runJags {polySegratioMM} | R Documentation |
Runs external program JAGS
and returns MCMC list for processing
by coda
.
runJags(jags.control, jags = "jags", quiet = FALSE, cmd.file = paste(jags.control$stem, ".cmd", sep = ""), timing = TRUE)
jags.control |
Object of class jagsControl containing MCMC
burn in, sample and thinning as well as relavant files for BUGS
commands, inits and data |
jags |
Name of JAGS program assumed to be in
PATH. However, jags may explicitly set here to include the full path
name |
quiet |
Locial to return program output (Default: FALSE) |
cmd.file |
JAGS .cmd commad file (Default: deduced from
jags.control ) |
timing |
Logical to return timing information such as date started and ended and elapsed user and system time |
Returns object of class runJAGS
with components
jags.control |
Object of class jagsControl |
exit |
integer indicating return error (0 if no errors) |
cmd.file |
JAGS command file |
start.time |
time JAGS run started |
end.time |
time JAGS run finished |
elapsed.time |
elapsed user and system time |
call |
function call |
Peter Baker p.baker1@uq.edu.au
setPriors
setInits
expected.segRatio
segRatio
setControl
dumpData
dumpInits
or for an easier way to
run a segregation ratio mixture model see
runSegratioMM
## simulate small autooctaploid data set a1 <- sim.autoMarkers(8,c(0.7,0.2,0.1),n.markers=100,n.individuals=50) sr <- segregationRatios(a1$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)