def test_simulated_disease():
""" Test fit for simulated disease data"""
# load model to test fitting
dm = DiseaseJson(file('tests/test_disease_1.json').read())
# filter and noise up data
cov = .5
data = []
for d in dm.data:
d['truth'] = d['value']
if dismod3.utils.clean(d['gbd_region']) == 'north_america_high_income':
if d['data_type'] == 'all-cause mortality data':
data.append(d)
else:
se = (cov * d['value'])
d['value'] = mc.rtruncnorm(d['truth'], se**-2, 0, np.inf)
d['age_start'] -= 5
d['age_end'] = d['age_start']+9
d['age_weights'] = np.ones(d['age_end']-d['age_start']+1)
d['age_weights'] /= float(len(d['age_weights']))
d['standard_error'] = se
data.append(d)
dm.data = data
# fit empirical priors and compare fit to data
from dismod3 import neg_binom_model
for rate_type in 'prevalence incidence remission excess-mortality'.split():
neg_binom_model.fit_emp_prior(dm, rate_type, '/dev/null')
check_emp_prior_fits(dm)
# fit posterior
delattr(dm, 'vars') # remove vars so that gbd_disease_model creates its own version
from dismod3 import gbd_disease_model
keys = dismod3.utils.gbd_keys(region_list=['north_america_high_income'],
year_list=[1990], sex_list=['male'])
gbd_disease_model.fit(dm, method='map', keys=keys, verbose=1) ## first generate decent initial conditions
gbd_disease_model.fit(dm, method='mcmc', keys=keys, iter=1000, thin=5, burn=5000, verbose=1, dbname='/dev/null') ## then sample the posterior via MCMC
print 'error compared to the noisy data (coefficient of variation = %.2f)' % cov
check_posterior_fits(dm)
for d in dm.data:
d['value'] = d['truth']
d['age_start'] += 5
d['age_end'] = d['age_start']
d['age_weights'] = np.ones(d['age_end']-d['age_start']+1)
d['age_weights'] /= float(len(d['age_weights']))
print 'error compared to the truth'
check_posterior_fits(dm)
return dm
def test_hep_c():
""" Test fit for subset of hep_c data
data is filtered to include only prevalence with
region == 'europe_western' and sex == 'all'
"""
# load model to test fitting
dm = DiseaseJson(file('tests/hep_c_europe_western.json').read())
# fit empirical priors
neg_binom_model.fit_emp_prior(dm, 'prevalence', '/dev/null')
# fit posterior
delattr(dm, 'vars') # remove vars so that gbd_disease_model creates its own version
from dismod3 import gbd_disease_model
keys = dismod3.utils.gbd_keys(region_list=['europe_western'],
year_list=[1990], sex_list=['male'])
gbd_disease_model.fit(dm, method='map', keys=keys, verbose=1) ## first generate decent initial conditions
gbd_disease_model.fit(dm, method='mcmc', keys=keys, iter=1000, thin=5, burn=5000, verbose=1, dbname='/dev/null') ## then sample the posterior via MCMC
# check that prevalence is smooth near age zero
prediction = dm.get_mcmc('mean', 'prevalence+europe_western+1990+male')
print prediction
return dm
assert prediction[100] < .1, 'prediction should not shoot up in oldest ages'
def test_dismoditis_wo_prevalence():
""" Test fit for simple example"""
# load model to test fitting
dm = DiseaseJson(file('tests/dismoditis.json').read())
# remove all prevalence data
dm.data = [d for d in dm.data if d['parameter'] != 'prevalence data']
# fit empirical priors
neg_binom_model.fit_emp_prior(dm, 'incidence', '/dev/null')
check_emp_prior_fits(dm)
neg_binom_model.fit_emp_prior(dm, 'excess-mortality', '/dev/null')
check_emp_prior_fits(dm)
# fit posterior
delattr(dm, 'vars') # remove vars so that gbd_disease_model creates its own version
from dismod3 import gbd_disease_model
keys = dismod3.utils.gbd_keys(region_list=['asia_southeast'],
year_list=[1990], sex_list=['male'])
#gbd_disease_model.fit(dm, method='map', keys=keys, verbose=1) ## first generate decent initial conditions
gbd_disease_model.fit(dm, method='mcmc', keys=keys, iter=1000, thin=5, burn=5000, verbose=1, dbname='/dev/null') ## then sample the posterior via MCMC
# compare fit to data
check_posterior_fits(dm)
def test_dismoditis():
""" Test fit for simple example"""
# load model to test fitting
dm = DiseaseJson(file('tests/dismoditis.json').read())
for d in dm.data:
d['standard_error'] = .01
# fit empirical priors
neg_binom_model.fit_emp_prior(dm, 'prevalence', '/dev/null')
check_emp_prior_fits(dm)
neg_binom_model.fit_emp_prior(dm, 'incidence', '/dev/null')
check_emp_prior_fits(dm)
neg_binom_model.fit_emp_prior(dm, 'excess-mortality', '/dev/null')
check_emp_prior_fits(dm)
