def test_tdist(testdata):
orig = Model(testdata / 'nonmem' / 'pheno.mod')
base = Model(testdata / 'nonmem' / 'qa' / 'pheno_linbase.mod')
td = Model(testdata / 'nonmem' / 'qa' / 'tdist.mod')
res = calculate_results(orig, base, tdist_model=td)
correct = """df,new_sd,old_sd
ETA(1),3.77,0.344951,0.333246
ETA(2),3.77,0.400863,0.448917
"""
correct = pd.read_csv(StringIO(correct), index_col=[0])
pd.testing.assert_frame_equal(res.tdist_parameters, correct)
assert res.dofv['dofv']['parameter_variability',
'tdist'] == pytest.approx(730.89472681373070 -
729.45800311609150)
assert res.dofv['df']['parameter_variability', 'tdist'] == 2
res = calculate_results(orig, base, tdist_model=None)
def test_boxcox(testdata):
orig = Model(testdata / 'nonmem' / 'pheno.mod')
base = Model(testdata / 'nonmem' / 'qa' / 'pheno_linbase.mod')
bc = Model(testdata / 'nonmem' / 'qa' / 'boxcox.mod')
res = calculate_results(orig, base, boxcox_model=bc)
correct = """lambda,new_sd,old_sd
ETA(1),-1.581460,0.296257,0.333246
ETA(2),0.645817,0.429369,0.448917
"""
correct = pd.read_csv(StringIO(correct), index_col=[0])
pd.testing.assert_frame_equal(res.boxcox_parameters, correct)
assert res.dofv['dofv']['parameter_variability',
'boxcox'] == pytest.approx(730.89472681373070 -
721.78812733817688)
assert res.dofv['df']['parameter_variability', 'boxcox'] == 2
res = calculate_results(orig, base, boxcox_model=None)
assert res.boxcox_parameters is None
def test_fullblock(testdata):
orig = Model(testdata / 'nonmem' / 'pheno.mod')
base = Model(testdata / 'nonmem' / 'qa' / 'pheno_linbase.mod')
fb = Model(testdata / 'nonmem' / 'qa' / 'fullblock.mod')
res = calculate_results(orig, base, fullblock_model=fb)
correct = """,new,old
"OMEGA(1,1)",0.486600,0.333246
"OMEGA(2,1)",0.846728,NaN
"OMEGA(2,2)",0.423262,0.448917
"""
correct = pd.read_csv(StringIO(correct), index_col=[0])
pd.testing.assert_frame_equal(res.fullblock_parameters, correct)
assert res.dofv['dofv']['parameter_variability',
'fullblock'] == pytest.approx(730.89472681373070 -
706.36113798726512)
assert res.dofv['df']['parameter_variability', 'fullblock'] == 1
res = calculate_results(orig, base, fullblock_model=None)
assert res.fullblock_parameters is None
def test_iov(testdata):
orig = Model(testdata / 'nonmem' / 'pheno.mod')
base = Model(testdata / 'nonmem' / 'qa' / 'pheno_linbase.mod')
iov = Model(testdata / 'nonmem' / 'qa' / 'iov.mod')
res = calculate_results(orig, base, iov_model=iov)
correct = """new_iiv_sd,orig_iiv_sd,iov_sd
ETA(1),0.259560,0.333246,0.555607
ETA(2),0.071481,0.448917,0.400451
"""
correct = pd.read_csv(StringIO(correct), index_col=[0])
pd.testing.assert_frame_equal(res.iov_parameters, correct)
assert res.dofv['dofv']['parameter_variability',
'iov'] == pytest.approx(42.314986)
assert res.dofv['df']['parameter_variability', 'iov'] == 2
def test_scm(testdata):
orig = Model(testdata / 'nonmem' / 'pheno.mod')
base = Model(testdata / 'nonmem' / 'qa' / 'pheno_linbase.mod')
scm_res = read_results(testdata / 'nonmem' / 'qa' / 'scm_results.json')
res = calculate_results(orig, base, scm_results=scm_res)
correct = """,,dofv,coeff
ETA(1),APGR,2.48792,-0.033334
ETA(1),WGT,0.48218,0.052342
ETA(2),APGR,0.59036,0.008371
ETA(2),WGT,0.00887,-0.003273
"""
correct = pd.read_csv(StringIO(correct), index_col=[0, 1])
correct.index.set_names(['parameter', 'covariate'], inplace=True)
pd.testing.assert_frame_equal(res.covariate_effects, correct, atol=1e-6)
assert res.dofv['dofv']['covariates',
'ET1APGR-2'] == pytest.approx(2.48792)
assert res.dofv['df']['covariates', 'ET1APGR-2'] == 1
def test_add_etas(testdata):
orig = Model(testdata / 'nonmem' / 'pheno.mod')
base = Model(testdata / 'nonmem' / 'qa' / 'pheno_linbase.mod')
add_etas = Model(testdata / 'nonmem' / 'qa' / 'add_etas_linbase.mod')
res = calculate_results(orig,
base,
add_etas_model=add_etas,
etas_added_to=['CL', 'V'])
correct = """added,new_sd,orig_sd
ETA(1),True,0.338974,0.333246
ETA(2),True,0.449430,0.448917
CL,False,0.010001,NaN
V,False,0.010000,NaN
"""
correct = pd.read_csv(StringIO(correct), index_col=[0])
pd.testing.assert_frame_equal(res.add_etas_parameters, correct, atol=1e-6)
assert res.dofv['dofv']['parameter_variability',
'add_etas'] == pytest.approx(730.89472681373070 -
730.84697789365532)
assert res.dofv['df']['parameter_variability', 'add_etas'] == 2