def test_prob_birth_death1(self):
"""Sampling and PDF for birth-death from single lineage."""
t = 1.0
birth = 0.5
death = 0.2
counts = [birthdeath.sample_birth_death_count(1, t, birth, death)
for i in xrange(10000)]
eq_sample_pmf(
counts,
lambda i: birthdeath.prob_birth_death1(i, t, birth, death),
pval=0.01)
def test_prob_birth_death1_eq(self):
"""
Sampling and PDF for birth-death from single lineage birth=death rate.
"""
t = 1.0
birth = 0.5
death = 0.5
counts = [
birthdeath.sample_birth_death_count(1, t, birth, death)
for i in xrange(10000)
]
eq_sample_pmf(
counts, lambda i: birthdeath.prob_birth_death1(i, t, birth, death))
def test_rannala1996_prob_birth_death1(self):
t = 1.0
birth = 0.5
death = 0.2
counts = [birthdeath.sample_birth_death_count(1, t, birth, death)
for i in xrange(10000)]
# original equation should fail
try:
eq_sample_pmf(
counts,
lambda i: rannala1996_prob_birth_death1(i, t, birth, death))
except:
pass
else:
raise AssertionError
eq_sample_pmf(
counts,
lambda i: rannala1996_prob_birth_death1_fix(i, t, birth, death))
def test_rannala1996_prob_birth_death1(self):
t = 1.0
birth = 0.5
death = 0.2
counts = [
birthdeath.sample_birth_death_count(1, t, birth, death)
for i in xrange(10000)
]
# original equation should fail
try:
eq_sample_pmf(
counts,
lambda i: rannala1996_prob_birth_death1(i, t, birth, death))
except:
pass
else:
raise AssertionError
eq_sample_pmf(
counts,
lambda i: rannala1996_prob_birth_death1_fix(i, t, birth, death))
