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Additional test for one-tailed permutation t-test #11575

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Merged
larsoner merged 9 commits into from
May 24, 2023
Merged

Additional test for one-tailed permutation t-test #11575

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f67e657
Additional test for one-tailed permutation t-test
jCalderTravis Mar 18, 2023
194e05c
Merge branch 'mne-tools:main' into main
jCalderTravis Mar 20, 2023
3459814
Clearer checking of all tails
jCalderTravis Mar 21, 2023
c3d4526
Adjusting parameterisation of test
jCalderTravis Mar 21, 2023
63c2ad9
Merge branch 'main' into main
jCalderTravis May 23, 2023
c5b0d4f
Marking fail as expected
jCalderTravis May 24, 2023
22fdfed
Merge branch 'mne-tools:main' into main
jCalderTravis May 24, 2023
0029a6b
Formatting with Black
jCalderTravis May 24, 2023
7444b67
gitMerge branch 'main' of https://github.com/jCalderTravis/mne-python…
jCalderTravis May 24, 2023
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21 changes: 19 additions & 2 deletions mne/stats/tests/test_permutations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from numpy.testing import assert_array_equal, assert_allclose
import numpy as np
from scipy import stats, sparse
import pytest

from mne.stats import permutation_cluster_1samp_test
from mne.stats.permutations import (
Expand Down Expand Up @@ -55,9 +56,25 @@ def test_permutation_t_test():
assert_allclose(t_obs_clust, t_obs)
assert_allclose(p_values_clust, p_values[keep], atol=1e-2)


@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")
),
],
)
def test_permutation_t_test_tail(tail_name, tail_code):
"""Test that tails work properly."""
X = np.random.randn(18, 1)
t_obs, p_values, H0 = permutation_t_test(X, n_permutations="all")
t_obs_scipy, p_values_scipy = stats.ttest_1samp(X[:, 0], 0)

t_obs, p_values, _ = permutation_t_test(X, n_permutations="all", tail=tail_code)
t_obs_scipy, p_values_scipy = stats.ttest_1samp(X[:, 0], 0, alternative=tail_name)
assert_allclose(t_obs[0], t_obs_scipy, 8)
assert_allclose(p_values[0], p_values_scipy, rtol=1e-2)

Expand Down