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Fix handling of tails in permutation test (issue 11511) #12216

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Fix handling of tails in permutation test (issue 11511) #12216

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7fd71cd
signed H0/Tmax collection and correct tail test
kimcoco Nov 15, 2023
25f7ef6
concatenate also signed T_obs absmax to H0
kimcoco Nov 15, 2023
2a6010d
tail tests work, sptemp-clu-test equivalence fails
kimcoco Nov 15, 2023
4a1a7ad
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 16, 2023
f7b8793
Merge branch 'main' into kimcoco/issue11511
hoechenberger May 21, 2024
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17 changes: 12 additions & 5 deletions mne/stats/permutations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,12 @@ def _max_stat(X, X2, perms, dof_scaling):
n_samples = len(X)
mus = np.dot(perms, X) / float(n_samples)
stds = np.sqrt(X2[None, :] - mus * mus) * dof_scaling # std with splitting
max_abs = np.max(np.abs(mus) / (stds / sqrt(n_samples)), axis=1) # t-max
tvals = mus / (stds / sqrt(n_samples))
max_abs = np.squeeze(
np.take_along_axis(
tvals, np.argmax(np.abs(tvals), axis=1, keepdims=True), axis=1
)
)
return max_abs


Expand Down Expand Up @@ -86,22 +91,24 @@ def permutation_t_test(
T_obs = np.mean(X, axis=0) / (std0 / sqrt(n_samples))
rng = check_random_state(seed)
orders, _, extra = _get_1samp_orders(n_samples, n_permutations, tail, rng)
perms = 2 * np.array(orders) - 1 # from 0, 1 -> 1, -1
perms = 2 * np.array(orders) - 1 # from 0, 1 -> -1, 1
logger.info("Permuting %d times%s..." % (len(orders), extra))
parallel, my_max_stat, n_jobs = parallel_func(_max_stat, n_jobs)
max_abs = np.concatenate(
parallel(
my_max_stat(X, X2, p, dof_scaling) for p in np.array_split(perms, n_jobs)
)
)
max_abs = np.concatenate((max_abs, [np.abs(T_obs).max()]))
max_abs = np.concatenate(
(max_abs, np.atleast_1d(T_obs.flat[np.abs(T_obs).argmax()]))
)
H0 = np.sort(max_abs)
if tail == 0:
p_values = (H0 >= np.abs(T_obs[:, np.newaxis])).mean(-1)
p_values = (np.abs(H0) >= np.abs(T_obs[:, np.newaxis])).mean(-1)
elif tail == 1:
p_values = (H0 >= T_obs[:, np.newaxis]).mean(-1)
elif tail == -1:
p_values = (-H0 <= T_obs[:, np.newaxis]).mean(-1)
p_values = (H0 <= T_obs[:, np.newaxis]).mean(-1)
return T_obs, p_values, H0


Expand Down
10 changes: 1 addition & 9 deletions mne/stats/tests/test_permutations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,15 +60,7 @@ def test_permutation_t_test():

@pytest.mark.parametrize(
"tail_name,tail_code",
[
("two-sided", 0),
pytest.param(
"less", -1, marks=pytest.mark.xfail(reason="Bug in permutation function")
),
pytest.param(
"greater", 1, marks=pytest.mark.xfail(reason="Bug in permutation function")
),
],
[("two-sided", 0), ("less", -1), ("greater", 1)],
)
def test_permutation_t_test_tail(tail_name, tail_code):
"""Test that tails work properly."""
Expand Down
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