runJags {polySegratioMM}

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

Author(s)

Peter Baker [e-mail]

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)