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user_trace_init.py¶
View page sourceUsing Initialization Trace Option¶
Purpose¶
This example shows how to use the trace_init_fit_model option.
Integrands¶
For this example there are one integrand, Sincidence .
Nodes¶
There three nodes.
The first is called world and is the parent node for this example.
The second (third) is called child_1 (child_2 )
and is a child of the parent node.
True Iota¶
For this example, the true model incidence rate iota is
def iota_true(age, node) :
import math
iota_parent = 0.01 * (1 + age / 100.0)
child_effect = 0.2
if node == 'world' :
return iota_parent
if node == 'child_1' :
return math.exp(+ child_effect) * iota_parent
if node == 'child_2' :
return math.exp(- child_effect) * iota_parent
assert False
Model¶
Parent Node¶
There is only one rate iota and it linear in age with knots at the age 0 and 100.
Child Nodes¶
There is only one rate iota and it constant.
Data¶
There are six data points measuring Sincidence with the true value of iota . These correspond to ages 0 and 100 at each of the three nodes.
trace_init_fit_model¶
The option trace_init_fit_model is set to true and the corresponding output is checked.
Source Code¶
# ------------------------------------------------------------------------
import sys
import os
import csv
import copy
import math
test_program = 'example/user/trace_init.py'
check_program = sys.argv[0].replace('\\', '/')
if check_program != test_program or len(sys.argv) != 1 :
usage = 'python3 ' + test_program + '\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(test_program)
#
# 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
#
# change into the build/example/user directory
if not os.path.exists('build/example/user') :
os.makedirs('build/example/user')
os.chdir('build/example/user')
# ------------------------------------------------------------------------
# Note that the a, t values are not used for this example
def example_db (file_name) :
def fun_iota_parent(a, t) :
return ('prior_iota_parent', None, None)
def fun_iota_child(a, t) :
return ('prior_iota_child', None, None)
# ----------------------------------------------------------------------
# age table:
age_list = [ 0.0, 100.0 ]
#
# time table:
time_list = [ 1990.0, 2020.0 ]
#
# integrand table:
integrand_table = [
{ 'name':'Sincidence' }
]
#
# node table:
node_table = [
{ 'name':'world', 'parent':'' } ,
{ 'name':'child_1', 'parent':'world' } ,
{ 'name':'child_2', 'parent':'world' } ,
]
#
# 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',
'weight': '',
'time_lower': 2000.,
'time_upper': 2000.,
'subgroup': 'world',
}
for age in [ 0.0 , 100.0 ] :
for node in [ 'world', 'child_1', 'child_2' ] :
# Sincidence
row['meas_value'] = iota_true(age, node)
row['meas_std'] = row['meas_value'] / 10.0
row['age_lower'] = age
row['age_upper'] = age
row['node'] = node
data_table.append( copy.copy(row) )
#
# ----------------------------------------------------------------------
# prior_table
prior_table = [
{ # prior_iota_parent
'name': 'prior_iota_parent',
'density': 'uniform',
'lower': iota_true(0, 'world') / 10.0,
'upper': iota_true(0, 'world') * 10.0,
'mean': iota_true(0, 'world') / 2.0 ,
}, {
# prior_iota_child
'name': 'prior_iota_child',
'density': 'uniform',
'mean': 0.0 ,
}
]
# ----------------------------------------------------------------------
# smooth table
smooth_table = [
{ 'name': 'smooth_iota_parent',
'age_id': [0, 1], # ages 0, 100
'time_id': [0],
'fun': fun_iota_parent
},{
'name': 'smooth_iota_child',
'age_id': [0],
'time_id': [0],
'fun': fun_iota_child
}
]
# ----------------------------------------------------------------------
# rate table:
rate_table = [
{ 'name': 'iota',
'parent_smooth': 'smooth_iota_parent',
'child_smooth': 'smooth_iota_child',
}
]
# ----------------------------------------------------------------------
# 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':'trace_init_fit_model', 'value':'true' },
]
# ----------------------------------------------------------------------
# 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
# ===========================================================================
# Create database
file_name = 'example.db'
example_db(file_name)
#
program = '../../devel/dismod_at'
dismod_at.system_command_prc([ program, file_name, 'init' ])
#
command = [ program, file_name, 'fit', 'both' ]
stdout = dismod_at.system_command_prc( command, return_stdout = True )
# -----------------------------------------------------------------------
# Check trace_init_fit_model results
check = 'Begin dismod_at: fit_model constructor\n'
check += 'Begin cppad_mixed::initialize\n'
check += 'init_ran_like_done_\n'
check += 'init_ran_jac_done_\n'
check += 'init_ran_hes_done_\n'
check += 'init_ldlt_ran_hes_done_\n'
check += 'init_hes_cross_done_\n'
check += 'init_fix_like_done_\n'
check += 'init_fix_con_done_\n'
check += 'End cppad_mixed::initialize\n'
check += 'End dismod_at: fit_model constructor\n'
check += 'Begin cppad_mixed::init_laplace_obj\n'
check += 'init_laplace_obj_fun_done_\n'
check += 'init_laplace_obj_hes_done_\n'
check += 'End cppad_mixed::init_laplace_obj\n'
assert stdout == check
# -----------------------------------------------------------------------
# read database
connection = dismod_at.create_connection(
file_name, new = False, readonly = True
)
node_table = dismod_at.get_table_dict(connection, 'node')
age_table = dismod_at.get_table_dict(connection, 'age')
var_table = dismod_at.get_table_dict(connection, 'var')
fit_var_table = dismod_at.get_table_dict(connection, 'fit_var')
connection.close()
#
# There are four values for iota in this model
assert len(var_table) == 4
assert len(fit_var_table) == 4
#
# check that the fit is accurate
for var_id in range( len(var_table) ) :
age_id = var_table[var_id]['age_id']
age = age_table[age_id]['age']
node_id = var_table[var_id]['node_id']
node_name = node_table[node_id]['node_name']
true_value = iota_true(age, node_name)
if node_name.startswith('child_') :
parent_value = iota_true(age, 'world')
true_value = math.log( true_value / parent_value )
fit_value = fit_var_table[var_id]['fit_var_value']
rel_error = 1.0 - fit_value/true_value
assert abs(rel_error) < 1e-6
# -----------------------------------------------------------------------------
print('trace_init.py: OK')
# -----------------------------------------------------------------------------