diversity: Diversity Index

In microbiome/microbiome: Microbiome Analytics

Diversity Index

Description

Various community diversity indices.

Usage

diversity(x, index = "all", zeroes = TRUE)

Arguments

x	A species abundance vector, or matrix (taxa/features x samples) with the absolute count data (no relative abundances), or phyloseq-class object
index	Diversity index. See details for options.
zeroes	Include zero counts in the diversity estimation.

Details

By default, returns all diversity indices. The available diversity indices include the following:

• inverse_simpson Inverse Simpson diversity: $1/lambda$ where $lambda=sum(p^2)$ and $p$ are relative abundances.

• gini_simpson Gini-Simpson diversity $1 - lambda$. This is also called Gibbs–Martin, or Blau index in sociology, psychology and management studies.

• shannon Shannon diversity ie entropy

• fisher Fisher alpha; as implemented in the vegan package

• coverage Number of species needed to cover 50% of the ecosystem. For other quantiles, apply the function coverage directly.

Value

A vector of diversity indices

Author(s)

Contact: Leo Lahti [e-mail]

References

Beisel J-N. et al. A Comparative Analysis of Diversity Index Sensitivity. Internal Rev. Hydrobiol. 88(1):3-15, 2003. URL: https://portais.ufg.br/up/202/o/2003-comparative_evennes_index.pdf

Bulla L. An index of diversity and its associated diversity measure. Oikos 70:167–171, 1994

Magurran AE, McGill BJ, eds (2011) Biological Diversity: Frontiers in Measurement and Assessment (Oxford Univ Press, Oxford), Vol 12.

Smith B and Wilson JB. A Consumer's Guide to Diversity Indices. Oikos 76(1):70-82, 1996.

See Also

dominance, richness, evenness, rarity, alpha

Examples

data(dietswap)
d <- alpha(dietswap, 'shannon')

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.