You can install the R package MeanRarity with the following command:
devtools::install_github("mikeroswell/MeanRarity")
This R package allows estimating and visualizing Hill diversity (aka “Hill numbers”) in terms of the average species “rarity.”
The average species rarity may be simpler to interpret than a transformed, generalized entropy. The rarity parameterization clarifies the role of the scaling exponent, and this R package provides illustration tools to visualize that scaling concretely. Furthermore, this framework may provide an entry point for developing and testing diversity estimators and their related interval estimates (e.g. confidence intervals); this package contains novel tools to simulate species abundance distributions that should streamline that process.
Three key functions
rarity() computes Hill diversity of a sample, parameterized in terms of the mean rarity.
rarity_plot() makes balance plots to visualize mean rarity.
fit_SAD() simulates a species abundance distribution with known richness, Hill-Simpson diversity, and a distributional assumption (lognormal or gamma).
Details
rarity(x, l) is equivalent to vegan::renyi(x, scale = 1-l, hill = T). Re-parameterizing Hill diversity in terms of species rarity can provide conceptual clarity.
“Balance plots” called with rarity_plot() illustrate the computation in rarity().
fit_SAD() is a potentially novel way to simulate abundance distributions that always gives precisely the same relative abundances for a given set of parameters, and may be a helpful tool for exploring the behavior of diversity metrics under different sampling scenarios.
Vignettes
We are working on vignettes now. Currently Estimating_Mean_Rarity provides code to make the figures in Roswell et al. 2021 Oikos https://doi.org/10.1111/oik.07202, Gods_estimator explores a playful extension of the tools in this package, and Using_MeanRarity is a more traditional, “user’s guide” -type vignette.
