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 THETA for |
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.