phylodiv.expect.secured: Expected Phylogenetic Diversity from conservation of...

In davidnipperess/PDcalc: An implementation of the Phylogenetic Diversity (PD) calculus in R

Description

Calculates expected Phylogenetic Diversity (PD) with and without successful management of a list of threatened species. Note that this function uses that version of PD that always includes the path to the root of the tree.

Usage

phylodiv.expect.secured(
  phy,
  species = phy$tip.label,
  managed = species,
  survival,
  feasibility = 1,
  success = 0.95
)

Arguments

phy	is a rooted phylogenetic tree with branch lengths stored as a phylo object (as in the ape package).
species	is an optional character vector of species names (tree will be trimmed to match). Each species must match to a tip label in phy. By default, all tip labels in phy will be included.
managed	is a character vector of species names to be managed for conservation. Each name must match to a name in species. By default, all names in species will be included.
survival	is a numeric vector of survival probabilities, given no management for conservation, corresponding to each species in species.
feasibility	is an optional numeric vector of probabilities of successfully managing each species in managed. By default, probability of success is assumed to be 1.
success	is a numeric vector of length 1, giving the probability of survival of a species if successfully managed for conservation. Value must be less than 1.

Details

phylodiv.expected.secured takes the probability of survival of species (before and after management) and a phylogenetic tree (rooted and with branch lengths) and calculates expected Phylogenetic Diversity (PD). PD is defined as the total length of all branches spanning a set of species (Faith, 1992). Expected PD is the summed branch length expected to survive given the probability of survival of species (Witting & Loeschcke 1995; Faith 2013). An optional argument (feasibility) allows for the gain of conserving any species to be down-weighted by the probability that management will be successful.

Value

A numeric vector giving three values corresponding to: expected PD with management; expected PD without management; and the gain in expected PD with management (i.e. the difference).

References

• Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61: 1-10.

• Faith DP. 2013. Biodiversity and evolutionary history: useful extensions of the PD phylogenetic diversity assessment framework. Annals of the New York Academy of Sciences 1289: 69-89.

• Witting L. & Loeschcke V. 1995. The optimization of biodiversity conservation. Biological Conservation 71: 205-207.

Examples

data(bandicoot_tree)
threatened <- c("Macrotis_lagotis","Rhynchomeles_prattorum","Peroryctes_broadbenti",
       "Isoodon_auratus","Perameles_gunnii","Perameles_bougainville")
probs <- c(0.01,0.90,0.01,0.30,0.99,0.99,0.99,0.99,0.99,0.99,0.30,0.99,0.90,0.99,0.99,0.99,0.90,0.01,0.90)
phylodiv.expect.secured(bandicoot_tree,managed=threatened,survival=probs)

davidnipperess/PDcalc documentation built on July 7, 2021, 1:07 p.m.