coverage {microbiome} | R Documentation

## Coverage Index

### 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 microbiome-admin@googlegroups.com

### See Also

dominance, alpha

### Examples

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

[Package microbiome version 1.12.0 Index]