def df(mi, settings):
alchemy = Alchemy(settings)
d = DismodFiller(path=Path('temp.db'),
settings_configuration=settings,
measurement_inputs=mi,
grid_alchemy=alchemy,
parent_location_id=70,
sex_id=2)
d.fill_for_parent_child()
return d
def main(args=None):
"""
Creates a dismod database using the saved inputs and the file
structure specified in the context.
Then runs an optional set of commands on the database passed
in the --commands argument.
Also passes an optional argument --options as a dictionary to
the dismod database to fill/modify the options table.
"""
args = get_args(args=args)
logging.basicConfig(level=LEVELS[args.loglevel])
if args.test_dir:
context = Context(model_version_id=args.model_version_id,
configure_application=False,
root_directory=args.test_dir)
else:
context = Context(model_version_id=args.model_version_id)
inputs, alchemy, settings = context.read_inputs()
# If we want to override the rate priors with posteriors from a previous
# database, pass them in here.
if args.prior_parent or args.prior_sex:
if not (args.prior_parent and args.prior_sex):
raise RuntimeError("Need to pass both prior parent and sex or neither.")
child_prior = DismodExtractor(path=context.db_file(
location_id=args.prior_parent,
sex_id=args.prior_sex
)).gather_draws_for_prior_grid(
location_id=args.parent_location_id,
sex_id=args.sex_id,
rates=[r.rate for r in settings.rate]
)
else:
child_prior = None
df = DismodFiller(
path=context.db_file(location_id=args.parent_location_id, sex_id=args.sex_id),
settings_configuration=settings,
measurement_inputs=inputs,
grid_alchemy=alchemy,
parent_location_id=args.parent_location_id,
sex_id=args.sex_id,
child_prior=child_prior
)
df.fill_for_parent_child(**args.options)
run_dismod_commands(dm_file=df.path.absolute(), commands=args.commands)
def fill_database(path: Union[str, Path], settings: SettingsConfig,
inputs: MeasurementInputs, alchemy: Alchemy,
parent_location_id: int, sex_id: int,
child_prior: Dict[str, Dict[str, np.ndarray]],
mulcov_prior: Dict[Tuple[str, str, str],
_Prior], options: Dict[str, Any]) -> None:
"""
Fill a DisMod database at the specified path with the inputs, model, and settings
specified, for a specific parent and sex ID, with options to override the priors.
"""
df = DismodFiller(
path=path,
settings_configuration=settings,
measurement_inputs=inputs,
grid_alchemy=alchemy,
parent_location_id=parent_location_id,
sex_id=sex_id,
child_prior=child_prior,
mulcov_prior=mulcov_prior,
)
df.fill_for_parent_child(**options)
def test_format_rate_grid_for_ihme(mi):
settings = load_settings(BASE_CASE)
alchemy = Alchemy(settings)
d = DismodFiller(
path='none',
settings_configuration=settings,
measurement_inputs=mi,
grid_alchemy=alchemy,
parent_location_id=70,
sex_id=2
)
grid = format_rate_grid_for_ihme(
rates=d.parent_child_model['rate'],
gbd_round_id=6,
location_id=70,
sex_id=2
)
assert all(grid.columns == ['location_id', 'year_id', 'age_group_id',
'sex_id', 'measure_id', 'mean', 'upper', 'lower'])