Using vegan to calculate alpha diversity metrics within the tidyverse in R (CC196)

March 17, 2022 • PD Schloss • 1 min read • •

Among the useful tools in the vegan R package are functions for calculating alpha diversity metrics and indices. In this episode of Code Club, Pat shows how to create our own versions of these functions and how we can implement either version in a group_by / summarize pipeline using dplyr. We’ll also take a look at whether there is an effect of sampling effort on the observed richness, shannon diversity, and simpson diversity. He’ll show how to synthesize and visualize the data using tools from vegan, dplyr, ggplot2 and other tidyverse packages.

Code

You can browse the state of the repository at the

• beginning of the episode
• end of the episode