chao1 {OTUtable}

Chao1 Richness

Description

Calculates Chao1 richness of a vector of relative abundance data. This alpha diversity metric takes into account the number of singletons and doubletons for a more accurate estimate than observed richness.

Usage

chao1(sample)

Arguments

sample

A vector of relative abundance data, typically a column in a matrix

Value

Returns a single number indicating the estimated richness in the tested sample based on the number of taxa appearing only once or twice

Note

Use apply functions to calculate Chao1 richness for all samples in a matrix

Author(s)

Alexandra Linz <[e-mail]>

Examples

data(otu_table)
chao1_richness <- apply(otu_table, 2, chao1)