def create_df(data_type,
db_table,
pivot=False,
index=['age', 'race_ethn', 'sex']):
"""
Create pandas DataFrame from database SQL query to select base population
or rate versions to be used in model.
Args:
data_type : string
type of data (e.g. birth, migration, population)
db_table : string
database table name
pivot : boolean, optional (default False)
Returns:
df_sql_result : pandas DataFrame
SQL query result
"""
# connect to database using SQLAlchemy
db_connection_string = database.get_connection_string(
'model_config.yml', 'in_db')
sql_in_engine = create_engine(db_connection_string)
# retrieve rate versions for current model and database table names to query
rate_versions = util.yaml_to_dict('model_config.yml', 'rate_versions')
tables = util.yaml_to_dict('model_config.yml', 'db_tables')
# build query from sql.py
# use database table name and rate versions from .yml file
in_query = getattr(
sql, data_type) % (tables[db_table], rate_versions[data_type])
# pandas DataFrame from query
df_sql_result = pd.read_sql(in_query, sql_in_engine)
# Special case for migration rates: pivot DataFrame since 4 rates in cols
# rates are: domestic in, domestic out, foreign in, foreign out
if pivot:
df_sql_result = util.apply_pivot(df_sql_result)
# create MultiIndex on cohort attributes
if index is not None:
df_sql_result = df_sql_result.set_index(index)
return df_sql_result
def create_df(data_type,db_table,pivot=False):
"""
Create pandas DataFrame from database SQL query to select base population
or rate versions to be used in model.
Args:
data_type : string
type of data (e.g. birth, migration, population)
db_table : string
database table name
pivot : boolean, optional (default False)
Returns:
df_sql_result : pandas DataFrame
SQL query result
"""
# connect to database using SQLAlchemy
db_connection_string = database.get_connection_string('model_config.yml', 'in_db')
sql_in_engine = create_engine(db_connection_string)
# retrieve rate versions for current model and database table names to query
rate_versions = util.yaml_to_dict('model_config.yml', 'rate_versions')
tables = util.yaml_to_dict('model_config.yml', 'db_tables')
# build query from sql.py
# use database table name and rate versions from .yml file
in_query = getattr(sql,data_type) % (tables[db_table],rate_versions[data_type])
# pandas DataFrame from query
df_sql_result = pd.read_sql(in_query, sql_in_engine)
# Special case for migration rates: pivot DataFrame since 4 rates in cols
# rates are: domestic in, domestic out, foreign in, foreign out
if pivot:
df_sql_result = util.apply_pivot(df_sql_result)
# create MultiIndex on cohort attributes
df_sql_result = df_sql_result.set_index(['age','race_ethn','sex'])
return df_sql_result
def run(self):
engine = create_engine(
get_connection_string("model_config.yml", 'output_database'))
db_connection_string = database.get_connection_string(
'model_config.yml', 'in_db')
sql_in_engine = create_engine(db_connection_string)
in_query = getattr(sql, 'max_run_id')
db_run_id = pd.read_sql(in_query, engine, index_col=None)
run_id = pd.Series([db_run_id['max'].iloc[0]])
run_id.to_hdf('temp/data.h5', 'run_id', mode='a')
rate_versions = util.yaml_to_dict('model_config.yml', 'rate_versions')
tables = util.yaml_to_dict('model_config.yml', 'db_tables')
in_query = getattr(
sql, 'inc_mil_gc_pop') % (tables['inc_pop_table'], run_id[0])
in_query2 = getattr(sql, 'inc_mil_hh_pop') % (
tables['population_table'], rate_versions['population'])
pop = pd.read_sql(in_query,
engine,
index_col=['age', 'race_ethn', 'sex'])
pop_mil = pd.read_sql(in_query2,
sql_in_engine,
index_col=['age', 'race_ethn', 'sex'])
pop_mil = pop_mil.loc[pop_mil['mildep'] == 'Y']
pop = pop.join(pop_mil)
pop.rename(columns={'persons': 'mil_gc_pop'}, inplace=True)
pop.rename(columns={'mil_mildep': 'mil_hh_pop'}, inplace=True)
pop = pop.reset_index(drop=False)
pop = pd.DataFrame(pop[['mil_gc_pop',
'mil_hh_pop']].groupby([pop['yr']]).sum())
pop.to_hdf('temp/data.h5', 'mil_pop', mode='a')
def run(self):
my_file = Path('temp/data.h5')
if my_file.is_file():
print'File exists'
else:
db_run_id = log.new_run(name='inc_run_log')
run_id = pd.Series([db_run_id])
run_id.to_hdf('temp/data.h5', 'run_id', mode='a')
engine = create_engine(get_connection_string("model_config.yml", 'output_database'))
db_connection_string = database.get_connection_string('model_config.yml', 'in_db')
sql_in_engine = create_engine(db_connection_string)
rate_versions = util.yaml_to_dict('model_config.yml', 'rate_versions')
tables = util.yaml_to_dict('model_config.yml', 'db_tables')
in_query = getattr(sql, 'inc_pop') % (tables['inc_pop_table'], rate_versions['inc_pop'])
in_query2 = getattr(sql, 'inc_pop_mil') % (tables['population_table'], rate_versions['population'])
pop = pd.read_sql(in_query, engine, index_col=['age', 'race_ethn', 'sex', 'mildep'])
pop_mil = pd.read_sql(in_query2, sql_in_engine, index_col=['age', 'race_ethn', 'sex', 'mildep'])
pop = pop.join(pop_mil)
pop['persons'] = (pop['persons'] - pop['mil_mildep'])
pop = pop.reset_index(drop=False)
pop = pop[pop['age'] >= 18]
pop['age_cat'] = ''
pop.loc[pop['age'].isin(list(range(18, 25))), ['age_cat']] = '18_24'
pop.loc[pop['age'].isin(list(range(25, 35))), ['age_cat']] = '25_34'
pop.loc[pop['age'].isin(list(range(35, 45))), ['age_cat']] = '35_44'
pop.loc[pop['age'].isin(list(range(45, 55))), ['age_cat']] = '45_54'
pop.loc[pop['age'].isin(list(range(55, 60))), ['age_cat']] = '55_59'
pop.loc[pop['age'].isin(list(range(60, 65))), ['age_cat']] = '60_64'
pop.loc[pop['age'].isin(list(range(65, 75))), ['age_cat']] = '65_74'
pop.loc[pop['age'].isin(list(range(75, 103))), ['age_cat']] = '75_99'
pop = pd.DataFrame(pop['persons'].groupby([pop['yr'], pop['age_cat']]).sum())
pop.to_hdf('temp/data.h5', 'pop', mode='a')
def new_run(name='runs'):
Base = declarative_base()
table_name = name
class Run(Base):
__tablename__ = table_name
__table_args__ = {'schema': 'defm'}
# define columns for the table
id = Column(Integer, primary_key=True)
base_rate_version = Column(Integer)
birth_rate_version = Column(Integer)
death_rate_version = Column(Integer)
migration_rate_version = Column(Integer)
householder_rate_version = Column(Integer)
#metadata = MetaData(schema="defm")
db_dir = 'results/'
if not os.path.exists(db_dir):
os.makedirs(db_dir)
engine = create_engine(
get_connection_string(
"model_config.yml",
'output_database')).execution_options(schema_translate_map={
None: "defm", # no schema name -> "defm"
})
Base.metadata.schema = 'defm'
if not engine.has_table(table_name, schema='defm'):
Base.metadata.create_all(engine)
db_session = sessionmaker(bind=engine)
session = db_session()
# Rate versions from yml file
rate_versions = util.yaml_to_dict('model_config.yml', 'rate_versions')
# Insert versions in database
model_run = Run(base_rate_version=rate_versions['population'],
birth_rate_version=rate_versions['birth'],
death_rate_version=rate_versions['death'],
migration_rate_version=rate_versions['migration'],
householder_rate_version=rate_versions['householder'])
session.add(model_run)
session.commit()
run_id = model_run.id
return run_id
def run(self):
engine = create_engine(get_connection_string("model_config.yml", 'output_database'))
db_connection_string = database.get_connection_string('model_config.yml', 'in_db')
sql_in_engine = create_engine(db_connection_string)
in_query = getattr(sql, 'max_run_id')
db_run_id = pd.read_sql(in_query, engine, index_col=None)
# db_run_id = log.new_run(name='inc_run_log', run_id=db_run_id['max'].iloc[0])
run_id = pd.Series([db_run_id['id'].iloc[0]])
run_id.to_hdf('temp/data.h5', 'run_id', mode='a')
dem_sim_rates = extract.create_df('dem_sim_rates', 'dem_sim_rates_table',
rate_id=self.dem_id, index=None)
dem_sim_rates.to_hdf('temp/data.h5', 'dem_sim_rates', mode='a')
econ_sim_rates = extract.create_df('econ_sim_rates', 'econ_sim_rates_table',
rate_id=self.econ_id, index=None)
econ_sim_rates.to_hdf('temp/data.h5', 'econ_sim_rates', mode='a')
tables = util.yaml_to_dict('model_config.yml', 'db_tables')
in_query = getattr(sql, 'inc_pop') % (tables['inc_pop_table'], run_id[0])
in_query2 = getattr(sql, 'inc_mil_hh_pop') % (tables['population_table'], dem_sim_rates.base_population_id[0])
pop = pd.read_sql(in_query, engine, index_col=['age', 'race_ethn', 'sex', 'mildep'])
pop_mil = pd.read_sql(in_query2, sql_in_engine, index_col=['age', 'race_ethn', 'sex', 'mildep'])
pop = pop.join(pop_mil)
pop['persons'] = (pop['persons'] - pop['mil_mildep'])
pop = pop.reset_index(drop=False)
pop = pop[pop['age'] >= 18]
pop['age_cat'] = ''
pop.loc[pop['age'].isin(list(range(18, 25))), ['age_cat']] = '18_24'
pop.loc[pop['age'].isin(list(range(25, 35))), ['age_cat']] = '25_34'
pop.loc[pop['age'].isin(list(range(35, 45))), ['age_cat']] = '35_44'
pop.loc[pop['age'].isin(list(range(45, 55))), ['age_cat']] = '45_54'
pop.loc[pop['age'].isin(list(range(55, 60))), ['age_cat']] = '55_59'
pop.loc[pop['age'].isin(list(range(60, 65))), ['age_cat']] = '60_64'
pop.loc[pop['age'].isin(list(range(65, 75))), ['age_cat']] = '65_74'
pop.loc[pop['age'].isin(list(range(75, 103))), ['age_cat']] = '75_99'
pop = pd.DataFrame(pop['persons'].groupby([pop['yr'], pop['age_cat']]).sum())
pop.to_hdf('temp/data.h5', 'pop', mode='a')
def new_run(db_name):
Base = declarative_base()
table_name = 'run_log'
class Run(Base):
__tablename__ = table_name
# define columns for the table
id = Column(Integer, primary_key=True)
base_rate_version = Column(Integer)
birth_rate_version = Column(Integer)
death_rate_version = Column(Integer)
migration_rate_version = Column(Integer)
householder_rate_version = Column(Integer)
db_dir = 'results/'
if not os.path.exists(db_dir):
os.makedirs(db_dir)
engine = create_engine('sqlite:///' + db_dir + db_name)
if not engine.has_table(table_name):
Base.metadata.create_all(engine)
db_session = sessionmaker(bind=engine)
session = db_session()
# Rate versions from yml file
rate_versions = util.yaml_to_dict('model_config.yml', 'rate_versions')
# Insert versions in database
model_run = Run(
base_rate_version=rate_versions['population'],
birth_rate_version=rate_versions['birth'],
death_rate_version=rate_versions['death'],
migration_rate_version=rate_versions['migration'],
householder_rate_version=rate_versions['householder'])
session.add(model_run)
session.commit()
run_id = model_run.id
return run_id
def run(self):
birth_rates = pd.read_hdf('temp/data.h5', 'birth_rates')
pop = pd.read_hdf('temp/data.h5', 'non_mig_pop')
pop = pop[(pop['type'] == 'HHP') & (pop['mildep'] == 'N')]
birth_rates = utils.rates_for_yr(pop, birth_rates, self.year)
birth_rates = birth_rates[(birth_rates['yr'] == self.year)]
rate_versions = util.yaml_to_dict('model_config.yml', 'rate_versions')
random_numbers = extract.create_df('random_numbers', 'random_numbers_table', rate_id=rate_versions['random_numbers'])
random_numbers = random_numbers[(random_numbers['yr'] == self.year)]
random_numbers = random_numbers[['random_number']]
births_per_cohort = cp.births_all(birth_rates, pop_col='non_mig_pop', rand_df=random_numbers)
death_rates = pd.read_hdf('temp/data.h5', 'death_rates')
death_rates = death_rates[(death_rates['yr'] == self.year)]
# sum newborn population across cohorts
newborn = cp.births_sum(births_per_cohort, self.year)
newborn = newborn.join(death_rates)
newborn['new_deaths'] = (newborn['new_born'] * newborn['death_rate']).round()
newborn['new_born_survived'] = (newborn['new_born'] - newborn['new_deaths']).round()
dead_pop = pd.read_hdf('temp/data.h5', 'dead_pop')
dead_pop = dead_pop.join(newborn['new_deaths'])
dead_pop = dead_pop.fillna(0)
dead_pop['deaths_hhp_non_mil'] = (dead_pop['deaths_hhp_non_mil'] + dead_pop['new_deaths']).round()
dead_pop = dead_pop.drop(['new_deaths'], 1)
dead_pop.to_hdf('temp/data.h5', 'dead_pop', mode='a')
newborn = newborn.drop(['new_deaths', 'death_rate'], 1)
newborn.to_hdf('temp/data.h5', 'new_born', mode='a')
# measure script time
start_time = time.time()
# change to current directory to find .yml input config file
full_path = os.path.abspath(inspect.getfile(inspect.currentframe()))
os.chdir(os.path.dirname(full_path))
# set console display to show MultiIndex for every row
pd.set_option('display.multi_sparse', False)
# rate versions to result database & return primary key for table
# db_run_id = log.new_run('model_summary.db')
db_run_id = log.new_run('defm.db')
years = util.yaml_to_dict('model_config.yml', 'years')
# Load rates for all years: SQL query to pandas DataFrame
# columns: 'age', 'race_ethn', 'sex' (cohort), 'rate', 'year'
# pivot migration DataFrame w 4 rates: domestic in & out, foreign in & out
birth_rates = extract.create_df('birth', 'rate_table')
death_rates = extract.create_df('death', 'rate_table')
mig_rates = extract.create_df('migration', 'rate_table', pivot=True)
# Load base population: SQL query to pandas DataFrame
# columns: 'age', 'race_ethn', 'sex' (cohort),
# 'gq.type', 'mildep', 'persons', 'households'
population = extract.create_df('population', 'population_table')
def run(self):
engine = create_engine(
get_connection_string("model_config.yml", 'output_database'))
db_connection_string = database.get_connection_string(
'model_config.yml', 'in_db')
sql_in_engine = create_engine(db_connection_string)
in_query = getattr(sql, 'max_run_id')
db_run_id = pd.read_sql(in_query, engine, index_col=None)
# db_run_id = log.new_run(name='emp_run_log', run_id=db_run_id['max'].iloc[0])
run_id = pd.Series([db_run_id['max'].iloc[0]])
run_id.to_hdf('temp/data.h5', 'run_id', mode='a')
rate_versions = util.yaml_to_dict('model_config.yml', 'rate_versions')
tables = util.yaml_to_dict('model_config.yml', 'db_tables')
in_query = getattr(sql,
'inc_pop') % (tables['inc_pop_table'], run_id[0])
in_query2 = getattr(sql, 'inc_mil_hh_pop') % (
tables['population_table'], rate_versions['population'])
pop = pd.read_sql(in_query,
engine,
index_col=['age', 'race_ethn', 'sex', 'mildep'])
pop_mil = pd.read_sql(in_query2,
sql_in_engine,
index_col=['age', 'race_ethn', 'sex', 'mildep'])
pop = pop.join(pop_mil)
pop['persons'] = (pop['persons'] - pop['mil_mildep'])
pop = pop.reset_index(drop=False)
pop['age_cat'] = ''
pop.loc[pop['age'].isin(list(range(0, 5))), ['age_cat']] = '00_04'
pop.loc[pop['age'].isin(list(range(5, 10))), ['age_cat']] = '05_09'
pop.loc[pop['age'].isin(list(range(10, 15))), ['age_cat']] = '10_14'
pop.loc[pop['age'].isin(list(range(15, 18))), ['age_cat']] = '15_17'
pop.loc[pop['age'].isin(list(range(18, 20))), ['age_cat']] = '18_19'
pop.loc[pop['age'].isin(list(range(20, 21))), ['age_cat']] = '20_20'
pop.loc[pop['age'].isin(list(range(21, 22))), ['age_cat']] = '21_21'
pop.loc[pop['age'].isin(list(range(22, 25))), ['age_cat']] = '22_24'
pop.loc[pop['age'].isin(list(range(25, 30))), ['age_cat']] = '25_29'
pop.loc[pop['age'].isin(list(range(30, 35))), ['age_cat']] = '30_34'
pop.loc[pop['age'].isin(list(range(35, 40))), ['age_cat']] = '35_39'
pop.loc[pop['age'].isin(list(range(40, 45))), ['age_cat']] = '40_44'
pop.loc[pop['age'].isin(list(range(45, 50))), ['age_cat']] = '45_49'
pop.loc[pop['age'].isin(list(range(50, 55))), ['age_cat']] = '50_54'
pop.loc[pop['age'].isin(list(range(55, 60))), ['age_cat']] = '55_59'
pop.loc[pop['age'].isin(list(range(60, 62))), ['age_cat']] = '60_61'
pop.loc[pop['age'].isin(list(range(62, 65))), ['age_cat']] = '62_64'
pop.loc[pop['age'].isin(list(range(65, 67))), ['age_cat']] = '65_66'
pop.loc[pop['age'].isin(list(range(67, 70))), ['age_cat']] = '67_69'
pop.loc[pop['age'].isin(list(range(70, 75))), ['age_cat']] = '70_74'
pop.loc[pop['age'].isin(list(range(75, 80))), ['age_cat']] = '75_79'
pop.loc[pop['age'].isin(list(range(80, 85))), ['age_cat']] = '80_84'
pop.loc[pop['age'].isin(list(range(85, 103))), ['age_cat']] = '85_99'
pop = pd.DataFrame(pop['persons'].groupby(
[pop['yr'], pop['age_cat'], pop['sex'], pop['race_ethn']]).sum())
pop.to_hdf('temp/data.h5', 'pop', mode='a')
# measure script time
start_time = time.time()
# change to current directory to find .yml input config file
full_path = os.path.abspath(inspect.getfile(inspect.currentframe()))
os.chdir(os.path.dirname(full_path))
# set console display to show MultiIndex for every row
pd.set_option('display.multi_sparse', False)
# rate versions to result database & return primary key for table
# db_run_id = log.new_run('model_summary.db')
db_run_id = log.new_run()
years = util.yaml_to_dict('model_config.yml', 'years')
# Load rates for all years: SQL query to pandas DataFrame
# columns: 'age', 'race_ethn', 'sex' (cohort), 'rate', 'year'
# pivot migration DataFrame w 4 rates: domestic in & out, foreign in & out
birth_rates = extract.create_df('birth', 'rate_table')
death_rates = extract.create_df('death', 'rate_table')
mig_rates = extract.create_df('migration', 'rate_table', pivot=True)
# Load base population: SQL query to pandas DataFrame
# columns: 'age', 'race_ethn', 'sex' (cohort),
# 'gq.type', 'mildep', 'persons', 'households'
population = extract.create_df('population', 'population_table')
def requires(self):
years = util.yaml_to_dict('model_config.yml', 'years')
return [ExportTables(y) for y in range(years['y1'], years['yf'] + 1)]
