def test_run_Continuous_231(self):
"""
Test suite for standard Continuous 2.3.1. models. This test contains
basic models, with very minimal modifications. It also assumes the
standard 1 SD BMR. Note that in the polynomial case, the
degree_poly value is overridden from the default.
"""
session = BMD_session(BMDS_version='2.31', bmrs=self.bmr_c)
run_suite = (
{
'type': 'Linear',
'fn': '2-continuous-tc-LinearCV-1SD.out'
},
{
'type': 'Polynomial',
'fn': '2-continuous-tc-Poly4CV-1SD.out',
'override': {
'degree_poly': 4,
'restrict_polynomial': 1
},
'override_text': ['Degree of Polynomial = 4']
},
{
'type': 'Power',
'fn': '2-continuous-tc-PowerCV-1SD.out'
},
{
'type': 'Hill',
'fn': '2-continuous-tc-HillCV-1SD.out'
},
{
'type': 'Exponential-M2',
'fn': '2-continuous-tc-M2M2ExpCV-1SD.out'
},
{
'type': 'Exponential-M3',
'fn': '2-continuous-tc-M3M3ExpCV-1SD.out'
},
{
'type': 'Exponential-M4',
'fn': '2-continuous-tc-M4M4ExpCV-1SD.out'
},
{
'type': 'Exponential-M5',
'fn': '2-continuous-tc-M5M5ExpCV-1SD.out'
},
)
for run in run_suite:
logging.debug('Testing ' + run['fn'])
m_run = self.v.models['C'][run['type']]()
if 'override' in run:
m_run.update_model(run['override'], run['override_text'],
self.bmr_c)
m = BMD_model_run(model_name=run['type'],
BMD_session=session,
option_override={},
option_override_text=[""])
m.run_model(self.v, m_run, self.dataset_continuous)
output_text = m.output_text.splitlines()[10:]
fn = os.path.join(BMDS_TEST_PATH, run['fn'])
gold_standard = self.import_bmds_output_file(fn)
# with open(os.path.join(BMDS_TEST_PATH, 'test_output.txt'), 'w') as f:
# f.write('\n'.join(output_text))
# with open(os.path.join(BMDS_TEST_PATH, 'gold_standard.txt'), 'w') as f:
# f.write('\n'.join(gold_standard))
self.assertTrue(output_text == gold_standard)
def test_run_Continuous_231(self):
"""
Test suite for standard Continuous 2.3.1. models. This test contains
basic models, with very minimal modifications. It also assumes the
standard 1 SD BMR. Note that in the polynomial case, the
degree_poly value is overridden from the default.
"""
session = BMD_session(BMDS_version='2.31', bmrs=self.bmr_c)
run_suite = (
{
'type': 'Linear',
'fn': '2-continuous-tc-LinearCV-1SD.out'
},
{
'type': 'Polynomial',
'fn': '2-continuous-tc-Poly4CV-1SD.out',
'override': {
'degree_poly': 4,
'restrict_polynomial': 1
},
'override_text': ['Degree of Polynomial = 4']
},
{
'type': 'Power',
'fn': '2-continuous-tc-PowerCV-1SD.out'
},
{
'type': 'Hill',
'fn': '2-continuous-tc-HillCV-1SD.out'
},
{
'type': 'Exponential-M2',
'fn': '2-continuous-tc-M2M2ExpCV-1SD.out'
},
{
'type': 'Exponential-M3',
'fn': '2-continuous-tc-M3M3ExpCV-1SD.out'
},
{
'type': 'Exponential-M4',
'fn': '2-continuous-tc-M4M4ExpCV-1SD.out'
},
{
'type': 'Exponential-M5',
'fn': '2-continuous-tc-M5M5ExpCV-1SD.out'
},
)
for run in run_suite:
logging.debug('Testing ' + run['fn'])
m_run = self.v.models['C'][run['type']]()
if 'override' in run:
m_run.update_model(run['override'], run['override_text'], self.bmr_c)
m = BMD_model_run(
model_name=run['type'],
BMD_session=session,
option_override={},
option_override_text=[""])
m.run_model(self.v, m_run, self.dataset_continuous)
output_text = m.output_text.splitlines()[10:]
fn = os.path.join(BMDS_TEST_PATH, run['fn'])
gold_standard = self.import_bmds_output_file(fn)
# with open(os.path.join(BMDS_TEST_PATH, 'test_output.txt'), 'w') as f:
# f.write('\n'.join(output_text))
# with open(os.path.join(BMDS_TEST_PATH, 'gold_standard.txt'), 'w') as f:
# f.write('\n'.join(gold_standard))
self.assertTrue(output_text == gold_standard)
def test_run_Dichotomous_231(self):
"""
Test suite for standard Dichotomous 2.3.1. models. This test contains
basic models, with very minimal modifications. It also assumes the
standard 10% BMR check. Note that in a few multistage cases, the
degree_poly value is overridden from the default.
