Skip to contents

Run JAGS from R

Source: R/utils.R
jags2_baker.Rd

The jags function takes data and starting values as input. It automatically writes a jags script, calls the model, and saves the simulations for easy access in R. Check the R2jags::jags2 for details about the argument.

Usage

jags2_baker(
  data,
  inits,
  parameters.to.save,
  model.file = "model.bug",
  n.chains = 3,
  n.iter = 2000,
  n.burnin = floor(n.iter/2),
  n.thin = max(1, floor((n.iter - n.burnin)/1000)),
  DIC = TRUE,
  jags.path = "",
  working.directory = NULL,
  clearWD = TRUE,
  refresh = n.iter/50
)

Arguments

data

(1) a vector or list of the names of the data objects used by the model, (2) a (named) list of the data objects themselves, or (3) the name of a "dump" format file containing the data objects, which must end in ".txt", see example below for details.

inits

a list with n.chains elements; each element of the list is itself a list of starting values for the BUGS model, or a function creating (possibly random) initial values. If inits is NULL, JAGS will generate initial values for parameters.

parameters.to.save

character vector of the names of the parameters to save which should be monitored.

model.file

file containing the model written in BUGS code. Alternatively, as in R2WinBUGS, model.file can be an R function that contains a BUGS model that is written to a temporary model file (see tempfile) using write.model

n.chains

number of Markov chains (default: 3)

n.iter

number of total iterations per chain (including burn in; default: 2000)

n.burnin

length of burn in, i.e. number of iterations to discard at the beginning. Default is n.iter/2, that is, discarding the first half of the simulations. If n.burnin is 0, jags() will run 100 iterations for adaption.

n.thin

thinning rate. Must be a positive integer. Set n.thin > 1 to save memory and computation time if n.iter is large. Default is max(1, floor(n.chains * (n.iter-n.burnin) / 1000)) which will only thin if there are at least 2000 simulations.

DIC

logical; if TRUE (default), compute deviance, pD, and DIC. The rule pD=var(deviance) / 2 is used.

jags.path

directory that contains the JAGS executable. The default is “”.

working.directory

sets working directory during execution of this function; This should be the directory where model file is.

clearWD

indicating whether the files data.txt, inits[1:n.chains].txt, codaIndex.txt, jagsscript.txt, and CODAchain[1:nchains].txt should be removed after jags has finished, default=TRUE.

refresh

refresh frequency for progress bar, default is n.iter/50

Value

Same as R2jags::jags()

Details

This modifies the jags2 function in R2jags package.

See also

R2jags::jags()