Check the status of NONMEM run(s)

Checks the status of bbi_base_model object(s) by looking for a bbi_config.json file. Other operations (such as returning messages or freezing the R console) may be done as a result.

check_nonmem_finished(.mod, ...)

get_model_status(.mod, max_print = 10, ...)

wait_for_nonmem(.mod, .time_limit = 300, .interval = 5, .delay = 1.5)

Arguments

.mod

a bbi_base_model or list of bbi_base_model objects. Other packages (e.g., bbr.bayes) may add additional methods.

...

Arguments passed to methods.

max_print

max number of models to explicitly print to the console. If the number of finished or incomplete models are greater than this number, just print the number of models.

.time_limit

integer for maximum number of seconds in total to wait before continuing (will exit after this time even if the run does not appear to have finished).

.interval

integer for number of seconds to wait between each check.

.delay

integer for number of seconds to wait before scanning the output directories. This function will exit early if no output directory exists, so this argument serves to delay this evaluation (e.g. if calling right after submit_model() in an Rmarkdown file).

Details

If the result of get_model_status() assigned to a variable, users can inspect the full list of runs to determine exactly which models are still running vs. have finished executing:

res <- get_model_status(mod_list)
res

Bootstrap Runs

When providing a bbi_nmboot_model object to get_model_status() or wait_for_nonmem(), the individual model runs (get_boot_models(.boot_run)) will be checked instead, returning more informative messages about the status of the bootstrap run.

Functions

• check_nonmem_finished(): Returns TRUE if the model appears to be finished running and FALSE otherwise.

• get_model_status(): Returns messages indicating which model(s) have finished executing and which are incomplete. Also invisibly returns a data.frame with a row for each model and a logical finished column.

• wait_for_nonmem(): Wait for NONMEM models to finish. i.e. freeze the user's console until the model(s) have finished running.

Examples

if (FALSE) {

# Check if model(s) or bootstrap run has finished:

check_nonmem_finished(.mod)
#> [1] TRUE

check_nonmem_finished(.boot_run)
#> [1] FALSE


# Inspect progress of model(s) or bootstrap run:

get_model_status(.mod)
#> The following model(s) have finished: `1`
#> 0 model(s) are incomplete

get_model_status(.boot_run)
#> 25 model(s) have finished
#> 75 model(s) are incomplete

get_model_status(list(.mod, .boot_run))
#> The following model(s) have finished: `1`
#> The following model(s) are incomplete: `1-boot`


# Freeze the `R` console until model(s) or bootstrap run has finished:

wait_for_nonmem(.mod)
#> Waiting for 1 model(s) to finish...
#> 1 model(s) have finished

# Batch submissions take longer to start
wait_for_nonmem(.boot_run, .delay = 6)
#> Waiting for 100 model(s) to finish...
#> Waiting for 50 model(s) to finish...
#> 100 model(s) have finished

}