MeanRarity-package: MeanRarity: A package for computing Hill diversity under the...

In mikeroswell/MeanRarity: Hill Diversity Estimation and Visualization

MeanRarity: A package for computing Hill diversity under the "mean rarity" framework.

Description

The MeanRarity package provides a suite of functions related to computing, estimating, and visualizing Hill diversity: For references on mean rarity, see \insertCiteRoswell2021MeanRarity, \insertCitePatil2012MeanRarity, and \insertCiteJost2006MeanRarity

Computing Hill diversity

rarity computes Hill diversity as parameterized by \insertCiteRoswell2021MeanRarity, by computing the generalized weighted mean of species rarities (i.e. the reciprocal of relative abundance). The "link" functions for the generalized mean are pfun and its inverse ipfun

Simulating Species Abundance Distributions

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Roswell2021MeanRarity developed a method to simulate a species abundance distribution (SAD) based on the [Hill] diversity of the assemblage. This method fits a discretization (based on quantile values) of a continuous parametric distribution (currently gamma or log-normal) based on the known, simulated richness and (currently) Hill-Simpson diversity. The function to do this is called fit_SAD

Visualizing Mean Rarity

The code for rarity balance plots, also in the web app https://mean-rarity.shinyapps.io/rshiny_app1/ is also contained in this package. rarity_plot makes rarity balance plots. radplot makes plots of rank-abundance distributions, with or without log-transforming abundances

Author(s)

Maintainer: Michael Roswell [e-mail] (ORCID)

Authors:

• Jonathan Dushoff [e-mail] (ORCID)

References

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See Also

Useful links:

• https://mikeroswell.github.io/MeanRarity

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