setControl function

Set up controls for a JAGS segregation ratio model run

Sets up directives for running JAGS which are subsequently put into a .cmd file. MCMC attributes such as the size of burn in, length of MCMC and thinning may be specified

setControl(model, stem = "test", burn.in = 2000, sample = 5000, thin = 1,
 bugs.file = paste(stem, ".bug", sep = ""),
 data.file = paste(stem, "-data.R", sep = ""),
 inits.file = paste(stem, "-inits.R", sep = ""),
 monitor.var = model$monitor.var, seed=1)

Arguments

• model: object of class modelSegratioMM specifying model parameters, ploidy etc
• stem: text to be used as part of JAGS .cmd file name
• burn.in: size of MCMC burn in (Default: 2000)
• sample: size of MCMC sample (default: 5000)
• thin: thinning interval between consecutive observations. Thinning may be a scalar or specified for each variable set by specifying a vector (default: 1 or no thinning)
• bugs.file: name of .bug file
• data.file: name of data file
• inits.file: name of inits file
• monitor.var: which variables to be monitored (Default: as per model)
• seed: seed for JAGS run for Windows only (for unix set seed in setInits)

Returns

Returns an object of class jagsControl which is a list with components - jags.code: Text containing control statements for JAGS

.cmd file

• model: object of class modelSegratioMM specifying model parameters, ploidy etc

• stem: text to be used as part of JAGS .cmd file name

• burn.in: size of MCMC burn in (Default: 2000)

• sample: size of MCMC sample (default: 5000)

• thin: thinning interval between consecutive observations

• bugs.file: name of .bug file

• data.file: name of data file

• inits.file: name of inits file

• monitor.var: which variables to be monitored

• call: function call

Author(s)

Peter Baker p.baker1@uq.edu.au

See Also

setModel 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)

## set up model with 3 components
x <- setModel(3,8)
x2 <- setPriors(x)

jc <- setControl(x)
print(jc)