div_phylo: Phylogenetic Diversity of a Community

In divent: Entropy Partitioning to Measure Diversity

Phylogenetic Diversity of a Community

Description

Estimate the diversity of species from abundance or probability data and a phylogenetic tree. Several estimators are available to deal with incomplete sampling.

Usage

div_phylo(x, tree, q = 1, ...)

## S3 method for class 'numeric'
div_phylo(
  x,
  tree,
  q = 1,
  normalize = TRUE,
  estimator = c("UnveilJ", "ChaoJost", "ChaoShen", "GenCov", "Grassberger", "Marcon",
    "UnveilC", "UnveiliC", "ZhangGrabchak", "naive", "Bonachela", "Holste"),
  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"),
  as_numeric = FALSE,
  ...,
  check_arguments = TRUE
)

## S3 method for class 'species_distribution'
div_phylo(
  x,
  tree,
  q = 1,
  normalize = TRUE,
  estimator = c("UnveilJ", "ChaoJost", "ChaoShen", "GenCov", "Grassberger", "Marcon",
    "UnveilC", "UnveiliC", "ZhangGrabchak", "naive", "Bonachela", "Holste"),
  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"),
  gamma = FALSE,
  as_numeric = FALSE,
  ...,
  check_arguments = TRUE
)

Arguments

x	An object, that may be a named numeric vector (names are species names) containing abundances or probabilities, or an object of class abundances or probabilities.
tree	an ultrametric, phylogenetic tree. May be an object of class phylo_divent, ape::phylo, ade4::phylog or stats::hclust.
q	a number: the order of diversity.
...	Unused.
normalize	if TRUE, phylogenetic is normalized: the height of the tree is set to 1.
estimator	An estimator of asymptotic 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.
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

Bias correction requires the number of individuals. See div_hill for estimators.

Entropy can be estimated at a specified level of interpolation or extrapolation, either a chosen sample size or sample coverage \insertCiteChao2014divent, rather than its asymptotic value. See accum_tsallis for details.

Value

A tibble with the site names, the estimators used and the estimated diversity

References

\insertAllCited

Examples

div_phylo(paracou_6_abd, tree = paracou_6_taxo, q = 2)

# At 80% coverage
div_phylo(paracou_6_abd, tree = paracou_6_taxo, q = 2, level = 0.8)

# Gamma entropy
div_phylo(paracou_6_abd, tree = paracou_6_taxo, q = 2, gamma = TRUE)

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