Calculate.Index: Indices values and Jack-knife indices for a single topology.
In jrich: Jack-Knife Support for Evolutionary Distinctiveness Indices I and W

Description Usage Arguments Author(s) Examples

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

1 2	Calculate.Index(tree = tree, distribution = distribution, jtip = 0, verbose = TRUE, standard = "distribution")

`tree`	is a single tree with n terminals, an ape phylo object.
`distribution`	species distributions in n 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

Miranda-Esquivel Daniel R.

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")