inst/explore-anacapa-output/docs/alpha-div-overview.md

In gauravsk/ranacapa: Utility Functions and 'shiny' App for Simple Environmental DNA Visualizations and Analyses

Background on alpha diversity

In ecology, the term alpha diversity refers simply to the diversity observed in a single site (or a single sample). Although this may seem like a very simple concept, it turns out that there's many ways to consider diversity. The most obvious way to measure alpha diversity is to count the number of species (or genera, or families, etc.) found in a sample. This is the metric calculated with the 'Observed' option on the left.

We may want to calculate diversity in a way that accounts for not only the number of species (or higher taxonomic groups) present in a sample, but also the relative abundance of each group. For example, consider, the following situation:

• You are comparing two communities, each community has 300 individuals in total, representing 3 species. In the Community A, each species is represented by 100 individuals each, for a total of 300 individuals. Community B also has 300 individuals, but in this case, there are 290 individuals of Species 1, nine individuals of Species 2, and just one individual of Species 3. Clearly, Communities A and B have the same species richness, but the abundances are more evenly distributed among species in Community A.

This is the type of diversity captured by a metric known as Shannon diversity, which you can select on the left.

For more information on alpha diversity, check out the following resources: - Measurement of Biodiversity, from the World Register of Marine Species. - Introduction to Alpha Diversity from Dr. Dan Knights, University of Minnesota. - For a lot more information, the book Biological Diversity: Frontiers in Measurement and Assessment is a fantastic resource.

In addition to inspecting alpha diversity per sample, you can also view the alpha diversity summarized by one of the characteristics of your samples. To do so, please choose a characteristic from the dropdown list on the left.

gauravsk/ranacapa documentation built on June 7, 2019, 4:03 a.m.