def test_hommola_vs_mantel(self):
# we don't compare p-values because the two methods use different
# permutation strategies
r_mantel, p_mantel, _ = mantel(self.hdist, self.pdist, method="pearson", permutations=0, alternative="greater")
r_hommola, p_hommola, _ = hommola_cospeciation(self.hdist, self.pdist, self.interact_1to1, permutations=0)
self.assertAlmostEqual(r_hommola, r_mantel)
npt.assert_equal(p_hommola, p_mantel)
def test_zero_permutations(self):
obs_r, obs_p, obs_perm_stats = hommola_cospeciation(self.hdist, self.pdist, self.interact, 0)
exp_p = np.nan
exp_r = 0.83170965463247915
exp_perm_stats = np.array([])
npt.assert_equal(obs_p, exp_p)
self.assertAlmostEqual(obs_r, exp_r)
npt.assert_equal(obs_perm_stats, exp_perm_stats)
def test_hommola_cospeciation_sig(self):
np.random.seed(1)
obs_r, obs_p, obs_perm_stats = hommola_cospeciation(self.hdist, self.pdist, self.interact, 9)
exp_p = 0.1
exp_r = 0.83170965463247915
exp_perm_stats = np.array(
[-0.14928122, 0.26299538, -0.21125858, 0.24143838, 0.61557855, -0.24258293, 0.09885203, 0.02858, 0.42742399]
)
self.assertAlmostEqual(obs_p, exp_p)
self.assertAlmostEqual(obs_r, exp_r)
npt.assert_allclose(obs_perm_stats, exp_perm_stats)
def test_hommola_cospeciation_no_sig(self):
np.random.seed(1)
obs_r, obs_p, obs_perm_stats = hommola_cospeciation(
self.hdist, self.pdist, self.interact_ns, 9)
exp_p = .6
exp_r = -0.013679391379114569
exp_perm_stats = np.array([-0.22216543, -0.14836061, -0.04434843,
0.1478281, -0.29105645, 0.56395839,
0.47304992, 0.79125657, 0.06804138])
self.assertAlmostEqual(obs_p, exp_p)
self.assertAlmostEqual(obs_r, exp_r)
npt.assert_allclose(obs_perm_stats, exp_perm_stats)
def test_hommola_vs_mantel(self):
# we don't compare p-values because the two methods use different
# permutation strategies
r_mantel, p_mantel, _ = mantel(self.hdist,
self.pdist,
method='pearson',
permutations=0,
alternative='greater')
r_hommola, p_hommola, _ = hommola_cospeciation(self.hdist,
self.pdist,
self.interact_1to1,
permutations=0)
self.assertAlmostEqual(r_hommola, r_mantel)
npt.assert_equal(p_hommola, p_mantel)
def test_hommola_cospeciation_asymmetric(self):
np.random.seed(1)
obs_r, obs_p, obs_perm_stats = hommola_cospeciation(
self.hdist_4x4, self.pdist, self.interact_5x4, 9)
exp_p = 0.2
exp_r = 0.85732140997411233
exp_perm_stats = np.array([-0.315244162496, -0.039405520312,
0.093429386594, -0.387835875941,
0.183711730709, 0.056057631956,
0.945732487487, 0.056057631956,
-0.020412414523])
self.assertAlmostEqual(obs_p, exp_p)
self.assertAlmostEqual(obs_r, exp_r)
npt.assert_allclose(obs_perm_stats, exp_perm_stats)
def test_permutations_too_few(self):
with self.assertRaises(ValueError):
hommola_cospeciation(self.h_dist_3x3, self.p_dist_3x3, self.interact_3x3, -1)
def test_par_interaction_not_equal(self):
with self.assertRaises(ValueError):
hommola_cospeciation(self.h_dist_3x3, self.p_dist_3x3, self.interact_3x2)
def test_dm_too_small(self):
with self.assertRaises(ValueError):
hommola_cospeciation(self.h_dist_2x2, self.p_dist_3x3, self.interact_3x3)