# fit posterior where there is no data
delattr(dm, 'vars') # remove vars so that gbd_disease_model creates its own version
from dismod3 import gbd_disease_model
keys = dismod3.utils.gbd_keys(region_list=['north_america_high_income'],
year_list=[1990], sex_list=['male'])
gbd_disease_model.fit(dm, method='map', keys=keys, verbose=1) ## first generate decent initial conditions
gbd_disease_model.fit(dm, method='mcmc', keys=keys, iter=1000, thin=5, burn=5000, verbose=1, dbname='/dev/null') ## then sample the posterior via MCMC
check_posterior_fits(dm)
# check that prevalence is smooth near age zero
prediction = dm.get_mcmc('mean', 'prevalence+north_america_high_income+1990+male')
assert prediction[1]-prediction[0] < .01, 'prediction should be smooth near zero'
def test_increasing_prior():
""" Test fit for empirical prior to data showing a linearly increasing age pattern with a fine age mesh"""
# load model to test fitting
dm = DiseaseJson(file('tests/single_low_noise.json').read())
dm.params['global_priors']['increasing']['incidence']['age_end'] = 100
# create linear age pattern data
import copy
d = dm.data.pop()
for a in range(10, 100, 10):
d = copy.copy(d)
d['age_start'] = a
d['age_end'] = a
d['parameter_value'] = .01*a
d['value'] = .01*a
dm.data.append(d)
# fit empirical priors
from dismod3 import neg_binom_model
neg_binom_model.fit_emp_prior(dm, 'prevalence', '/dev/null')
# compare fit to data, and check that it is increasing
check_emp_prior_fits(dm)
assert np.all(np.diff(dm.get_mcmc('emp_prior_mean', dismod3.utils.gbd_key_for('prevalence', 'asia_southeast', 1990, 'male'))) >= 0), 'expert prior says increasing'
def test_ihd():
""" Test fit for subset of ihd data
data is filtered to include only data for
region == 'europe_western' and sex == 'male'
"""
# load model to test fitting
dm = DiseaseJson(file('tests/ihd.json').read())
fit_model(dm, 'europe_western', 1990, 'male')
# check that prevalence is smooth around age 90
prediction = dm.get_mcmc('mean', 'prevalence+europe_western+1990+male')
print prediction
assert prediction[89]/prediction[90] < .05, 'prediction should not change greatly at age 90'
return dm
def test_opi():
""" Test fit for subset of opi_dep data
data is filtered to include only data for
region == 'europe_central' and sex == 'male'
"""
# load model to test fitting
dm = DiseaseJson(file('tests/opi.json').read())
dm.params['global_priors']['decreasing']['prevalence']['age_start'] = 60
dm.params['global_priors']['decreasing']['prevalence']['age_end'] = 100
fit_model(dm, 'europe_central', 1990, 'male')
# check that prevalence is smooth near age zero
prediction = dm.get_mcmc('mean', 'prevalence+europe_central+1990+male')
print prediction
assert prediction[80] > prediction[100], 'prediction should decrease at oldest ages'
return dm
def test_mesh_refinement():
""" Compare fit for coarse and fine age mesh"""
# load model and fit it
dm1 = DiseaseJson(file('tests/single_low_noise.json').read())
dm1.set_param_age_mesh(arange(0,101,20))
from dismod3 import neg_binom_model
neg_binom_model.fit_emp_prior(dm1, 'prevalence', '/dev/null')
# load another copy and fit it with a finer age mesh
dm2 = DiseaseJson(file('tests/single_low_noise.json').read())
dm2.set_param_age_mesh(arange(0,101,5))
from dismod3 import neg_binom_model
neg_binom_model.fit_emp_prior(dm2, 'prevalence', '/dev/null')
# compare fits
p1 = dm1.get_mcmc('emp_prior_mean', dismod3.utils.gbd_key_for('prevalence', 'asia_southeast', 1990, 'male'))
p2 = dm2.get_mcmc('emp_prior_mean', dismod3.utils.gbd_key_for('prevalence', 'asia_southeast', 1990, 'male'))
print p1[::20]
print p2[::20]
assert np.all(abs(p1[::20] / p2[::20] - 1.) < .05), 'Prediction should be closer to data'
def fit_simulated_disease(n=300, cv=2.):
""" Test fit for simulated disease data with noise and missingness"""
# load model to test fitting
dm = DiseaseJson(file('tests/simulation_gold_standard.json').read())
# adjust any priors and covariates as desired
dm.set_param_age_mesh(arange(0,101,2))
for type in 'incidence prevalence remission excess_mortality'.split():
dm.params['global_priors']['heterogeneity'][type] = 'Very'
dm.params['covariates']['Country_level']['LDI_id']['rate']['value'] = 0
# filter and noise up data
mort_data = []
all_data = []
for d in dm.data:
d['truth'] = d['value']
d['age_weights'] = array([1.])
