BAT (version 2.5.1)

coverage: 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

An hclust or phylo object (used only for PD or FD).

Value

A vector with coverage values per site.

Details

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

References

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

Examples

# NOT RUN {
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)
# }