diverdist: beta and gamma Diversity Distance
In jarioksa/natto: An Extreme 'vegan' Package of Experimental Code

diverdist

R Documentation

beta and gamma Diversity Distance

Description

The distance between two sampling units is the increase in diversity when these are merged together, or the beta diversity between two SUs. Alternatively, the function can find the total diversity or distance from the origin which is known as gamma diversity for two SUs. Any Renyi diversity can be used.

Usage

diverdist(x, renyi = 1, equalize = TRUE, beta = TRUE, hill = FALSE)

Arguments

`x`	Community data.
`renyi`	The scale of Renyi diversity index as defined in `renyi`. Value `0` gives diversity based on species richness, `1` diversity based on Shannon entropy, `2` diversity based on Simpson index, and `Inf` diversity based on Berger-Parker index. Other non-negative values are also allowed, but they may not define a well known standard diversity index.
`equalize`	Equalize data rows so that they can be meaningfully pooled and averaged. If this is `FALSE`, raw data will be used, and beta diversities may be negative. The equalization depends on the value of `renyi`, and each row of `x` is divided by `(rowSums(x^renyi))^(1/renyi)`. In borderline cases `renyi=0` the data are presence-absence tranformed (but can be left untransformed), and with `renyi=Inf` the rows are divided by row maxima (see `decostand`).
`beta`	Use beta diversities: the average alpha diversity of cluster members is subtracted from the pooled diversity. If this is `FALSE`,the clustering is based on pooled diversity, also known as gamma diversity.
`hill`	Use Hill numbers instead of Renyi diversity (see `renyi`). For `renyi = 0` these are species richess values instead of their logarithms, and for `renyi = 1` they are exponents of Shannon diversity instead of Shannon diversities. In general, a Hill number is an exponent of Renyi diversity. The Hill numbers may not be strictly additive, and beta diversities may be negative (except with `renyi = 0`).