomonas Project
Date: 2022-04-04

Richness estimation has been proposed as an alternative to rarefaction because the estimate should be independent of sampling effort. But is it? In this episode of Code Club, I use the breakaway package in the context of nest, mutate, map, and unnest to assess the sensitivity of richness estimation to sampling effort. 
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/2022-04-04-estimation. 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).

#breakaway #tidyverse #R #Rstudio #Rstats

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0:00 Using breakaway to estimate richness
2:05 Installing and using breakaway
5:29 Using nest/mutate/map to analyze data
8:00 Using nest/mutate/map/unnest with breakaway
10:21 Visualizing estimated richness values
13:29 Estimating richness with Chao1