alphaDiv_calc: Calculates Alpha Diversity Indices
In pmartR/pmartRseq: Analysis and Visualization of 16S Data

Description Usage Arguments Details Value Author(s) Examples

This function calculates Shannon's, Simpson's, and/or Inverse Simpson's alpha diversity indices.

1	alphaDiv_calc(omicsData, index = c("shannon", "simpson", "invsimpson"))

`omicsData`	an object of the class 'seqData' created by `as.seqData`.
`index`	a character vector stating which of the calculations to perform - "shannon" for Shannon's diversity index, "simpson" for Simpson's diversity index, and/or "invsimpson" for the inverse Simpson's diversity index. Default is to perform all 3 calculations.

Alpha diversity is calculated for each sample in the data, using Shannon's diversity index (Shannon's H), Simpson's diversity index (Simpson's D), and/or inverse Simpson's diversity index.

Shannon or Shannon–Weaver (or Shannon–Wiener) index is defined as H = -sum(p_i*log(p_i)), where p_i is the proportional abundance of species i.

Both variants of Simpson's index are based on D = sum(p_i^2). Choice simpson returns 1-D and invsimpson returns 1/D.

An object of class alphaRes (also a data.frame) containing the diversity value(s) for every sample in the data object.

Allison Thompson

## Not run: 
library(mintJansson)
data(rRNA_data)
rRNA_diversity <- alphaDiv_calc(omicsData = rRNA_data)
rRNA_diversity
summary(rRNA_diversity)
plot(rRNA_diversity)

## End(Not run)