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user_other_database.py¶
View page sourceUsing Data Interval Compression¶
Purpose¶
This example shows how to use the Other Database options.
Integrands¶
For this example there are one integrand, Sincidence .
Nodes¶
There is only one node called world for this example.
There are no random effects because there are no child nodes.
True Iota¶
For this example, the true incidence rate iota is the following constant value:
iota_true = 0.01
Model¶
There is only one rate iota and it constant w.r.t age and time.
Data¶
There is one data point measuring Sincidence with the true value of iota . but faster to compute.
other_input_table¶
For this example, the other_input_table is
other_input_table = 'data node'
Source Code¶
# ------------------------------------------------------------------------
import sys
import shutil
import os
import csv
import copy
import math
source_file = 'example/user/other_database.py'
if sys.argv[0] != source_file or len(sys.argv) != 1 :
usage = 'python3 ' + source_file + '\n'
usage += 'where python3 is the python 3 program on your system\n'
usage += 'and working directory is the dismod_at distribution directory\n'
sys.exit(usage)
print(source_file)
#
# import dismod_at
local_dir = os.getcwd() + '/python'
if( os.path.isdir( local_dir + '/dismod_at' ) ) :
sys.path.insert(0, local_dir)
import dismod_at
#
# work_directory
work_directory = 'build/example/user'
# ------------------------------------------------------------------------
# Note that the a, t values are not used for this example
def example_db (file_name) :
# note that the a, t values are not used for this case
def fun_iota(a, t) :
return ('prior_iota', None, None)
# ----------------------------------------------------------------------
# age table:
age_list = [ 0.0, 50.0, 100.0 ]
#
# time table:
time_list = [ 1990.0, 2000.0, 2010.0, 2020.0 ]
#
# integrand table:
integrand_table = [
{ 'name':'Sincidence' }
]
#
# node table:
node_table = [ { 'name':'world', 'parent':'' } ]
#
# weight table:
weight_table = list()
#
# covariate table:
covariate_table = list()
#
# mulcov table:
mulcov_table = list()
#
# avgint table: empty
avgint_table = list()
#
# nslist_dict:
nslist_dict = dict()
# ----------------------------------------------------------------------
# data table:
data_table = list()
#
# values that are the same for all data points
row = {
'integrand': 'Sincidence',
'hold_out': False,
'density': 'gaussian',
'meas_std': iota_true / 10.,
'weight': '',
'time_lower': 2000.,
'time_upper': 2000.,
'node': 'world',
'subgroup': 'world',
'meas_value': iota_true,
'age_lower': 50.0,
'age_upper': 50.0,
'time_lower': 2000.0,
'time_upper': 2000.0,
}
data_table.append(row)
#
# ----------------------------------------------------------------------
# prior_table
prior_table = [
{ # prior_iota
'name': 'prior_iota',
'density': 'uniform',
'lower': iota_true / 10.0,
'upper': iota_true * 10.0,
'mean': iota_true * 2.0,
}
]
# ----------------------------------------------------------------------
# smooth table
name = 'smooth_iota'
fun = fun_iota
smooth_table = [
{ 'name':name,
'age_id':[0],
'time_id':[0],
'fun':fun
}
]
# ----------------------------------------------------------------------
# rate table:
rate_table = [
{ 'name': 'iota',
'parent_smooth': 'smooth_iota',
}
]
# ----------------------------------------------------------------------
# option_table
option_table = [
{ 'name':'rate_case', 'value':'iota_pos_rho_zero' },
{ 'name':'parent_node_name', 'value':'world' },
{ 'name':'quasi_fixed', 'value':'false' },
{ 'name':'max_num_iter_fixed', 'value':'50' },
{ 'name':'print_level_fixed', 'value':'0' },
{ 'name':'tolerance_fixed', 'value':'1e-9' },
{ 'name':'max_num_iter_random', 'value':'50' },
{ 'name':'print_level_random', 'value':'0' },
{ 'name':'tolerance_random', 'value':'1e-10' },
{ 'name':'other_database', 'value':'other.db' },
{ 'name':'other_input_table', 'value':other_input_table },
]
# ----------------------------------------------------------------------
# subgroup_table
subgroup_table = [ { 'subgroup':'world', 'group':'world' } ]
# ----------------------------------------------------------------------
# create database
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_dict,
rate_table,
mulcov_table,
option_table
)
# ----------------------------------------------------------------------
return
# ===========================================================================
#
# example_db, example.db
database = f'{work_directory}/example.db'
example_db(database)
#
# other_db, other.db
other_db = f'{work_directory}/other.db'
shutil.copyfile(database, other_db)
#
# example.db
connection = dismod_at.create_connection(
database, new = False, readonly = False
)
for table_name in other_input_table.split() :
command = 'DROP TABLE ' + table_name
dismod_at.sql_command(connection, command)
command = 'VACUUM;'
dismod_at.sql_command(connection, command)
connection.close()
#
assert os.stat(database).st_size < os.stat(other_db).st_size
#
#
program = 'build/devel/dismod_at'
dismod_at.system_command_prc([ program, database, 'init' ])
dismod_at.system_command_prc([ program, database, 'fit', 'fixed' ])
# -----------------------------------------------------------------------
# read database
connection = dismod_at.create_connection(
database, new = False, readonly = True
)
var_table = dismod_at.get_table_dict(connection, 'var')
fit_var_table = dismod_at.get_table_dict(connection, 'fit_var')
connection.close()
#
# There is only one variables, iota
assert len(var_table) == 1
assert len(fit_var_table) == 1
#
# check that the fit is accurate
for var_id in range( len(var_table) ) :
true_value = iota_true
fit_value = fit_var_table[var_id]['fit_var_value']
rel_error = 1.0 - fit_value/true_value
assert abs(rel_error) < 1e-6
#
# Test db2csv
dismod_at.db2csv_command(database)
# -----------------------------------------------------------------------------
print('other_database.py: OK')
# -----------------------------------------------------------------------------