ent_gen_simpson {divent} | R Documentation |
Generalized Simpson's Entropy
Description
Estimate the Generalized Simpson's entropy of species from abundance or probability data.
Usage
ent_gen_simpson(x, ...)
## S3 method for class 'numeric'
ent_gen_simpson(
x,
k = 1,
estimator = c("Zhang", "naive"),
as_numeric = FALSE,
...,
check_arguments = TRUE
)
## S3 method for class 'species_distribution'
ent_gen_simpson(
x,
k = 1,
estimator = c("Zhang", "naive"),
gamma = FALSE,
as_numeric = FALSE,
...,
check_arguments = TRUE
)
Arguments
x |
An object, that may be a numeric vector containing abundances or probabilities, or an object of class abundances or probabilities. |
... |
Unused. |
k |
the order of Hurlbert's diversity. |
estimator |
An estimator of entropy. |
as_numeric |
if |
check_arguments |
if |
gamma |
if |
Details
The Generalized Simpson's Entropy (Zhang and Zhou 2010) of order k
is,
in the species accumulation curve,the probability for the individual sampled
in rank k + 1
to belong to a new species.
It is a measure of diversity so long as k
is lower than the number
of species (Grabchak et al. 2017).
Bias correction requires the number of individuals.
It is limited to orders r
less than or equal to the number of individuals
in the community (Zhang and Grabchak 2016).
Generalized Simpson's diversity cannot be estimated at a specified level of interpolation or extrapolation, and diversity partitioning is not available.
Value
A tibble with the site names, the estimators used and the estimated entropy.
Note
The unbiased estimator is calculated by the EntropyEstimation::GenSimp.z function of the EntropyEstimation package.
See Also
#' @references
Grabchak M, Marcon E, Lang G, Zhang Z (2017).
“The Generalized Simpson's Entropy Is a Measure of Biodiversity.”
Plos One, 12(3), e0173305.
doi:10.1371/journal.pone.0173305.
Zhang Z, Grabchak M (2016).
“Entropic Representation and Estimation of Diversity Indices.”
Journal of Nonparametric Statistics, 28(3), 563–575.
doi:10.1080/10485252.2016.1190357.
Zhang Z, Zhou J (2010).
“Re-Parameterization of Multinomial Distributions and Diversity Indices.”
Journal of Statistical Planning and Inference, 140(7), 1731–1738.
doi:10.1016/j.jspi.2009.12.023.
Examples
# Entropy of each community
ent_gen_simpson(paracou_6_abd, k = 50)
# gamma entropy
ent_gen_simpson(paracou_6_abd, k = 50, gamma = TRUE)