coverage {BAT}R Documentation

Coverage of datasets.

Description

Coverage is a measure of completeness of a dataset.

Usage

coverage(comm, tree)

Arguments

comm

A matrix of sites x species with abundance values.

tree

A phylo or hclust object (used only for PD or FD) or alternatively a species x traits matrix or data.frame to build a functional tree.

Details

Calculated as the estimated proportion of individuals that belong to the species (or phylogenetic, or functional diversity) already collected (Chao and Jost 2012).

Value

A vector with coverage values per site.

References

Chao, A. & Jost, L. (2012). Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size. Ecology, 93: 2533-2547.

Examples

comm <- matrix(c(2,1,0,0,100,1,2,0,0,3,1,2,4,0,0,0,0,0,2,2), nrow = 4, ncol = 5, byrow = TRUE)
tree <- hclust(dist(c(1:5), method="euclidean"), method="average")
coverage(comm)
coverage(comm, tree)

[Package BAT version 2.6.0 Index]