ips (version 0.0.13)

mrbayes.mcmc: MCMC Settings for MrBayes

Description

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

Usage

mrbayes.mcmc(...)

Value

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

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.

MCMC Parameters

ngen

"NUMERIC"

nruns

"NUMERIC"

nchains

"NUMERIC"

temp

"NUMERIC"

% # reweight <number>,<number> 0.00 v 0.00 ^,

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"

% # filename = filename,

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"

Author

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()