def test_phi_table(pheno_phi):
phi_table_file = table.NONMEMTableFile(pheno_phi)
phi_table = phi_table_file.table
assert phi_table.problem == 1
assert phi_table.subproblem == 0
assert phi_table.iteration2 == 0
assert phi_table.method == "First Order Conditional Estimation with Interaction"
assert phi_table.goal_function is None
def test_cov_table(pheno_cov):
cov_table_file = table.NONMEMTableFile(pheno_cov)
cov_table = cov_table_file.table
df = cov_table.data_frame
paramnames = ['THETA(1)', 'THETA(2)', 'THETA(3)', 'OMEGA(1,1)', 'OMEGA(2,2)', 'SIGMA(1,1)']
assert list(df.columns) == paramnames
assert list(df.index) == paramnames
assert df.values[0][0] == 4.41151e-8
assert df.values[0][3] == -1.09343e-6
def test_nonmem_table(pheno_ext):
ext_table_file = table.NONMEMTableFile(pheno_ext)
assert list(ext_table_file.table.data_frame.columns) == [
'ITERATION',
'THETA(1)',
'THETA(2)',
'THETA(3)',
'OMEGA(1,1)',
'OMEGA(2,1)',
'OMEGA(2,2)',
'SIGMA(1,1)',
'OBJ',
]
def test_ext_table(pheno_ext):
ext_table_file = table.NONMEMTableFile(pheno_ext)
ext_table = ext_table_file.table
assert ext_table.problem == 1
assert ext_table.subproblem == 0
assert ext_table.iteration2 == 0
assert ext_table.method == "First Order Conditional Estimation with Interaction"
assert ext_table.goal_function == "MINIMUM VALUE OF OBJECTIVE FUNCTION"
assert ext_table.final_parameter_estimates['THETA(1)'] == 0.00469555
assert list(
ext_table.fixed) == [False, False, False, False, True, False, False]
assert ext_table.final_ofv == 586.27605628188053
assert ext_table.initial_ofv == 587.36644134661617
def test_create_phi_table(fs):
df = pd.DataFrame({'ETA(1)': [1, 2], 'ETA(2)': [5, 6]}, index=[1, 2])
df.index.name = 'ID'
phi = table.PhiTable(df=df)
phi.create_content()
correct = ''' SUBJECT_NO ID ETA(1) ETA(2)
1 1 1.00000E+00 5.00000E+00
2 2 2.00000E+00 6.00000E+00
''' # noqa W291
assert phi.content == correct
table_file = table.NONMEMTableFile(tables=[phi])
table_file.write('my.phi')
with open('my.phi', 'r') as fp:
cont = fp.read()
correct = 'TABLE NO. 1\n' + correct
assert cont == correct
def test_ofv_table_gap(testdata):
p = Path(testdata / 'nonmem' / 'modelfit_results' / 'multPROB' /
'multEST' / 'withSIM')
rfile = rf.NONMEMResultsFile(p / 'multprobmix_nm730.lst')
assert rfile.estimation_status(2) == {
'minimization_successful': False,
'estimate_near_boundary': False,
'rounding_errors': False,
'maxevals_exceeded': True,
'significant_digits': nan,
'function_evaluations': 16,
'warning': False,
}
table_numbers = (1, 2, 3, 4, 6, 8, 10, 11, 12, 13)
ext_table_file = table.NONMEMTableFile(p / 'multprobmix_nm730.ext')
for n in table_numbers:
assert rfile.ofv(n) == pytest.approx(
ext_table_file.table_no(n).final_ofv)