readJags: Read MCMC sample(s) from a JAGS run

In polySegratioMM: Bayesian Mixture Models for Marker Dosage in Autopolyploids

Read MCMC sample(s) from a JAGS run

Description

wrapper to read.openbugs which returns object of class mcmc.list and so can be used to specify the start and end iterations for the MCMC sample(s) and also specify thinning

Usage

readJags(run.jags, quiet = TRUE, ...)

Arguments

run.jags	object of class runJAGS produced by running JAGS
quiet	logical to return program output (Default: TRUE)
...	other options for read.openbugs

Value

Returns object of class segratioMCMC with components

run.jags	object of class runJAGS produced by running JAGS
mcmc.list	object of class mcmc.list containing the MCMC sample(s)

Author(s)

Peter Baker [e-mail]

See Also

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

Examples

library(polySegratio)

## simulate small autooctaploid data set
a1 <- sim.autoMarkers(8,c(0.7,0.2,0.1),n.markers=100,n.individuals=50)
##print(a1)
sr <-  segregationRatios(a1$markers)
x <- setModel(3,8)
x2 <- setPriors(x)
cat(x$bugs.code,x2$bugs.code,sep="\n")


x3 <- setModel(3,8, random.effect = TRUE)
x4 <- setPriors(x3, type="strong")

## Not run: 
## write control files for JAGs run
dumpData(sr, x3)
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

xj <- readJags(rj)
print(xj)

## End(Not run)

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