mrbayes.mcmc: MrBayes MCMC settings

In ips: Interfaces to Phylogenetic Software in R

MrBayes MCMC settings

Description

Specify the MCMC settings for mrbayes.

Usage

mrbayes.mcmc(
  ngen = 1e+06,
  nruns = 2,
  nchains = 4,
  temp = 0.1,
  reweight = c(0, 0),
  swapfreq = 1,
  nswaps = 1,
  samplefreq = 500,
  printfreq = 1000,
  printall = TRUE,
  printmax = 8,
  mcmcdiagn = TRUE,
  diagnfreq = 5000,
  diagnstat = "avgstddev",
  minpartfreq = 0.1,
  allchains = FALSE,
  allcomps = FALSE,
  relburnin = TRUE,
  burnin = 0,
  burninfrac = 0.25,
  stoprule = FALSE,
  stopval = 0.05,
  savetrees = FALSE,
  checkpoint = TRUE,
  checkfreq = 2000,
  startparams = "current",
  starttree = "current",
  nperts = 0,
  data = TRUE,
  ordertaxa = FALSE,
  append = FALSE,
  autotune = TRUE,
  tunefreq = 100
)

Arguments

ngen	A character string
nruns	xxx
nchains	xxx
temp	xxx
reweight	xxx
swapfreq	xxx
nswaps	xxx
samplefreq	xxx
printfreq	xxx
printall	xxx
printmax	xxx
mcmcdiagn	xxx
diagnfreq	xx
diagnstat	xxx
minpartfreq	xxx
allchains	xxx
allcomps	xxx
relburnin	xxx
burnin	xxx
burninfrac	xxx
stoprule	xxx
stopval	xxx
savetrees	xxx
checkpoint	xxx
checkfreq	xxx
startparams	xxx
starttree	xxx
nperts	xxx
data	xxx
ordertaxa	xxx
append	xxx
autotune	xxx
tunefreq	xxx

Details

xxx

Value

A list of MCMC parameters.

See Also

mrbayes, mrbayes.lset , mrbayes.prset.

ips documentation built on July 8, 2026, 5:07 p.m.