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

In polySegratioMM: Bayesian Mixture Models for Marker Dosage in Autopolyploids

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)

## Not run: 

## write control files for JAGs run
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)

## End(Not run)

polySegratioMM documentation built on Feb. 25, 2026, 5:08 p.m.