polySegratioMM (version 0.6-2)

runJags: Run JAGS to create MCMC sample for segregation ratio mixture model

Description

Runs external program JAGS and returns MCMC list for processing by coda.

Usage

runJags(jags.control, jags = "jags", quiet = FALSE,
 cmd.file = paste(jags.control$stem, ".cmd", sep = ""), timing = TRUE)

Arguments

jags.control

Object of class jagsControl containing MCMC burn in, sample and thinning as well as relavant files for BUGS commands, inits and data

jags

Name of JAGS program assumed to be in PATH. However, jags may explicitly set here to include the full path name

quiet

Locial to return program output (Default: FALSE)

cmd.file

JAGS .cmd commad file (Default: deduced from jags.control)

timing

Logical to return timing information such as date started and ended and elapsed user and system time

Value

• Returns object of class runJAGS with components
• jags.control
  Object of class jagsControl
• exit
  integer indicating return error (0 if no errors)
• cmd.file
  JAGS command file
• start.time
  time JAGS run started
• end.time
  time JAGS run finished
• elapsed.time
  elapsed user and system time
• call
  function call

concept

• segregation ratio
• dominant marker
• autopolyploid

See Also

setPriors setInits expected.segRatio segRatio setControl dumpData dumpInits or for an easier way to run a segregation ratio mixture model see runSegratioMM

Examples

## simulate small autooctaploid data set
a1 <- sim.autoMarkers(8,c(0.7,0.2,0.1),n.markers=100,n.individuals=50)
sr <-  segregationRatios(a1$markers)

## set up model with 3 components
x <- setModel(3,8)
x2 <- setPriors(x)
dumpData(sr, x)
inits <- setInits(x,x2)
dumpInits(inits)
##x.priors <- setPriors(x, "vague")
writeJagsFile(x, x2, stem="test")

small <- setControl(x, burn.in=20, sample=50)
writeControlFile(small)
rj <- runJags(small)  ## just run it
print(rj)