def test_compute_harrells_c():
dummy_z = pd.DataFrame(
[
[1, 1, 1, 0, 0, 0, 1, 0, 1],
[1, 1, 1, 1, 0, 1, 1, 1, 0],
[1, 1, 1, 1, 0, 1, 1, 1, 0],
[1, 1, 1, 1, 0, 1, 1, 1, 0],
[1, 1, 1, 1, 0, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 0, 0, 1, 0],
[0, 0, 0, 1, 0, 0, 1, 1, 0],
[0, 0, 0, 1, 0, 0, 1, 1, 0],
[0, 0, 0, 1, 0, 0, 1, 1, 0],
[0, 0, 0, 1, 0, 0, 1, 1, 0],
[0, 0, 0, 1, 0, 1, 1, 1, 1],
],
index=[f'sample {i}' for i in range(11)],
columns=[f'LF{i}' for i in range(9)]
) # here the first 3 factors separate the groups and the last 6 do not
durations = [
1, 2, 3, 4, 5, 6, 1000, 2000, 3000, 4000, 5000
] # here the first 3 have short durations, the last 3 longer ones
observed = [True] * 11 # all events observed
survival = pd.DataFrame(dict(duration=durations, observed=observed),
index=[f'sample {i}' for i in range(11)])
z_clinical = utils.select_clinical_factors(dummy_z,
survival,
cox_penalizer=1)
np.random.seed(0)
c = utils.compute_harrells_c(z_clinical, survival, cv_folds=2)
assert np.allclose(c, [.8, .8])
def test_select_clinical_factors():
dummy_z = pd.DataFrame(
[
[1, 1, 1, 0, 0, 0, 1, 0, 1],
[1, 1, 1, 1, 0, 1, 1, 1, 0],
[1, 1, 1, 1, 0, 1, 1, 1, 0],
[1, 1, 1, 1, 0, 1, 1, 1, 0],
[1, 1, 1, 1, 0, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 0, 0, 1, 0],
[0, 0, 0, 1, 0, 0, 1, 1, 0],
[0, 0, 0, 1, 0, 0, 1, 1, 0],
[0, 0, 0, 1, 0, 0, 1, 1, 0],
[0, 0, 0, 1, 0, 0, 1, 1, 0],
[0, 0, 0, 1, 0, 1, 1, 1, 1],
],
index=[f"sample {i}" for i in range(11)],
columns=[f"LF{i}" for i in range(9)],
) # here the first 3 factors separate the groups and the last 6 do not
durations = [
1,
2,
3,
4,
5,
6,
1000,
2000,
3000,
4000,
5000,
] # here the first 3 have short durations, the last 3 longer ones
observed = [True] * 11 # all events observed
survival = pd.DataFrame(
dict(duration=durations, observed=observed),
index=[f"sample {i}" for i in range(11)],
)
z_clinical = utils.select_clinical_factors(dummy_z,
survival,
cox_penalizer=1)
assert "LF0" in z_clinical.columns
assert "LF1" in z_clinical.columns
assert "LF2" in z_clinical.columns
assert "LF3" not in z_clinical.columns
assert "LF4" not in z_clinical.columns
assert "LF5" not in z_clinical.columns