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Run a batch of iterations for a jags model and return only strategic output.

Source: R/tar_jags_rep.R
tar_jags_rep_run.Rd

Not a user-side function. Do not invoke directly.

Usage

tar_jags_rep_run(
  jags_lines,
  jags_name,
  jags_file,
  parameters.to.save,
  data,
  variables = NULL,
  summaries = NULL,
  summary_args = NULL,
  transform = NULL,
  reps,
  output,
  n.cluster = n.cluster,
  n.chains = n.chains,
  n.iter = n.iter,
  n.burnin = n.burnin,
  n.thin = n.thin,
  jags.module = jags.module,
  inits = inits,
  RNGname = RNGname,
  stdout = stdout,
  stderr = stderr,
  progress.bar = progress.bar,
  refresh = refresh
)

Arguments

jags_lines

Character vector of lines from a JAGS file.

jags_name

Friendly suffix of the jags model target.

jags_file

Original path to the input jags file.

parameters.to.save

Model parameters to save, passed to R2jags::jags() or R2jags::jags.parallel(). See the argument documentation of the R2jags::jags() and R2jags::jags.parallel() help files for details.

data

A list, the original JAGS dataset.

variables

Character vector of model parameter names. The output posterior summaries are restricted to these variables.

summaries

List of summary functions passed to ... in posterior::summarize_draws() through $summary() on the CmdStanFit object.

summary_args

List of summary function arguments passed to .args in posterior::summarize_draws() through $summary() on the CmdStanFit object.

transform

Symbol or NULL, name of a function that accepts arguments data and draws and returns a data frame. Here, data is the JAGS data list supplied to the model, and draws is a data frame with one column per model parameter and one row per posterior sample. Any arguments other than data and draws must have valid default values because jagstargets will not populate them. See the simulation-based calibration discussion thread at https://github.com/ropensci/jagstargets/discussions/31 for an example.

output

Character of length 1 denoting the type of output tibble to return: "draws" for MCMC samples (which could take up a lot of space) "summary" for lightweight posterior summary statistics, and "dic" for the overall deviance information criterion and effective number of parameters.

n.cluster

Number of parallel processes, passed to R2jags::jags() or R2jags::jags.parallel(). See the argument documentation of the R2jags::jags() and R2jags::jags.parallel() help files for details.

n.chains

Number of MCMC chains, passed to R2jags::jags() or R2jags::jags.parallel(). See the argument documentation of the R2jags::jags() and R2jags::jags.parallel() help files for details.

n.iter

Number if iterations (including warmup), passed to R2jags::jags() or R2jags::jags.parallel(). See the argument documentation of the R2jags::jags() and R2jags::jags.parallel() help files for details.

n.burnin

Number of warmup iterations, passed to R2jags::jags() or R2jags::jags.parallel(). See the argument documentation of the R2jags::jags() and R2jags::jags.parallel() help files for details.

n.thin

Thinning interval, passed to R2jags::jags() or R2jags::jags.parallel(). See the argument documentation of the R2jags::jags() and R2jags::jags.parallel() help files for details.

jags.module

Character vector of JAGS modules to load, passed to R2jags::jags() or R2jags::jags.parallel(). See the argument documentation of the R2jags::jags() and R2jags::jags.parallel() help files for details.

inits

Initial values of model parameters, passed to R2jags::jags() or R2jags::jags.parallel(). See the argument documentation of the R2jags::jags() and R2jags::jags.parallel() help files for details.

RNGname

Choice of random number generator, passed to R2jags::jags() or R2jags::jags.parallel(). See the argument documentation of the R2jags::jags() and R2jags::jags.parallel() help files for details.

stdout

Character of length 1, file path to write the stdout stream of the model when it runs. Set to NULL to print to the console. Set to R.utils::nullfile() to suppress stdout. Does not apply to messages, warnings, or errors.

stderr

Character of length 1, file path to write the stderr stream of the model when it runs. Set to NULL to print to the console. Set to R.utils::nullfile() to suppress stderr. Does not apply to messages, warnings, or errors.

progress.bar

Type of progress bar, passed to R2jags::jags() or R2jags::jags.parallel(). See the argument documentation of the R2jags::jags() and R2jags::jags.parallel() help files for details.

refresh

Frequency for refreshing the progress bar, passed to R2jags::jags() or R2jags::jags.parallel(). See the argument documentation of the R2jags::jags() and R2jags::jags.parallel() help files for details.

Value

A data frame of posterior summaries.