Chao_Hill_abu: Estimate asymptotic Hill diversity

In mikeroswell/MeanRarity: Hill Diversity Estimation and Visualization

Estimate asymptotic Hill diversity

Description

Computes an estimate of the true community diversity based on a finite sample assuming that individuals are randomly and independently sampled, after Chao and Jost 2015. SpadeR source code modified to match our use of \ell instead of q to parameterize Hill diversity. Code taken from SpadeR:::Chao_Hill_abu()From the R package SpadeR 0.1.1 by Anne Chao, K. H. Ma, T. C. Hsieh and Chun-Huo Chiu

Usage

Chao_Hill_abu(ab, l, q = NULL)

Arguments

ab	A numeric vector of species abundances or relative abundances.
l	Scaling exponent for the mean, can be any real number.
q	Scalar, traditional Hill number scaling exponent, q = 1-l where l is the scaling parameter for the generalized mean. Can be any real number.

Value

Scalar estimate of Hill diversity given \ell

References

\insertRef

Chao2015MeanRarity

Examples

# generate sample
abs <- sample_infinite(fit_SAD(rich = 50, simpson = 20)[[3]], 150)

# estimate true Hill diversity
Chao_Hill_abu(abs, l = 1) # Chao1 estimate of richness lower bound
Chao_Hill_abu(abs, l = 0) # Asymptotic estimate of Hill-Shannon diversity
Chao_Hill_abu(abs, l = -1) # Asymptotic estimate of Hill-Simpson diversity

mikeroswell/MeanRarity documentation built on May 5, 2024, 4:50 p.m.