def test_birthDeathCounts(self):
"""birthDeathCounts"""
l = 3.0
u = .5
t = 1.0
print spidir.birthDeathCount(1, t, l, u)
for s in range(1, 10):
for e in range(0, 10):
p1 = spidir.birthDeathCounts(s, e, t, l, u)
p2 = birthdeath.prob_birth_death(s, e, t, l, u)
print s, e, p1, p2
fequal(p1, p2, .01)
def test_birthDeathCounts(self):
"""birthDeathCounts"""
l = 3.0
u = .5
t = 1.0
print spidir.birthDeathCount(1, t, l, u)
for s in range(1, 10):
for e in range(0, 10):
p1 = spidir.birthDeathCounts(s, e, t, l, u)
p2 = birthdeath.prob_birth_death(s, e, t, l, u)
print s, e, p1, p2
fequal(p1, p2, .01)
def test_birthDeathCount(self):
"""birthDeathCount"""
l = 3
u = .5
for t in frange(0, 5, .01):
for s in range(0, 20):
p1 = spidir.birthDeathCount(s, t, l, u)
p2 = birthdeath.prob_birth_death1(s, t, l, u)
fequal(p1, p2, .01)
def test_birthDeathCount(self):
"""birthDeathCount"""
l = 3
u = .5
for t in frange(0, 5, .01):
for s in range(0, 20):
p1 = spidir.birthDeathCount(s, t, l, u)
p2 = birthdeath.prob_birth_death1(s, t, l, u)
fequal(p1, p2, .01)
def test_sample_birth_times(self):
stree = read_tree("test/data/flies.stree")
birth = 8.1
death = 2.1 * 1.0001
print spidir.birthDeathCount(4, .005, birth, death)
print spidir.birthDeathCounts(1, 4, .005, birth, death)
maxgenes = [5, 10, 20, 40, 50]
tic("time")
counts = [2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 2]
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree,
counts,
birth,
death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl
toc()
counts = [1] * 12
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree,
counts,
birth,
death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl
counts = [4] * 12
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree,
counts,
birth,
death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl
def test_sample_birth_times(self):
stree = read_tree("test/data/flies.stree")
birth = 8.1
death = 2.1 * 1.0001
print spidir.birthDeathCount(4, .005, birth, death)
print spidir.birthDeathCounts(1, 4, .005, birth, death)
maxgenes = [5, 10, 20, 40, 50]
tic("time")
counts = [2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 2]
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree, counts,
birth, death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl
toc()
counts = [1] * 12
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree, counts,
birth, death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl
counts = [4] * 12
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree, counts,
birth, death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl