abd_freq_count: Abundance Frequency Count of a Community

In divent: Entropy Partitioning to Measure Diversity

Abundance Frequency Count of a Community

Description

Count the number of species observed the same number of times.

Usage

abd_freq_count(
  abd,
  level = NULL,
  probability_estimator = c("Chao2015", "Chao2013", "ChaoShen", "naive"),
  unveiling = c("geometric", "uniform", "none"),
  richness_estimator = c("jackknife", "iChao1", "Chao1", "rarefy", "naive"),
  jack_alpha = 0.05,
  jack_max = 10,
  coverage_estimator = c("ZhangHuang", "Chao", "Turing", "Good"),
  check_arguments = TRUE
)

Arguments

abd	A numeric vector containing species abundances.
level	the level of interpolation or extrapolation. It may be a sample size (an integer) or a sample coverage (a number between 0 and 1). If not NULL, the asymptotic estimator is ignored.
probability_estimator	a string containing one of the possible estimators of the probability distribution (see probabilities). Used only for extrapolation.
unveiling	a string containing one of the possible unveiling methods to estimate the probabilities of the unobserved species (see probabilities). Used only for extrapolation.
richness_estimator	A string containing an estimator recognized by div_richness to evaluate the total number of species in probabilities. Used only for extrapolation.
jack_alpha	the risk level, 5% by default, used to optimize the jackknife order.
jack_max	the highest jackknife order allowed. Default is 10.
coverage_estimator	an estimator of sample coverage used by coverage.
check_arguments	if TRUE, the function arguments are verified. Should be set to FALSE to save time when the arguments have been checked elsewhere.

Details

The Abundance Frequency Count \insertCiteChao2015divent is the number of species observed each number of times. It is a way to summarize the species distribution.

It can be estimated at a specified level of interpolation or extrapolation. Extrapolation relies on the estimation of the estimation of the asymptotic distribution of the community by probabilities and eq. (5) of \insertCiteChao2014divent.

Value

A two-column tibble. The first column contains the number of observations, the second one the number of species observed this number of times.

References

\insertAllCited

Examples

abd_freq_count(as.numeric(paracou_6_abd[1, ]))

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