"""
session = BMD_session(BMDS_version='2.31', bmrs=self.bmr_d)
run_suite = (
{
'type': 'Logistic',
'fn': '1-dichotomous-tc-Logistic-10%.out'
},
{
'type': 'LogLogistic',
'fn': '1-dichotomous-tc-LogLogistic-10%.out'
},
{
'type': 'Weibull',
'fn': '1-dichotomous-tc-Weibull-10%.out'
},
{
'type': 'Probit',
'fn': '1-dichotomous-tc-Probit-10%.out'
},
{
'type': 'LogProbit',
'fn': '1-dichotomous-tc-LogProbit-10%.out'
},
{
'type': 'Gamma',
'fn': '1-dichotomous-tc-Gamma-10%.out'
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi1-10%.out',
'override': {
'degree_poly': 1
},
'override_text': ['Degree of Polynomial = 1']
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi2-10%.out',
'override': {
'degree_poly': 2
}, # todo: these lines shouldn't be required, think parent class needs to update child class
'override_text': ['Degree of Polynomial = 2']
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi3-10%.out',
'override': {
'degree_poly': 3
},
'override_text': ['Degree of Polynomial = 3']
},
)
for run in run_suite:
logging.debug('Testing ' + run['fn'])
m_run = self.v.models['D'][run['type']]()
if 'override' in run:
m_run.update_model(run['override'], run['override_text'],
self.bmr_d)
m = BMD_model_run(model_name=run['type'],
BMD_session=session,
option_override={},
option_override_text=[""])
m.run_model(self.v, m_run, self.dataset_dichotomous)
output_text = m.output_text.splitlines()[10:]
fn = os.path.join(BMDS_TEST_PATH, run['fn'])
gold_standard = self.import_bmds_output_file(fn)
# f = file(os.path.join(BMDS_TEST_PATH, 'test_output.txt'), 'w')
# f.write('\n'.join(output_text))
# f.close()
# f = file(os.path.join(BMDS_TEST_PATH, 'gold_standard.txt'), 'w')
# f.write('\n'.join(gold_standard))
# f.close()
self.assertTrue(output_text == gold_standard)
def test_run_Dichotomous_231(self):
"""
Test suite for standard Dichotomous 2.3.1. models. This test contains
basic models, with very minimal modifications. It also assumes the
standard 10% BMR check. Note that in a few multistage cases, the
degree_poly value is overridden from the default.
"""
session = BMD_session(BMDS_version='2.31', bmrs=self.bmr_d)
run_suite = (
{
'type': 'Logistic',
'fn': '1-dichotomous-tc-Logistic-10%.out'
},
{
'type': 'LogLogistic',
'fn': '1-dichotomous-tc-LogLogistic-10%.out'
},
{
'type': 'Weibull',
'fn': '1-dichotomous-tc-Weibull-10%.out'
},
{
'type': 'Probit',
'fn': '1-dichotomous-tc-Probit-10%.out'
},
{
'type': 'LogProbit',
'fn': '1-dichotomous-tc-LogProbit-10%.out'
},
{
'type': 'Gamma',
'fn': '1-dichotomous-tc-Gamma-10%.out'
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi1-10%.out',
'override': {'degree_poly': 1},
'override_text': ['Degree of Polynomial = 1']
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi2-10%.out',
'override': {'degree_poly': 2}, # todo: these lines shouldn't be required, think parent class needs to update child class
'override_text': ['Degree of Polynomial = 2']
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi3-10%.out',
'override': {'degree_poly': 3},
'override_text': ['Degree of Polynomial = 3']
},
)
for run in run_suite:
logging.debug('Testing ' + run['fn'])
m_run = self.v.models['D'][run['type']]()
if 'override' in run:
m_run.update_model(run['override'], run['override_text'], self.bmr_d)
m = BMD_model_run(
model_name=run['type'],
BMD_session=session,
option_override={},
option_override_text=[""])
m.run_model(self.v, m_run, self.dataset_dichotomous)
output_text = m.output_text.splitlines()[10:]
fn = os.path.join(BMDS_TEST_PATH, run['fn'])
gold_standard = self.import_bmds_output_file(fn)
# f = file(os.path.join(BMDS_TEST_PATH, 'test_output.txt'), 'w')
# f.write('\n'.join(output_text))
# f.close()
# f = file(os.path.join(BMDS_TEST_PATH, 'gold_standard.txt'), 'w')
# f.write('\n'.join(gold_standard))
# f.close()
self.assertTrue(output_text == gold_standard)
