[Scipy-svn] r6907 - trunk/scipy/stats/tests
scipy-svn at scipy.org
scipy-svn at scipy.org
Thu Nov 18 06:40:53 EST 2010
Author: rgommers
Date: 2010-11-18 05:40:52 -0600 (Thu, 18 Nov 2010)
New Revision: 6907
Modified:
trunk/scipy/stats/tests/test_stats.py
Log:
TST: clean up fisher_exact test. An unused for-loop was left in.
Modified: trunk/scipy/stats/tests/test_stats.py
===================================================================
--- trunk/scipy/stats/tests/test_stats.py 2010-11-17 20:49:26 UTC (rev 6906)
+++ trunk/scipy/stats/tests/test_stats.py 2010-11-18 11:40:52 UTC (rev 6907)
@@ -416,36 +416,24 @@
res = fisher_exact([[19000, 80000], [20000, 90000]])[1]
assert_approx_equal(res, 3.319e-9, significant=1)
- tablelist = ( [[100, 2], [1000, 5]],
- [[2, 7], [8, 2]],
- [[5, 1], [10, 10]],
- [[5, 15], [20, 20]],
- [[5, 16], [20, 25]],
- [[10, 5], [10, 1]],
- [[10, 5], [10, 0]],
- [[5,0], [1, 4]],
- [[0,5], [1, 4]],
- [[5,1], [0, 4]],
- [[0, 1], [3, 2]] )
- for table in tablelist:
- # results from R
- #
- # R defines oddsratio differently (see Notes section of fisher_exact
- # docstring), so those will not match. We leave them in anyway, in
- # case they will be useful later on. We test only the p-value.
- tablist = [
- ([[100, 2], [1000, 5]], (2.505583993422285e-001, 1.300759363430016e-001)),
- ([[2, 7], [8, 2]], (8.586235135736206e-002, 2.301413756522114e-002)),
- ([[5, 1], [10, 10]], (4.725646047336584e+000, 1.973244147157190e-001)),
- ([[5, 15], [20, 20]], (3.394396617440852e-001, 9.580440012477637e-002)),
- ([[5, 16], [20, 25]], (3.960558326183334e-001, 1.725864953812994e-001)),
- ([[10, 5], [10, 1]], (2.116112781158483e-001, 1.973244147157190e-001)),
- ([[10, 5], [10, 0]], (0.000000000000000e+000, 6.126482213438734e-002)),
- ([[5, 0], [1, 4]], (np.inf, 4.761904761904762e-002)),
- ([[0, 5], [1, 4]], (0.000000000000000e+000, 1.000000000000000e+000)),
- ([[5, 1], [0, 4]], (np.inf, 4.761904761904758e-002)),
- ([[0, 1], [3, 2]], (0.000000000000000e+000, 1.000000000000000e+000))
- ]
+ # results from R
+ #
+ # R defines oddsratio differently (see Notes section of fisher_exact
+ # docstring), so those will not match. We leave them in anyway, in
+ # case they will be useful later on. We test only the p-value.
+ tablist = [
+ ([[100, 2], [1000, 5]], (2.505583993422285e-001, 1.300759363430016e-001)),
+ ([[2, 7], [8, 2]], (8.586235135736206e-002, 2.301413756522114e-002)),
+ ([[5, 1], [10, 10]], (4.725646047336584e+000, 1.973244147157190e-001)),
+ ([[5, 15], [20, 20]], (3.394396617440852e-001, 9.580440012477637e-002)),
+ ([[5, 16], [20, 25]], (3.960558326183334e-001, 1.725864953812994e-001)),
+ ([[10, 5], [10, 1]], (2.116112781158483e-001, 1.973244147157190e-001)),
+ ([[10, 5], [10, 0]], (0.000000000000000e+000, 6.126482213438734e-002)),
+ ([[5, 0], [1, 4]], (np.inf, 4.761904761904762e-002)),
+ ([[0, 5], [1, 4]], (0.000000000000000e+000, 1.000000000000000e+000)),
+ ([[5, 1], [0, 4]], (np.inf, 4.761904761904758e-002)),
+ ([[0, 1], [3, 2]], (0.000000000000000e+000, 1.000000000000000e+000))
+ ]
for table, res_r in tablist:
res = fisher_exact(np.asarray(table))
np.testing.assert_almost_equal(res[1], res_r[1], decimal=11,
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