\(\newcommand{\B}[1]{ {\bf #1} }\) \(\newcommand{\R}[1]{ {\rm #1} }\) \(\newcommand{\W}[1]{ \; #1 \; }\)
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')
# -----------------------------------------------------------------------------