treeOperators | R Documentation |

These functions provide tools for tree rearrangement to be used as operators in a MCMC run.

NeighborhoodRearrangement(phy, n, THETA, brtimes) TipInterchange(phy, n)

`phy` |
a tree of class |

`n` |
the number of tips in |

`THETA` |
The estimate of |

`brtimes` |
the branching times of |

`NeighborhoodRearrangement`

performs a rearrangement as described
by Kuhner et al. (1995).

`TipInterchange`

interchanges two tips under the condition that
they are not sisters.

`EdgeLengthJittering`

alters the branch lengths by adding a
random value from a uniform distribution defined by
`range(phy$edge.length)`

(the ultrametric nature of the tree is
conserved).

an object of class `"phylo"`

.

Emmanuel Paradis

Kuhner, M. K., Yamato, J. and Felsenstein, J. (1995) Estimating
effective population size and mutation rate from sequence data using
Metropolis-Hastings sampling. *Genetics*, **140**, 1421–1430.

`coalescentMCMC`

, `dcoal`

tr <- rcoal(10) ts <- NeighborhoodRearrangement(tr, 10, 1, branching.times(tr)) layout(matrix(1:2, 2)) plot(tr); plot(ts) layout(1)

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