Calculate.Index: Indices values and Jack-knife indices for a single topology.

In Dmirandae/jrich: Jack-Knife Support for Evolutionary Distinctiveness Indices I and W

Description

The funtion calculates standard and terminal jack-knifed indices I and W [see Miranda-Esquivel 2016], along with Posadas et al. (2001) modifications.

Usage

Calculate.Index(tree = tree, distribution = distribution, jtip = 0,
  verbose = TRUE, standard = "distribution")

Arguments

tree	is a single tree with n terminals, an ape phylo object.
distribution	species distributions in m areas, a data.frame
jtip	is the proportion of terminals to delete, real (range 0-1).
verbose	Boolean. If TRUE, the output reports the number of deleted terminals/topologies.
standard	"distribution" or "tree" to standarize by the by the sum of indices in the distribution or the sum of indices in the tree.

Author(s)

Miranda-Esquivel Daniel R.

Examples

library(jrich)

data(tree)
data(distribution)

## Standarized by the sum of indices in the distribution
Calculate.Index(tree=tree, distribution = distribution, verbose=TRUE, standard = "distribution")

## Standarized by the sum of indices in the tree (as figure 1 in Miranda-Esquivel 2016)
Calculate.Index(tree=tree, distribution = distribution, verbose=TRUE, standard = "tree")

Dmirandae/jrich documentation built on May 6, 2019, 2:50 p.m.