ips (version 0.1.1)

mrbayes.mcmc: 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
)

Value

A list of MCMC parameters.

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

See Also

mrbayes, mrbayes.lset , mrbayes.prset.