Whittaker: Whittaker's index of overall association in a community...

In petrkeil/spasm: Species association measures for various data types

Description

This metric is equivalent to calculating the classical Whittaker's beta diversity on a transposed matrix. The impulse to use this metric for species associations arose during a discussion with Aniko Toth at IBS 2019 conference in Malaga. We then found out that Arita (2015) also used the same idea. Note: Before the calculation, species (rows) with zero occurrences, and sites (columns) with zero species are removed from m.

Usage

Whittaker(m, clean = TRUE)

Arguments

m	Community data matrix with species as rows and sites as columns. Can contain either incidences (1/0) or abundances (natural numbers).
clean	Logical. Do you want to remove zero-sum rows or columns? When the index needs the "d" fraction (sites where no species occurs), only zero-sum rows are removed.

Value

A single number, which is the ratio of mean occupancy and the number of

References

Arita H. (2015) Multisite and multispecies measures of overlap, co-occurrence and co-diversity. Ecography 40: 709-718.

petrkeil/spasm documentation built on Jan. 15, 2021, 6:08 p.m.