alpha_div: Alpha diversity measure

In umerijaz/microbiomeSeq: Microbial community analysis in an environmental context.

Description

This function calculates alpha diversity of provided community data using selected indices/method.

Usage

alpha_div(physeq, method)

Arguments

physeq	(Required). A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.
method	(Required). A list of character strings specifying method to be used to calculate for alpha diversity in the data. Available methods are: "richness", "fisher", "simpson", "shannon" and "evenness".

Value

It returns a data frame of diversity measure and corresponding indices/methods

Author(s)

Alfred Ssekagiri [e-mail],Umer Zeeshan Ijaz [e-mail]

References

http://userweb.eng.gla.ac.uk/umer.ijaz/, Umer Ijaz, 2015

umerijaz/microbiomeSeq documentation built on May 30, 2019, 3:13 p.m.