setControl {polySegratioMM} | R Documentation |
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)
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 ) |
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 |
Peter Baker p.baker1@uq.edu.au
setModel
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) ## set up model with 3 components x <- setModel(3,8) x2 <- setPriors(x) jc <- setControl(x) print(jc)