mrbayes.mcmc: MCMC Settings for MrBayes

In ips: Interfaces to Phylogenetic Software in R

MCMC Settings for MrBayes

Description

Set Markov chain Monte Carlo (MCMC) parameters for mrbayes.

Usage

mrbayes.mcmc(...)

Arguments

...	arguments in tag = value form, or a list of tagged values. The tags must come from the names of MCMC parameters described in the ‘MCMC Parameters’ section.

Value

a list containing a subset (including the empty and the full set) of model parameters.

MCMC Parameters

ngen

"NUMERIC"

nruns

"NUMERIC"

nchains

"NUMERIC"

temp

"NUMERIC"

swapfreq

"NUMERIC"

nswaps

"NUMERIC"

samplefreq

"NUMERIC"

printfreq

"NUMERIC"

printall

"yes" or "no"

printmax

"NUMERIC"

mcmcdiagn

"yes" or "no"

diagnfreq

"NUMERIC"

diagnstat

"avgstddev" or "maxstddev"

minpartfreq

"NUMERIC"

allchains

"yes" or "no"

allcomps

"yes" or "no"

relburnin

"yes" or "no"

burnin

"NUMERIC"

burninfrac

"NUMERIC"

stoprule

"yes" or "no"

stopval

"NUMERIC"

savetrees

"yes" or "no"

checkpoint

"yes" or "no"

checkfreq

"NUMERIC"

startparams

"current" or "reset"

starttree

"current", "random", or "parsimony"

nperts

"NUMERIC"

data

"yes" or "no"

ordertaxa

"yes" or "no"

append

"yes" or "no"

autotune

"yes" or "no"

tunefreq

"NUMERIC"

Note

The parameters reweight and filename cannot be set via mrbayes.mcmc.

Author(s)

Christoph Heibl

References

J.P. Huelsenbeck & Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.

Ronquist F. & J.P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Biometrics 19: 1572-1574.

MrBayes website: https://mrbayes.sourceforge.net/.

See Also

mrbayes.lset to set model parameters, mrbayes.prset to set prior distributions, and mrbayes to run MrBayes locally or prepare input files for a computer cluster.

Examples

mrbayes.mcmc()

ips documentation built on May 29, 2024, 4:39 a.m.