setControl {polySegratioMM}R Documentation

Set up controls for a JAGS segregation ratio model run

Description

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

Usage

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 R data file
inits.file name of R 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)

Value

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 R data file
inits.file name of R 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)

[Package polySegratioMM version 0.5-2 Index]