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BUG: fixed calculation of ranks in spearman, added option to use midr… #192

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BUG: fixed calculation of ranks in spearman, added option to use midr… #192

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fcb607e
BUG: fixed calculation of ranks in spearman, added option to use midr…
pbstark Nov 9, 2021
a4334c4
BUG: fixed namespace issue for rankdata
pbstark Nov 9, 2021
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13 changes: 9 additions & 4 deletions permute/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
import numpy as np
import warnings
from scipy.optimize import brentq, fsolve
from scipy.stats import ttest_ind, ttest_1samp
from scipy.stats import ttest_ind, ttest_1samp, rankdata
from fractions import Fraction

from .utils import get_prng, potential_outcomes, permute
Expand Down Expand Up @@ -52,7 +52,7 @@ def corr(x, y, alternative='greater', reps=10**4, seed=None, plus1=True):
return tst, pvalue, sims


def spearman_corr(x, y, alternative='greater', reps=10**4, seed=None, plus1=True):
def spearman_corr(x, y, alternative='greater', reps=10**4, seed=None, plus1=True, method='average'):
r"""
Simulate permutation p-value for Spearman correlation coefficient

Expand All @@ -72,15 +72,20 @@ def spearman_corr(x, y, alternative='greater', reps=10**4, seed=None, plus1=True
flag for whether to add 1 to the numerator and denominator of the
p-value based on the empirical permutation distribution.
Default is True.
method : {‘average’, ‘min’, ‘max’, ‘dense’, ‘ordinal’}
passed to scipy.stats.rankdata. 'average' uses midranks.
'ordinal' uses distinct ranks, with ties broken by order
of appearance in the original list.
Default is 'average'.

Returns
-------
tuple
Returns test statistic, p-value, simulated distribution
"""

xnew = np.argsort(x)+1
ynew = np.argsort(y)+1
xnew = rankdata(x, method=method)
ynew = rankdata(y, method=method)
return corr(xnew, ynew, alternative=alternative, reps=reps, seed=seed)


Expand Down