div_pd: Faith's Phylogenetic Diversity of a Community
In divent: Entropy Partitioning to Measure Diversity

div_pd

R Documentation

Faith's Phylogenetic Diversity of a Community

Description

Estimate PD \insertCiteFaith1992divent or FD \insertCitePetchey2002divent from abundance or probability data and a phylogenetic or functional dendrogram.

Usage

div_pd(x, tree, ...)

## S3 method for class 'numeric'
div_pd(x, tree, prune = FALSE, as_numeric = FALSE, ..., check_arguments = TRUE)

## S3 method for class 'species_distribution'
div_pd(
  x,
  tree,
  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.
`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 div_hill with argument q = 0 if they are needed.

PD and FD are defined as the total length of the branches of the tree.

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 diversity.

References

\insertAllCited

Examples

# diversity of each community
div_pd(paracou_6_abd, tree = paracou_6_taxo)

# gamma diversity
div_pd(paracou_6_abd, tree = paracou_6_taxo, gamma = TRUE)

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