def _agg_pop_wtd_ages_birth(self, age_group_id):
age_tree = agetree(age_group_id)
age_tree.add_node(age.BIRTH, {}, age_tree.root.id)
# make the source and sink
source = self.gen_draw_source()
source.add_transform(convert_to_counts, self.population,
self.dimensions.data_list())
sink = self.gen_draw_sink()
sink.add_transform(convert_to_rates, self.population,
self.dimensions.data_list())
# constuct aggregator obj
operator = Sum(index_cols=[
col for col in self.dimensions.index_names if col != "age_group_id"
],
value_cols=self.dimensions.data_list())
aggregator = AggSynchronous(draw_source=source,
draw_sink=sink,
index_cols=[
col
for col in self.dimensions.index_names
if col != "age_group_id"
],
aggregate_col="age_group_id",
operator=operator)
aggregator.run(age_tree)
def compute_sex_aggregates(self):
sex_tree = sextree()
# make the source and sink
source = self.gen_draw_source()
source.add_transform(
fill_square,
index_cols=[
col for col in self.dimensions.index_names if col != "sex_id"
],
square_col="sex_id",
square_col_vals=[node.id for node in sex_tree.leaves()])
sink = self.gen_draw_sink()
# construct aggregator obj
operator = WtdSum(
index_cols=[
col for col in self.dimensions.index_names if col != "sex_id"
],
value_cols=self.dimensions.data_list(),
weight_df=self.population,
weight_name="population",
merge_cols=["location_id", "year_id", "age_group_id", "sex_id"])
aggregator = AggSynchronous(draw_source=source,
draw_sink=sink,
index_cols=[
col
for col in self.dimensions.index_names
if col != "sex_id"
],
aggregate_col="sex_id",
operator=operator)
# run the tree
aggregator.run(sex_tree)
def _agg_age_std_ages(self):
age_tree = agetree(27)
# make the source and sink
source = self.gen_draw_source()
source.add_transform(
fill_square,
index_cols=[
col for col in self.dimensions.index_names
if col != "age_group_id"
],
square_col="age_group_id",
square_col_vals=[node.id for node in age_tree.leaves()])
sink = self.gen_draw_sink()
# constuct aggregator obj
operator = WtdSum(index_cols=[
col for col in self.dimensions.index_names if col != "age_group_id"
],
value_cols=self.dimensions.data_list(),
weight_df=self.std_age_weights,
weight_name="age_group_weight_value",
merge_cols=["age_group_id"])
aggregator = AggSynchronous(draw_source=source,
draw_sink=sink,
index_cols=[
col
for col in self.dimensions.index_names
if col != "age_group_id"
],
aggregate_col="age_group_id",
operator=operator)
# run the tree
aggregator.run(age_tree)
def _get_population(
version: MachineParameters,
location_set_id: int = constants.LocationSetId.OUTPUTS,
agg_loc_sets: Optional[List[int]] = (
constants.LocationAggregation.Ids.SPECIAL_LOCATIONS +
[constants.LocationSetId.OUTPUTS])
) -> pd.DataFrame:
"""
Unpacks arguments from version object to use with get_population
function. Requests most detailed ages and most detailed sexes because
age-sex population aggregates are created in the summarize module.
Dependant on demographics team to upload population for majority of
aggregate locations but currently uses AggSynchronous to create population
information for select Norway locations in LocationSetId.OUTPUTS.
Arguments:
version (MachineParameters): object containing all the demographic
and configuration data needed to query population
estimates.
location_set_id (int): The id for hierarchy to aggregate up
agg_loc_sets (list): Additional location sets to create special
aggregates
Return:
pd.DataFrame
"""
pop = get_population(age_group_id=version.most_detailed_age_group_ids,
location_id=version.location_ids,
year_id=version.year_ids,
sex_id=version.sex_ids,
run_id=version.population_version_id,
decomp_step=version.decomp_step,
gbd_round_id=version.gbd_round_id)
io_mock = {}
source = DrawSource({"draw_dict": io_mock, "name": "tmp"}, mem_read_func)
sink = DrawSink({"draw_dict": io_mock, "name": "tmp"}, mem_write_func)
index_cols = constants.Columns.DEMOGRAPHIC_INDEX
data_cols = [constants.Columns.POPULATION]
sink.push(pop[index_cols + data_cols])
# location
if agg_loc_sets:
assert len(agg_loc_sets) == len(set(agg_loc_sets))
assert agg_loc_sets[-1] == constants.LocationSetId.OUTPUTS
for set_id in agg_loc_sets:
loc_tree = dbtrees.loctree(location_set_id=set_id,
gbd_round_id=version.gbd_round_id)
operator = Sum(index_cols=([
col for col in index_cols
if col != constants.Columns.LOCATION_ID
]),
value_cols=data_cols)
aggregator = AggSynchronous(
draw_source=source,
draw_sink=sink,
index_cols=([
col for col in index_cols
if col != constants.Columns.LOCATION_ID
]),
aggregate_col=constants.Columns.LOCATION_ID,
operator=operator)
aggregator.run(loc_tree)
special_locations = source.content()
else:
special_locations = pd.DataFrame()
return pd.concat([
pop, special_locations.
