richness {microbiome}R Documentation

Richness Index

Description

Community richness index.

Usage

richness(x, detection = NULL)

Arguments

x

A species abundance vector, or matrix (taxa/features x samples) with the absolute count data (no relative abundances), or phyloseq-class object

detection

Detection threshold.

Details

By default, returns the richness for multiple detection thresholds defined by the data quantiles. If the detection argument is provided, returns richness with that detection threshold.

Value

A vector of richness indices

Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

See Also

global

Examples

data(dietswap)
d <- richness(dietswap, detection=0)

[Package microbiome version 1.2.1 Index]