readJags function

Read MCMC sample(s) from a JAGS run

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

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

Returns

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 p.baker1@uq.edu.au

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")

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)
## Not run:

rj <- runJags(small)  ## just run it

xj <- readJags(rj)
print(xj)
## End(Not run)