Submits a group of models to be run in batch by calling out to bbi
in as
few external calls as possible (see "Details").
submit_models(
.mods,
.bbi_args = NULL,
.mode = getOption("bbr.bbi_exe_mode"),
...,
.overwrite = NULL,
.config_path = NULL,
.wait = TRUE,
.dry_run = FALSE
)
# S3 method for list
submit_models(
.mods,
.bbi_args = NULL,
.mode = getOption("bbr.bbi_exe_mode"),
...,
.overwrite = NULL,
.config_path = NULL,
.wait = TRUE,
.dry_run = FALSE
)
The model objects to submit.
A named list specifying arguments to pass to bbi
formatted like list("nm_version" = "nm74gf_nmfe", "json" = T, "threads" = 4)
. Run print_bbi_args()
to see valid arguments. Note that bbr does
not support changing the output directory (including through the model or
global YAML files).
Either "sge"
, the default, to submit model(s) to the grid or
"local"
for local execution. This can be passed directly to this argument
or set globally with options("bbr.bbi_exe_mode")
.
args passed through to bbi_exec()
Logical to specify whether or not to overwrite existing
model output from a previous run. If NULL
, the default, will defer to
setting in .bbi_args
or bbi.yaml
. If not NULL
will override any
settings in .bbi_args
or bbi.yaml
. The exception to this are
bootstrap runs (bbi_nmboot_model
objects). For bootstrap runs, this
defaults to FALSE
and does not respect any setting passed via
.bbi_args
or a bbi.yaml
config file. To overwrite existing bootstrap
output, a user must pass TRUE
through this argument.
Path to a bbi configuration file. If NULL
, the
default, will attempt to use a bbi.yaml
in the same directory as the
model.
If TRUE
, the default, wait for the bbi process to return
before this function call returns. If FALSE
function will return while
bbi process runs in the background.
Returns an object detailing the command that would be run, insted of running it. This is primarily for testing but also a debugging tool.
The number of bbi
calls to make is determined by the number of
distinct sets of bbi
arguments passed to the submission calls, either
explicitly through .bbi_args
, as specified in the bbi_args
field of the
model YAML, or specified globally in bbi.yaml
.
submit_models(list)
: Takes a list of bbi_base_model
objects.
NONMEM
model extensionsBefore executing the model, bbi
first copies the control stream file to a
subdirectory. Whether a relative path to the data file in the control stream
is adjusted for this change in directory depends on the control stream's file
extension:
For a model with a .mod
extension, bbi
automatically adjusts a
relative data path to make it relative to the execution directory,
following the behavior of PsN
.
For a model with a .ctl
extension, bbi
does not adjust the data
path. A relative data path in the control stream must be specified
one level deeper (i.e. with an additional ../
) to account for the
model being executed in a subdirectory.
Other NONMEM
model extensions:
get_data_path()
,
submit_model()