runJags function

Run JAGS to create MCMC sample for segregation ratio mixture model

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

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

Returns

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

Author(s)

Peter Baker p.baker1@uq.edu.au

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")

## Not run:

small <- setControl(x, burn.in=20, sample=50)
writeControlFile(small)
rj <- runJags(small)  ## just run it
print(rj)
## End(Not run)