div_part: Diversity partition
In divent: Entropy Partitioning to Measure Diversity

div_part

R Documentation

Diversity partition

Description

Calculate \gamma, \beta and \alpha diversities of a metacommunity.

Usage

div_part(
  abundances,
  q = 1,
  estimator = c("UnveilJ", "ChaoJost", "ChaoShen", "GenCov", "Grassberger", "Holste",
    "Marcon", "UnveilC", "UnveiliC", "ZhangGrabchak"),
  level = NULL,
  probability_estimator = c("Chao2015", "Chao2013", "ChaoShen", "naive"),
  unveiling = c("geometric", "uniform", "none"),
  richness_estimator = c("jackknife", "iChao1", "Chao1", "naive"),
  jack_alpha = 0.05,
  jack_max = 10,
  coverage_estimator = c("ZhangHuang", "Chao", "Turing", "Good"),
  q_threshold = 10,
  check_arguments = TRUE
)

Arguments

`abundances`	an object of class abundances.
`q`	a number: the order of diversity.
`estimator`	An estimator of diversity.
`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`	an estimator of richness to evaluate the total number of species, see div_richness. used for interpolation and 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.
`q_threshold`	the value of `q` above which diversity is computed directly with the naive estimator `(\sum{p_s^q}^{\frac{1}{(1-q)}}`, without computing entropy. When `q` is great, the exponential of entropy goes to `0^{\frac{1}{(1-q)}}`, causing rounding errors while the naive estimator of diversity is less and less biased.
`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 function computes \gamma diversity after building a metacommunity from local communities according to their weight \insertCiteMarcon2014adivent. \alpha entropy is the weighted mean local entropy, converted into Hill numbers to obtain \alpha diversity. \beta diversity is obtained as the ratio of \gamma to \alpha.