run_nm: Run NONMEM jobs
In tsahota/NMproject: Script Based 'NONMEM' Model Development

run_nm

R Documentation

Run NONMEM jobs

Description

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

Usage

run_nm(
  m,
  threads = Inf,
  ignore.stdout = FALSE,
  quiet = getOption("quiet_run"),
  intern = getOption("intern"),
  force = FALSE,
  cache_ignore_cmd = FALSE,
  cache_ignore_ctl = FALSE,
  cache_ignore_data = FALSE
)

Arguments

`m`	An nm object.
`threads`	Numeric. Number of jobs to run concurrently (default = `Inf`). Will block the console until all jobs are submitted.
`ignore.stdout`	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?

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 with a gap of getOption("job_time_spacing") seconds (default = 0). This could overwhelm resources if not in a grid environment.

run_nm is a variant of run_nm_single() containing a threads argument that will submit run_nm()'s in batches and wait for them to complete. If you need all the runs to complete ensure you use a wait_finish() statement afterwards as R console will only be blocked for until the last batch has been submitted which will be before all runs have completed.

The job_time_spacing argument

Value

m with job_info fields populated.

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)

tsahota/NMproject documentation built on Oct. 1, 2022, 11:51 a.m.