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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import unittest
import numpy as np
import numpy.testing as npt
from skbio.stats.distance import mantel
from skbio.stats.evolve import hommola_cospeciation
from skbio.stats.evolve._hommola import _get_dist, _gen_lists
class HommolaCospeciationTests(unittest.TestCase):
def setUp(self):
# Test matrices, as presented in original paper by Hommola et al.
self.hdist = np.array([[0, 3, 8, 8, 9], [3, 0, 7, 7, 8], [
8, 7, 0, 6, 7], [8, 7, 6, 0, 3], [9, 8, 7, 3, 0]])
self.pdist = np.array([[0, 5, 8, 8, 8], [5, 0, 7, 7, 7], [
8, 7, 0, 4, 4], [8, 7, 4, 0, 2], [8, 7, 4, 2, 0]])
self.interact = np.array([[1, 0, 0, 0, 0], [0, 1, 0, 0, 0], [
0, 0, 1, 0, 0], [0, 0, 0, 1, 0], [0, 0, 0, 1, 1]])
# Reduced-size host matrix for testing asymmetric interaction matrix
self.hdist_4x4 = np.array([[0, 3, 8, 8], [3, 0, 7, 7], [8, 7, 0, 6],
[8, 7, 6, 0]])
self.interact_5x4 = np.array([[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0],
[0, 0, 0, 1], [0, 0, 0, 1]])
# One to one interaction matrix for comparing against Mantel output
self.interact_1to1 = np.array([[1, 0, 0, 0, 0], [0, 1, 0, 0, 0], [
0, 0, 1, 0, 0], [0, 0, 0, 1, 0], [0, 0, 0, 0, 1]])
# interaction matrix yielding non-significant results.
# this matrix was picked because it will generate an r value that's
# less than a standard deviation away from the mean of the normal
# distribution of r vals
self.interact_ns = np.array(
[[0, 0, 0, 1, 0], [0, 0, 0, 0, 1], [1, 0, 0, 0, 0],
[1, 0, 0, 0, 0], [0, 0, 0, 0, 1]])
# minimal size matrices for sanity checks of inputs
self.h_dist_3x3 = np.array([[0, 1, 2], [1, 0, 1], [2, 1, 0]])
self.h_dist_2x2 = np.array([[0, 3], [3, 0]])
self.p_dist_3x3 = np.array([[0, 3, 2], [3, 0, 1], [2, 1, 0]])
self.interact_3x3 = np.array([[0, 1, 1], [1, 0, 1], [0, 0, 1]])
self.interact_3x2 = np.array([[0, 1], [1, 0], [1, 1]])
self.interact_2x3 = np.array([[0, 1, 1], [1, 0, 1]])
self.interact_zero = np.array([[0, 0, 0], [0, 0, 0], [0, 0, 0]])
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 = .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_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_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_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_get_dist(self):
labels = np.array([0, 1, 1, 2, 3])
k_labels, t_labels = _gen_lists(labels)
dists = np.array([[0, 2, 6, 3], [2, 0, 5, 4], [6, 5, 0, 7],
[3, 4, 7, 0]])
index = np.array([2, 3, 1, 0])
expected_vec = np.array([7, 7, 5, 6, 0, 4, 3, 4, 3, 2])
actual_vec = _get_dist(k_labels, t_labels, dists, index)
npt.assert_allclose(actual_vec, expected_vec)
def test_gen_lists(self):
exp_pars_k_labels = np.array([0, 0, 0, 0, 0, 1, 1, 1,
1, 2, 2, 2, 3, 3, 4])
exp_pars_t_labels = np.array([1, 2, 3, 4, 4, 2, 3, 4,
4, 3, 4, 4, 4, 4, 4])
exp_host_k_labels = np.array([0, 0, 0, 0, 0, 1, 1, 1,
1, 2, 2, 2, 3, 3, 3])
exp_host_t_labels = np.array([1, 2, 3, 3, 4, 2, 3, 3,
4, 3, 3, 4, 3, 4, 4])
pars, hosts = np.nonzero(self.interact)
obs_pars_k_labels, obs_pars_t_labels = _gen_lists(pars)
obs_hosts_k_labels, obs_hosts_t_labels = _gen_lists(hosts)
npt.assert_allclose(exp_pars_k_labels, obs_pars_k_labels)
npt.assert_allclose(exp_pars_t_labels, obs_pars_t_labels)
npt.assert_allclose(exp_host_k_labels, obs_hosts_k_labels)
npt.assert_allclose(exp_host_t_labels, obs_hosts_t_labels)
def test_dm_too_small(self):
with self.assertRaises(ValueError):
hommola_cospeciation(self.h_dist_2x2, self.p_dist_3x3,
self.interact_3x3)
def test_host_interaction_not_equal(self):
with self.assertRaises(ValueError):
hommola_cospeciation(self.h_dist_3x3, self.p_dist_3x3,
self.interact_2x3)
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_interaction_too_few(self):
with self.assertRaises(ValueError):
hommola_cospeciation(self.h_dist_3x3, self.p_dist_3x3,
self.interact_zero)
def test_permutations_too_few(self):
with self.assertRaises(ValueError):
hommola_cospeciation(self.h_dist_3x3, self.p_dist_3x3,
self.interact_3x3, -1)
if __name__ == '__main__':
unittest.main()
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