if d['data_type'] == 'all-cause mortality data':
mort_data.append(d)
else:
if d['value'] > 0:
se = (cv / 100.) * d['value']
Y_i = mc.rtruncnorm(d['truth'], se**-2, 0, np.inf)
d['value'] = Y_i
d['standard_error'] = se
d['effective_sample_size'] = Y_i * (1-Y_i) / se**2
all_data.append(d)
sampled_data = random.sample(all_data, n) + mort_data
dm.data = sampled_data
# fit empirical priors and compare fit to data
from dismod3 import neg_binom_model
for rate_type in 'prevalence incidence remission excess-mortality'.split():
#neg_binom_model.fit_emp_prior(dm, rate_type, iter=1000, thin=1, burn=0, dbname='/dev/null')
neg_binom_model.fit_emp_prior(dm, rate_type, iter=30000, thin=15, burn=15000, dbname='/dev/null')
check_emp_prior_fits(dm)
# fit posterior
delattr(dm, 'vars') # remove vars so that gbd_disease_model creates its own version
from dismod3 import gbd_disease_model
keys = dismod3.utils.gbd_keys(region_list=['north_america_high_income'],
year_list=[1990], sex_list=['male'])
gbd_disease_model.fit(dm, method='map', keys=keys, verbose=1) ## first generate decent initial conditions
gbd_disease_model.fit(dm, method='mcmc', keys=keys, iter=30000, thin=15, burn=15000, verbose=1, dbname='/dev/null') ## then sample the posterior via MCMC
#gbd_disease_model.fit(dm, method='mcmc', keys=keys, iter=1000, thin=1, burn=0, verbose=1, dbname='/dev/null') ## fast for dev
print 'error compared to the noisy data (coefficient of variation = %.2f)' % cv
check_posterior_fits(dm)
dm.data = all_data
for d in dm.data:
if d['data_type'] != 'all-cause mortality data':
d['noisy_data'] = d['value']
d['value'] = d['truth']
print 'error compared to the truth'
are, coverage = check_posterior_fits(dm)
print
print 'Median Absolute Relative Error of Posterior Predictions:', median(are)
print 'Pct coverage:', 100*mean(coverage)
f = open('score_%d_%f.txt' % (n, cv), 'a')
f.write('%10.10f,%10.10f\n' % (median(are), mean(coverage)))
f.close()
dm.all_data = all_data
dm.data = sampled_data
for d in dm.data:
if d['data_type'] != 'all-cause mortality data':
d['value'] = d['noisy_data']
generate_figure(dm, n, cv)
return dm
col_names = sorted(data_dict_for_csv(data[0]).keys())
csv_f.writerow(col_names)
for d in data:
dd = data_dict_for_csv(d)
csv_f.writerow([dd[c] for c in col_names])
f_file.close()
except:
print "couldn't write file"
# create the disease model based on this data
dm = DiseaseJson(json.dumps({'params':
{"id": 1,
"sex": "male",
"region": "asia_southeast",
"year": "2005",
"condition": "type_ii_diabetes"},
"data": data}))
for year in [1990, 2005]:
for sex in ['male', 'female']:
key = dismod3.utils.gbd_key_for('%s', dm.get_region(), year, sex)
dm.set_initial_value(key % 'all-cause_mortality', m)
# set semi-informative priors on the rate functions
dm.set_priors(key % 'remission', ' zero 0 100, ')
dm.set_priors(key % 'case-fatality', ' zero 0 10, smooth 100, ')
dm.set_priors(key % 'incidence', ' zero 0 2, smooth 100, increasing 50 100, ')
dm.set_priors(key % 'prevalence', ' zero 0 2, smooth 100, ')
csv_f.writerow(col_names)
for d in data:
dd = data_dict_for_csv(d)
csv_f.writerow([dd[c] for c in col_names])
f_file.close()
except:
print "couldn't write file"
# create the disease model based on this data
dm = DiseaseJson(
json.dumps({
'params': {
"id": 1,
"sex": "male",
"region": "asia_southeast",
"year": "2005",
"condition": "type_ii_diabetes"
},
"data": data
}))
for year in [1990, 2005]:
for sex in ['male', 'female']:
key = dismod3.utils.gbd_key_for('%s', dm.get_region(), year, sex)
dm.set_initial_value(key % 'all-cause_mortality', m)
# set semi-informative priors on the rate functions
dm.set_priors(key % 'remission', ' zero 0 100, ')
dm.set_priors(key % 'case-fatality', ' zero 0 10, smooth 100, ')
dm.set_priors(key % 'incidence',
