jrich (version 0.60-35)

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

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 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

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")