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Fix RBC sign in mwu
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raphaelvallat committed May 25, 2024
1 parent 790ae3f commit 4e24aa7
Showing 1 changed file with 21 additions and 13 deletions.
34 changes: 21 additions & 13 deletions src/pingouin/nonparametric.py
Original file line number Diff line number Diff line change
Expand Up @@ -172,7 +172,7 @@ def mwu(x, y, alternative="two-sided", **kwargs):
-------
stats : :py:class:`pandas.DataFrame`
* ``'U-val'``: U-value
* ``'U-val'``: U-value corresponding with sample x
* ``'alternative'``: tail of the test
* ``'p-val'``: p-value
* ``'RBC'`` : rank-biserial correlation
Expand All @@ -193,7 +193,8 @@ def mwu(x, y, alternative="two-sided", **kwargs):
The rank biserial correlation [2]_ is the difference between
the proportion of favorable evidence minus the proportion of unfavorable
evidence.
evidence. Values range from -1 to 1, with negative values indicating that `y > x`, and
positive values indicating `x > y`.
The common language effect size is the proportion of pairs where ``x`` is
higher than ``y``. It was first introduced by McGraw and Wong (1992) [3]_.
Expand Down Expand Up @@ -238,8 +239,8 @@ def mwu(x, y, alternative="two-sided", **kwargs):
>>> x = np.random.uniform(low=0, high=1, size=20)
>>> y = np.random.uniform(low=0.2, high=1.2, size=20)
>>> pg.mwu(x, y, alternative='two-sided')
U-val alternative p-val RBC CLES
MWU 97.0 two-sided 0.00556 0.515 0.2425
U-val alternative p-val RBC CLES
MWU 97.0 two-sided 0.00556 -0.515 0.2425
Compare with SciPy
Expand All @@ -250,18 +251,24 @@ def mwu(x, y, alternative="two-sided", **kwargs):
One-sided test
>>> pg.mwu(x, y, alternative='greater')
U-val alternative p-val RBC CLES
MWU 97.0 greater 0.997442 0.515 0.2425
U-val alternative p-val RBC CLES
MWU 97.0 greater 0.997442 -0.515 0.2425
>>> pg.mwu(x, y, alternative='less')
U-val alternative p-val RBC CLES
MWU 97.0 less 0.00278 0.515 0.7575
U-val alternative p-val RBC CLES
MWU 97.0 less 0.00278 -0.515 0.7575
Passing keyword arguments to :py:func:`scipy.stats.mannwhitneyu`:
>>> pg.mwu(x, y, alternative='two-sided', method='exact')
U-val alternative p-val RBC CLES
MWU 97.0 two-sided 0.004681 0.515 0.2425
U-val alternative p-val RBC CLES
MWU 97.0 two-sided 0.004681 -0.515 0.2425
Reversing the order of `x` and `y`.
>>> pg.mwu(y, x)
U-val alternative p-val RBC CLES
MWU 303.0 two-sided 0.00556 0.515 0.7575
"""
x = np.asarray(x)
y = np.asarray(y)
Expand All @@ -279,7 +286,7 @@ def mwu(x, y, alternative="two-sided", **kwargs):
raise ValueError(
"Since Pingouin 0.4.0, the 'tail' argument has been renamed to 'alternative'."
)
uval, pval = scipy.stats.mannwhitneyu(x, y, alternative=alternative, **kwargs)
uval_x, pval = scipy.stats.mannwhitneyu(x, y, alternative=alternative, **kwargs)

# Effect size 1: Common Language Effect Size
# CLES is tail-specific and calculated according to the formula given in
Expand All @@ -292,11 +299,12 @@ def mwu(x, y, alternative="two-sided", **kwargs):
cles = 1 - cles if alternative == "less" else cles

# Effect size 2: rank biserial correlation (Wendt 1972)
rbc = 1 - (2 * uval) / diff.size # diff.size = x.size * y.size
uval_y = x.shape[0] * y.shape[0] - uval_x
rbc = 1 - (2 * uval_y) / diff.size # diff.size = x.size * y.size

# Fill output DataFrame
stats = pd.DataFrame(
{"U-val": uval, "alternative": alternative, "p-val": pval, "RBC": rbc, "CLES": cles},
{"U-val": uval_x, "alternative": alternative, "p-val": pval, "RBC": rbc, "CLES": cles},
index=["MWU"],
)
return _postprocess_dataframe(stats)
Expand Down

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