def test_toProbs(self):
"""Rates toProbs should return correct probability matrix"""
a = self.abc_pairs
p = Probs([0.75, 0.1, 0.15, 0.2, 0.7, 0.1, 0.05, 0.1, 0.85], a)
q = p.toRates()
self.assertEqual(q._data, logm(p._data))
p2 = q.toProbs()
self.assertFloatEqual(p2._data, p._data)
#test a case that didn't work for DNA
q = Rates(array(
[[-0.64098451, 0.0217681 , 0.35576469, 0.26345171],
[ 0.31144238, -0.90915091, 0.25825858, 0.33944995],
[ 0.01578521, 0.43162879, -0.99257581, 0.54516182],
[ 0.13229986, 0.04027147, 0.05817791, -0.23074925]]),
DnaPairs)
self.assertFloatEqual(q.toProbs(0.5)._data, expm(q._data)(t=0.5))
def test_toProbs(self):
"""Rates toProbs should return correct probability matrix"""
a = self.abc_pairs
p = Probs([0.75, 0.1, 0.15, 0.2, 0.7, 0.1, 0.05, 0.1, 0.85], a)
q = p.toRates()
self.assertEqual(q._data, logm(p._data))
p2 = q.toProbs()
self.assertFloatEqual(p2._data, p._data)
#test a case that didn't work for DNA
q = Rates(
array([[-0.64098451, 0.0217681, 0.35576469, 0.26345171],
[0.31144238, -0.90915091, 0.25825858, 0.33944995],
[0.01578521, 0.43162879, -0.99257581, 0.54516182],
[0.13229986, 0.04027147, 0.05817791, -0.23074925]]),
DnaPairs)
self.assertFloatEqual(q.toProbs(0.5)._data, expm(q._data)(t=0.5))
