run_nm_single: Run NONMEM jobs (single job)

In NMproject: Script Based 'NONMEM' Model Development

Run NONMEM jobs (single job)

Description

Run nm objects. Uses system_nm() to submit the cmd() value of object.

Usage

run_nm_single(
  m,
  ignore.stdout = FALSE,
  ignore.stderr = FALSE,
  quiet = getOption("quiet_run"),
  intern = getOption("intern"),
  force = FALSE,
  cache_ignore_cmd = FALSE,
  cache_ignore_ctl = FALSE,
  cache_ignore_data = FALSE,
  return_cmd_only = FALSE
)

Arguments

m	An nm object.
ignore.stdout	Logical (default=TRUE). Parameter passed to system_nm().
ignore.stderr	Logical (default=TRUE). Parameter passed to system_nm().
quiet	Logical (default=FALSE). Should system_nm() output be piped to screen?
intern	Logical. intern argument to be passed to system_nm().
force	Logical (default = FALSE). Force run even results unchanged.
cache_ignore_cmd	Logical (default = FALSE). Should check cmd field with cache?
cache_ignore_ctl	Logical (default = FALSE). Should check control file contents with cache?
cache_ignore_data	Logical (default = FALSE). Should check dataset with cache?
return_cmd_only	Logical. Instead of running cmd, return the command information in the form of a tibble. This is intended for use in run_nm() batch submission.

Details

In grid environment it is recommended to run nm_tran() via the RStudio 'Addin' prior to executing this code.

By default, when highlighting code and evaluating it via an RStudio app, run_nm() will not execute and will just return the nm object.

For vector nm objects of length more than 1, all runs will be launched at the same time. This could overwhelm resources if not in a grid environment. In this case see run_nm() for batched execution of a vector valued nm object.

Value

m with job_info fields populated.

See Also

nm_tran()

Examples

## requires NONMEM to be installed
## Not run: 
m1 <- new_nm(
  run_id = "m1",
  based_on = "staging/Models/ADVAN2.mod",
  data_path = "DerivedData/data.csv"
) %>%
  cmd("execute {ctl_name} -dir={run_dir}") %>%
  fill_input() %>%
  run_nm()

## End(Not run)

NMproject documentation built on Sept. 30, 2022, 1:06 a.m.