ent_gen_simpson: Generalized Simpson's Entropy

In divent: Entropy Partitioning to Measure Diversity

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 TRUE, a number or a numeric vector is returned rather than a tibble.
check_arguments	if TRUE, the function arguments are verified. Should be set to FALSE to save time when the arguments have been checked elsewhere.
gamma	if TRUE, \gamma diversity, i.e. diversity of the metacommunity, is computed.

Details

The Generalized Simpson's Entropy \insertCiteZhang2010divent 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 \insertCiteGrabchak2016divent.

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 \insertCiteZhang2014divent.

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

div_gen_simpson

#' @references \insertAllCited

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)

divent documentation built on April 3, 2025, 7:40 p.m.