tar_jags_rep_run: Run a batch of iterations for a jags model and return only...
In jagstargets: Targets for JAGS Pipelines

tar_jags_rep_run

R Documentation

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

Description

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.