coverage: Coverage Index

In microbiome: Microbiome Analytics

Description

Community coverage index.

Usage

coverage(x, threshold = 0.5)

Arguments

x	A species abundance vector, or matrix (taxa/features x samples) with the absolute count data (no relative abundances), or phyloseq-class object
threshold	Indicates the fraction of the ecosystem to be occupied by the N most abundant species (N is returned by this function). If the detection argument is a vector, then a data.frame is returned, one column for each detection threshold.

Details

The coverage index gives the number of groups needed to have a given proportion of the ecosystem occupied (by default 0.5 ie 50

Value

A vector of coverage indices

Author(s)

Contact: Leo Lahti [e-mail]

See Also

dominance, alpha

Examples

data(dietswap)
d <- coverage(dietswap, threshold=0.5)

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