shipunov (version 1.0)

MrBayes: Calls MrBayes

Description

A slight improvement of 'ips::mrbayes()'

Usage

MrBayes(x, file="", nst=6, rates="invgamma", ngammacat=4, nruns=2, ngen=1e+06,
 printfreq=100, samplefreq=10, nchains=4, savebrlens="yes", temp=0.2, burnin=10,
 contype="allcompat", run=FALSE, simple=TRUE, exec="mb-mpi")

Arguments

x

The object to process (must be 'DNAbin' class)

file

A character string, giving the name of the MrBayes input file.

nst

An integer giving the number of rates in the model of sequence evolution.

rates

A character string; allowed are "equal", "gamma", "propinv", "invgamma", and "adgamma"; the default is "equal".

ngammacat

An integer; the number rate categories for the discretized Gamma distribution; the default is '4'.

nruns

An integer; the number of runs.

ngen

An integer; the number of states of the MCMC.

printfreq

An integer; the interval between states of the MCMC to be printed on the screen

samplefreq

An integer; the interval between states of the MCMC to be sampled.

nchains

An integer; number of Metropolis coupled MCMCs in each run.

savebrlens

Logical; shall branch lengths be saved.

temp

0.2

burnin

An integer; the number of samples from the MCMC to be discarded prior to further analysis.

contype

A character string; the type of consensus tree calculated from the posterior distribution of trees

run

Logical; 'run = FALSE' will only print the NEXUS file, 'run = TRUE' will also start the MCMC runs, if the 'path' argument is correctly specified.

simple

New option: if TRUE (default), then outputs tree in the format readable by functions from 'ape' package

exec

New option: name of UNIX executable (to appow multithreaded version)

Details

'MrBayes()' is a slight improvement of 'ips::mrbayes()'. Please see its documentation for clarity and other options.

'MrBayes()' has two more options, it also both views and saves output (this works only on UNIX).

See Also

ips::mrbayes

Examples

# NOT RUN {
require(ips)
data(ips.cox1)
x <- ips.cox1[, 100:140]
# }
# NOT RUN {
## requires MrBayes installation
MrBayes(x, file="cox1", ngen=100, run=TRUE)
# }