MeanRarity-package.RdThe MeanRarity package provides a suite of functions related to computing, estimating, and visualizing Hill diversity: For references on mean rarity, see (Roswell et al. 2021) , (Patil and Taillie 1982) , and (Jost 2006)
rarity computes Hill
diversity as parameterized by (Roswell et al. 2021)
, 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
(Roswell et al. 2021)
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
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
Jost L (2006).
“Entropy and diversity.”
Oikos, 113, 363--375.
doi:10.1111/j.2006.0030-1299.14714.x
.
Patil GP, Taillie C (1982).
“Diversity as a concept and its measurement.”
Journal of the American Statistical Association, 77(379), 548--561.
doi:10.1080/01621459.1982.10477845
, http://www.tandfonline.com/loi/uasa20%5Cnhttp://dx.doi.org/10.1080/01621459.1982.10477845%5Cnhttp://www.tandfonline.com/.
Roswell M, Dushoff J, Winfree R (2021).
“A conceptual guide to measuring species diversity.”
Oikos, 130(3), 321--338.
ISSN 0030-1299, doi:10.1111/oik.07202
, https://onlinelibrary.wiley.com/doi/10.1111/oik.07202.
Useful links: