\(\newcommand{\B}[1]{ {\bf #1} }\) \(\newcommand{\R}[1]{ {\rm #1} }\) \(\newcommand{\W}[1]{ \; #1 \; }\)
create_database.py¶
View page sourcecreate_database: Example and Test¶
#
def constant_weight_fun(a, t) :
return 1.0
def smooth_uniform_01_fun(a, t) :
# note that the da and dt values are not used
return ('uniform_01', 'uniform_01', 'uniform_01')
def smooth_gaussian_01_fun(a, t) :
# note that the da and dt values are not used
return ('gaussian_01', 'gaussian_01', 'gaussian_01')
def column_as_list(row_list, column) :
ret = list()
for row in row_list :
ret.append( row[column] )
return ret
# ------------------------------------------------------------------------
def create_database() :
import dismod_at
import copy
#
# file_name, age_list, time_list, integrand_table
file_name = 'example.db'
age_list = [ 50.0 ]
time_list = [ 2000.0 ]
integrand_table = [
{ 'name':'mtother', 'minimum_meas_cv':0.0 }
]
#
# node_table
node_table = [
{ 'name':'world', 'parent':'' },
{ 'name':'north_america', 'parent':'world' },
{ 'name':'united_states', 'parent':'north_america' },
{ 'name':'canada', 'parent':'north_america' }
]
# weight_table
fun = constant_weight_fun
weight_table = [
{ 'name':'constant', 'age_id':[0], 'time_id':[0], 'fun':fun }
]
# covariate_table
covariate_table = [
{ 'name':'sex', 'reference':0.0, 'max_difference':0.6 }
]
# data_table
data_table = []
row = {
'integrand':'mtother',
'density':'log_gaussian',
'weight':'constant',
'hold_out':False,
'meas_std':1e-5,
'age_lower':0.0,
'age_upper':100.0,
'time_lower':1990.0,
'time_upper':2010.0,
'sex':0.5,
'subgroup':'world',
}
row['data_name'] = 'one'
row['node'] = 'north_america'
row['meas_value'] = 1.0e-5
data_table.append( copy.copy(row) )
row['data_name'] = 'two'
row['node'] = 'united_states'
row['meas_value'] = 1.5e-5
data_table.append( copy.copy(row) )
row['data_name'] = 'three'
row['node'] = 'canada'
row['meas_value'] = 0.5e-5
data_table.append( copy.copy(row) )
#
# prior_table
prior_table = [
{ 'name':'zero',
'density':'uniform',
'lower':0.0,
'upper':0.0,
'mean':0.0,
},{ 'name':'one',
'density':'uniform',
'lower':1.0,
'upper':1.0,
'mean':1.0,
},{ 'name':'uniform_01',
'density':'uniform',
'lower':0.0,
'upper':1.0,
'mean':0.1,
},{ 'name':'gaussian_01',
'density':'gaussian',
'mean':0.0,
'std':1.0,
},{ 'name':'log_gaussian',
'density':'log_gaussian',
'mean':0.0,
'eta':1e-6
}
]
#
# smooth list
smooth_table = [
{ 'name':'uniform_01_constant',
'age_id':[0],
'time_id':[0],
'mulstd_value_prior_name':None,
'mulstd_dage_prior_name':None,
'mulstd_dtime_prior_name':None,
'fun':smooth_uniform_01_fun
},{ 'name':'gaussian_01_constant',
'age_id':[0],
'time_id':[0],
'mulstd_value_prior_name':None,
'mulstd_dage_prior_name':None,
'mulstd_dtime_prior_name':None,
'fun':smooth_gaussian_01_fun
}
]
#
# rate_table
rate_table = [
{
'name':'pini',
'parent_smooth':'uniform_01_constant',
'child_smooth':'gaussian_01_constant',
'child_nslist':None
},{
'name':'iota',
'parent_smooth':'uniform_01_constant',
'child_smooth':'gaussian_01_constant',
'child_nslist':None
},{
'name':'rho',
'parent_smooth':'uniform_01_constant',
'child_smooth':'gaussian_01_constant',
'child_nslist':None
},{
'name':'chi',
'parent_smooth':'uniform_01_constant',
'child_smooth':'gaussian_01_constant',
'child_nslist':None
},{
'name':'omega',
'parent_smooth':'uniform_01_constant',
'child_smooth':'gaussian_01_constant',
'child_nslist':None
}
]
#
# mulcov_table
mulcov_table = [
{ 'covariate':'sex',
'type':'rate_value',
'effected':'omega',
'group':'world',
'smooth':'uniform_01_constant'
}
]
#
# option_table
option_table = [
{ 'name':'parent_node_name','value':'world' },
{ 'name':'ode_step_size', 'value':'10.0' },
{ 'name':'random_seed', 'value':'0' },
{ 'name':'rate_case', 'value':'iota_pos_rho_pos' },
{ 'name':'tolerance', 'value':'1e-8' },
{ 'name':'max_num_iter', 'value':'100' },
{ 'name':'print_level', 'value':'0' },
{ 'name':'derivative_test', 'value':'second-order' }
]
# avgint_table
avgint_table = []
row = {
'integrand':'mtother',
'weight':'constant',
'age_lower':0.0,
'age_upper':100.0,
'time_lower':1990.0,
'time_upper':2010.0,
'sex':0.5,
'subgroup':'world',
}
row['node'] = 'north_america'
avgint_table.append( copy.copy(row) )
row['node'] = 'united_states'
avgint_table.append( copy.copy(row) )
row['node'] = 'canada'
row['meas_value'] = 0.5e-5
avgint_table.append( copy.copy(row) )
# nslist_table
nslist_table = dict()
#
# ----------------------------------------------------------------------
# subgroup_table
subgroup_table = [ { 'subgroup':'world', 'group':'world' } ]
# ----------------------------------------------------------------------
dismod_at.create_database(
file_name,
age_list,
time_list,
integrand_table,
node_table,
subgroup_table,
weight_table,
covariate_table,
avgint_table,
data_table,
prior_table,
smooth_table,
nslist_table,
rate_table,
mulcov_table,
option_table
)
# ----------------------------------------------------------------------
# Check database
# ----------------------------------------------------------------------
#
# connection
connection = dismod_at.create_connection(
file_name, new = False, readonly = True
)
#
# age_table
tbl_name = 'age'
col_name = [ 'age' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
col_list = column_as_list(row_list, 0)
assert col_list == age_list
#
# time_table
tbl_name = 'time'
col_name = [ 'time' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
col_list = column_as_list(row_list, 0)
assert col_list == time_list
#
# intergrand_table
tbl_name = 'integrand'
col_name = [ 'integrand_name' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [ ['mtother'] ]
assert row_list == check_list
#
# weight_table
tbl_name = 'weight'
col_name = [ 'weight_name', 'n_age', 'n_time' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [ [ 'constant', 1, 1 ] ]
assert row_list == check_list
#
# weight_grid_table
tbl_name = 'weight_grid'
col_name = [ 'weight_id', 'age_id', 'time_id', 'weight' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [ [ 0, 0, 0, 1.0 ] ]
assert row_list == check_list
#
# covariate_table
tbl_name = 'covariate'
col_name = [ 'covariate_name', 'reference' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [ [ 'sex', 0.0 ] ]
assert row_list == check_list
#
# node_table
tbl_name = 'node'
col_name = [ 'node_name', 'parent' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [
['world', None],
['north_america', 0],
['united_states', 1],
['canada', 1]
]
assert row_list == check_list
#
# data_table
tbl_name = 'data'
col_name = [ 'integrand_id', 'node_id', 'meas_value', 'meas_std' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [
[ 0, 1, 1.0e-5, 1e-5 ],
[ 0, 2, 1.5e-5, 1e-5 ],
[ 0, 3, 0.5e-5, 1e-5 ]
]
assert row_list == check_list
#
# prior_table
tbl_name = 'prior'
col_name = [ 'prior_name', 'density_id', 'lower', 'upper' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [
[ 'zero', 0, 0.0, 0.0 ],
[ 'one', 0, 1.0, 1.0 ],
[ 'uniform_01', 0, 0.0, 1.0 ],
[ 'gaussian_01', 2, None, None ],
[ 'log_gaussian', 5, None, None ]
]
assert row_list == check_list
#
# smooth_table
tbl_name = 'smooth'
col_name = [
'smooth_name',
'n_age',
'n_time',
'mulstd_value_prior_id',
'mulstd_dage_prior_id',
'mulstd_dtime_prior_id'
]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [
[ 'uniform_01_constant', 1, 1, None, None, None],
[ 'gaussian_01_constant', 1, 1, None, None, None]
]
assert row_list == check_list
#
# smooth_grid_table
tbl_name = 'smooth_grid'
col_name = [
'smooth_id', 'age_id', 'time_id',
'value_prior_id', 'dage_prior_id', 'dtime_prior_id'
]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [
[ 0, 0, 0, 2, None, None ] ,
[ 1, 0, 0, 3, None, None ]
]
assert row_list == check_list
#
# rate_table
tbl_name = 'rate'
col_name = [ 'rate_name', 'parent_smooth_id', 'child_smooth_id' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [
[ 'pini', 0, 1 ],
[ 'iota', 0, 1 ],
[ 'rho', 0, 1 ],
[ 'chi', 0, 1 ],
[ 'omega', 0, 1 ]
]
assert row_list == check_list
#
# mulcov_table
tbl_name = 'mulcov'
col_name = [
'mulcov_type', 'rate_id', 'integrand_id', 'covariate_id',
'group_id', 'subgroup_smooth_id', 'group_smooth_id'
]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [ [ 'rate_value', 4, None, 0, 0, None, 0 ] ]
assert row_list == check_list
#
# option_table
tbl_name = 'option'
col_name = [ 'option_name', 'option_value' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [
[ 'parent_node_name', 'world' ],
[ 'ode_step_size', '10.0' ],
[ 'random_seed', '0' ],
[ 'rate_case', 'iota_pos_rho_pos' ],
[ 'tolerance', '1e-8' ],
[ 'max_num_iter', '100' ],
[ 'print_level', '0' ],
[ 'derivative_test', 'second-order' ]
]
assert row_list == check_list
#
# avgint_table
tbl_name = 'avgint'
col_name = [ 'integrand_id', 'node_id', 'age_lower', 'age_upper' ]
row_list = dismod_at.get_row_list(connection, tbl_name, col_name)
check_list = [
[ 0, 1, 0.0, 100.0 ],
[ 0, 2, 0.0, 100.0 ],
[ 0, 3, 0.0, 100.0 ]
]
assert row_list == check_list
# ----------------------------------------------------------------------
connection.close()
print('create_database: OK')