richness: Richness Index

In microbiome: Microbiome Analytics

Description

Community richness index.

Usage

richness(x, index = c("observed", "chao1"), detection = 0)

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	"observed" or "chao1"
detection	Detection threshold. Used for the "observed" index.

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. The "observed" richness corresponds to index="observed", detection=0.

Value

A vector of richness indices

Author(s)

Contact: Leo Lahti [e-mail]

See Also

alpha

Examples

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

microbiome documentation built on Nov. 8, 2020, 5:08 p.m.