Is phylogenetic diversity any better than richness or Shannon diversity? (CC210) скачать в хорошем качестве

Is phylogenetic diversity any better than richness or Shannon diversity? (CC210)

Phylogenetic diversity is an approach to quantifying alpha diversity based on a phylogenetic tree generated from sequences. But is it much different from traditional alpha diversity metrics like richness or Shannon diversity? In this Code Club, Pat will use R to quantify the difference between these metrics using the same tools. He'll answer the question using data generated with mothur and R functions from vegan, dplyr, and ggplot2. 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). #microbiome #tidyverse #vegan #R #Rstudio #Rstats #ggplot2 Want more practice on the concepts covered in Code Club? You can sign up for my weekly newsletter at https://shop.riffomonas.org/youtube to get practice problems, tips, and insights. 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 Introduction 2:36 Getting rarefied phylogenetic diversity 5:03 Generating rarefied richness 7:58 Generating rarefied Shannon diversity 11:33 Comparing alpha diversity metrics 14:32 Measuring correlation between metrics