Calculate phylogenetic diversity

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Description

Returns the phylogenetic diversity of a tree for the tips specified.

Usage

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calcPhyDv(tree, tids, ...)

Arguments

tree

TreeMan object

tids

tip ids

...

plyr arguments

Details

Faith's phylogenetic diversity is calculated as the sum of all connected branches for specified tips in a tree. It can be used to investigate how biodviersity as measured by the phylogeny changes. Parallelizable.

References

Faith, D. (1992). Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.

See Also

calcFrPrp, calcOvrlp https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

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library(treeman)
tree <- randTree(10)
calcPhyDv(tree, tree['tips'])

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