def test_mpd(self):
"""Test if mean phylogenetic distance (mpd) is calculated correctly.
Notes:
The formula used is found Webb et al. 2002. Paper available at:
http://www.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.33.010802.150448
"""
distmat = array([[0.0, 0.4, 2.0, 1.3], [0.4, 0.0, 1.6, 0.2], [2.0, 1.6, 0.0, 1.1], [1.3, 0.2, 1.1, 0.0]])
self.assertFloatEqual(6.6 / 6.0, mpd(distmat))
def test_mpd(self):
"""Test if mean phylogenetic distance (mpd) is calculated correctly.
Notes:
The formula used is found Webb et al. 2002. Paper available at:
http://www.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.33.010802.150448
"""
distmat = array([[0.0, 0.4, 2.0, 1.3], [0.4, 0.0, 1.6, 0.2],
[2.0, 1.6, 0.0, 1.1], [1.3, 0.2, 1.1, 0.0]])
assert_almost_equal(6.6 / 6., mpd(distmat))
def test_mpd(self):
"""tests mpd walks through input matrices correctly"""
#define data
dist_mat = array([[0, 1, 2, 3, 4], [5, 6, 7, 8, 9],
[10, 11, 12, 13, 14], [15, 16, 17, 18, 19],
[20, 21, 22, 23, 24]])
expected_out_m = 8
actual_out_m = mpd(dist_mat)
self.assertEqual(expected_out_m, actual_out_m)
def test_mpd(self):
"""tests mpd walks through input matrices correctly"""
#define data
dist_mat = array([[ 0, 1, 2, 3, 4],
[ 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14],
[15, 16, 17, 18, 19],
[20, 21, 22, 23, 24]])
expected_out_m = 8
actual_out_m = mpd(dist_mat)
self.assertEqual(expected_out_m, actual_out_m)
