Description Usage Arguments Author(s) Examples

View source: R/Calculate.Index.R

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.

1 2 3 4 5 6 7 8 | ```
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")
``` |

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