treeOperators {coalescentMCMC} | R Documentation |
Trees Operators for Running MCMC
Description
These functions provide tools for tree rearrangement to be used as operators in a MCMC run.
Usage
NeighborhoodRearrangement(phy, n, THETA, brtimes)
TipInterchange(phy, n)
Arguments
phy |
a tree of class |
n |
the number of tips in |
THETA |
The estimate of |
brtimes |
the branching times of |
Details
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).
Value
an object of class "phylo"
.
Author(s)
Emmanuel Paradis
References
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.
See Also
Examples
tr <- rcoal(10)
ts <- NeighborhoodRearrangement(tr, 10, 1, branching.times(tr))
layout(matrix(1:2, 2))
plot(tr); plot(ts)
layout(1)