Description Usage Arguments Details Value References

A pruning algorithm that seeks to maximise Phylogenetic Diversity (PD) for a set of species of a given size. The algorithm proceeds in a step-wise fashion, removing species that contribute the least to PD until the desired set size is achieved.

1 | ```
phyloprunr(phy, size, iterations = 1, trees = TRUE)
``` |

`phy` |
is a rooted phylogenetic tree with branch lengths stored as a
phylo object (as in the |

`size` |
is the number of tips (species/OTUs) to prune the tree to. |

`iterations` |
is the number of iterations of the algorithm (to resolve ties). Default is 1. |

`trees` |
is a |

`phyloprunr`

takes a phylogenetic tree (rooted and with branch
lengths) and determines the optimal set of tips (species/OTUs) of a given
size that maximises Phylogenetic Diversity (PD). The algorithm determines
step-wise which tip contributes the least to PD (has the shortest terminal
branch) and then removes it, adjusting the terminal branch lengths of the
remaining tips (to accommodate the tip removal) as it goes. The algorithm
will continue until the stipulated set size is achieved. The resulting set
is the set that maximises PD for its size. At each step, ties are resolved
by choosing at random from the available options. For this reason, the user
can repeat the algorithm (using the `iterations`

argument) to generate
several equally optimal sets. For a fully resolved ultrametric tree, there
will be 2^(n-k) possible solutions (where *n* is the number of tips
and *k* is the desired set size), so a large number of iterations of
the algorithm may be needed to explore the range of possible solutions. The
algorithm is descibed in Minh et al. (2006).

If `trees = TRUE`

, a multiphylo object (see `ape`

package)
is returned, consisting of one tree for each iteration of the algorithm. If
`trees = FALSE`

, a list of length `iterations`

is returned where
each element is a vector of tip labels / species names corresponding to an
optimal set.

Minh B., Klaere S. & Haeseler A. (2006). Phylogenetic Diversity within Seconds.

*Systematic Biology*55: 769–773.

davidnipperess/PDcalc documentation built on July 1, 2018, 3:59 p.m.

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