Description Usage Arguments Details Value Author(s) See Also Examples

This function generates a specified number of trees by permutation or random generation, then checks to make sure that they are unique before returning the original tree plus the generated trees

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`x` |
an object of class |

`N` |
number of new trees to return |

`filebase` |
base name of the file to which trees will be written |

`method` |
method of generating the trees, either nearest neighbor interchange (nni) or random |

`maxmoves` |
maximum number nni moves |

`perms` |
number of permutations per nni stratum; defaults to the number of single-step nni trees, then the remainder of N divided by the number of nni strata requested (negatives not allowed) |

`software` |
not currently used; in an earlier version, would write out analysis file for PAUP or RAxML |

`...` |
further arguments to be passed to rtree |

The main need for this function is to ensure that the trees you get back are unique... mainly just a wrapper to rNNI and rtree.
`perms`

defaults to:

`c(length(nni(x)), max(1, as.integer(N - (length(nni(x))))))`

an object of class `"multiPhylo"`

Andrew Hipp

`gen.RAD.loci.datasets`

,
`compare.all.trees`

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RADami documentation built on May 30, 2017, 8:23 a.m.

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