mrbayes.mcmc: MCMC Settings for MrBayes
In ips: Interfaces to Phylogenetic Software in R

Description Usage Arguments Value MCMC Parameters Note Author(s) References See Also Examples

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

1	mrbayes.mcmc(...)

...

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.

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

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

Christoph Heibl

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: http://mrbayes.sourceforge.net/.

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.