phangornMCMC: phangornMCMC This function runs a Markov chain Monte Carlo...

In KlausVigo/phangornMCMC: phangorn MCMC

Description

phangornMCMC This function runs a Markov chain Monte Carlo (MCMC) algorithm to generate a set of trees which is returned with their likelihoods.

Usage

phangornMCMC(x, ntrees = 3000, burnin = 1000, frequency = 1,
  tree0 = NULL, model = NULL, printevery = 100, bf = baseFreq(x),
  Q = rep(1, 6), optBf = TRUE, optQ = TRUE, rooted = TRUE)

Arguments

x	a set of DNA sequences, typically an object of class "DNAbin".
ntrees	the number of trees to output.
burnin	the number of trees to discard as <e2><80><9c>burn-in<e2><80><9d>.
frequency	the frequency at which trees are sampled.
tree0	the initial tree of the chain; by default, a fastME / UPGMA tree from a JC69 distance is generated.
model	the transition model
printevery	an integer specifying the frequency at which to print the numbers of trees proposed and accepted; set to 0 to cancel all printings.
bf	base frequencies
Q	rate matrix

Examples

## Not run: 
data(yeast)
out <- phangornMCMC(yeast)
plot(out)
getMCMCtrees()

## End(Not run)

KlausVigo/phangornMCMC documentation built on May 23, 2019, 4:23 p.m.