loc[~special_locations.location_id.isin(pop.location_id.unique())]
],
ignore_index=True)
def new_population(self, location_set_id, agg_loc_sets=[]):
dim = self.nonfatal_dimensions.get_simulation_dimensions(
self.measure_id)
df = get_population(
age_group_id=(
dim.index_dim.get_level("age_group_id") + [164]),
location_id=dbtrees.loctree(location_set_id=location_set_id,
gbd_round_id=self.gbd_round_id
).node_ids,
sex_id=dim.index_dim.get_level("sex_id"),
year_id=dim.index_dim.get_level("year_id"))
index_cols = ["location_id", "year_id", "age_group_id", "sex_id"]
data_cols = ["population"]
io_mock = {}
source = DrawSource({"draw_dict": io_mock, "name": "tmp"},
mem_read_func)
sink = DrawSink({"draw_dict": io_mock, "name": "tmp"}, mem_write_func)
sink.push(df[index_cols + data_cols])
# location
for set_id in agg_loc_sets:
loc_tree = dbtrees.loctree(
location_set_id=set_id,
gbd_round_id=self.gbd_round_id)
operator = Sum(
index_cols=[col for col in index_cols if col != "location_id"],
value_cols=data_cols)
aggregator = AggSynchronous(
draw_source=source,
draw_sink=sink,
index_cols=[col for col in index_cols if col != "location_id"],
aggregate_col="location_id",
operator=operator)
aggregator.run(loc_tree)
# age
for age_group_id in ComoSummaries._gbd_compare_age_group_list:
age_tree = dbtrees.agetree(age_group_id)
operator = Sum(
index_cols=[col for col in index_cols if col != "age_group_id"
],
value_cols=data_cols)
aggregator = AggSynchronous(
draw_source=source,
draw_sink=sink,
index_cols=[col for col in index_cols if col != "age_group_id"
],
aggregate_col="age_group_id",
operator=operator)
aggregator.run(age_tree)
# sex
sex_tree = dbtrees.sextree()
operator = Sum(
index_cols=[col for col in index_cols if col != "sex_id"],
value_cols=data_cols)
aggregator = AggSynchronous(
draw_source=source,
draw_sink=sink,
index_cols=[col for col in index_cols if col != "sex_id"],
aggregate_col="sex_id",
operator=operator)
aggregator.run(sex_tree)
df = source.content()
df.to_hdf(
"{}/info/population.h5".format(self.como_dir),
'draws',
mode='w',
format='table',
data_columns=["location_id", "year_id", "age_group_id", "sex_id"])
def location_aggregate_birth_counts(gbd_round_id: int, decomp_step: str,
constants_path: pathlib.PosixPath,
location_set_id: int) -> None:
"""
for given gbd_round, decomp_step, location_set_id, get a complete
set of location-aggregated live births
"""
logger.info(f'aggregating for location_set_id {location_set_id}')
multiple_tree_flag = (location_set_id
in mmr_constants.MULTIPLE_ROOT_LOCATION_SET_IDS)
scalars = get_regional_scalars(gbd_round_id, decomp_step)
index_cols = ['location_id', 'year_id', 'age_group_id', 'sex_id']
cov_estimate_filename = (
mmr_constants.COV_ESTIMATES_FORMAT_FILENAME.format(location_set_id))
region_locs, most_detailed_locs = get_location_level_sets(
gbd_round_id=gbd_round_id,
decomp_step=decomp_step,
location_set_id=location_set_id)
save_birth_count_estimates(gbd_round_id=gbd_round_id,
decomp_step=decomp_step,
cov_estimate_filepath=constants_path /
cov_estimate_filename,
location_set_id=location_set_id,
most_detailed_locs=most_detailed_locs)
loc_trees = dbtrees.loctree(location_set_id=location_set_id,
gbd_round_id=gbd_round_id,
decomp_step=decomp_step,
return_many=multiple_tree_flag)
if not multiple_tree_flag:
loc_trees = [loc_trees]
draw_source = DrawSource(params={
'draw_dir': str(constants_path),
'file_pattern': cov_estimate_filename
})
i = 1
output_filenames = []
for loc_tree in loc_trees:
output_filename = f'{location_set_id}_{i}.h5'
i += 1
draw_sink = DrawSink(params={
'draw_dir': str(constants_path),
'file_pattern': output_filename
})
draw_sink.add_transform(
_apply_regional_scalars,
regional_scalars_df=scalars.query('location_id in @region_locs'),
gbd_round_id=gbd_round_id,
decomp_step=decomp_step)
op = Sum(index_cols=[s for s in index_cols if s != 'location_id'],
value_cols=[mmr_constants.Columns.LIVE_BIRTH_VALUE_COL])
AggSynchronous(
draw_source=draw_source,
draw_sink=draw_sink,
index_cols=[s for s in index_cols if s != 'location_id'],
aggregate_col='location_id',
operator=op).run(loc_tree, include_leaves=True)
output_filenames.append(output_filename)
return output_filenames