ent_allen: Allen et al.'s Phylogenetic Entropy of a Community

In divent: Entropy Partitioning to Measure Diversity

Allen et al.'s Phylogenetic Entropy of a Community

Description

Estimate entropy \insertCiteAllen2009divent from abundance or probability data and a phylogenetic or functional dendrogram.

Usage

ent_allen(x, tree, ...)

## S3 method for class 'numeric'
ent_allen(
  x,
  tree,
  q = 1,
  normalize = TRUE,
  prune = FALSE,
  as_numeric = FALSE,
  ...,
  check_arguments = TRUE
)

## S3 method for class 'species_distribution'
ent_allen(
  x,
  tree,
  q = 1,
  normalize = TRUE,
  prune = FALSE,
  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.
...	Unused.
q	a number: the order of diversity.
normalize	if TRUE, phylogenetic is normalized: the height of the tree is set to 1.
prune	What to do when some species are in the tree but not in x? If TRUE, the tree is pruned to keep species of x only. The height of the tree may be changed if a pruned branch is related to the root. If FALSE (default), the length of branches of missing species is not summed but the height of the tree is never changed.
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

Estimators to deal with incomplete sampling are not implemented. Use function ent_phylo with argument if they are needed.

The phylogenetic entropy is calculated following \insertCiteAllen2009;textualdivent for order q=1 and \insertCiteLeinster2012;textualdivent for other orders. The result is identical to the total entropy calculated by ent_phylo. It is much faster but no bias correction is available.

All species of the species_distribution must be found in the tips of the tree.

Value

A tibble with the site names, the estimators used and the estimated entropy.

References

\insertAllCited

Examples

# entropy of each community
ent_allen(paracou_6_abd, tree = paracou_6_taxo)

# gamma entropy
ent_allen(paracou_6_abd, tree = paracou_6_taxo, gamma = TRUE)

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