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_birth_death(self):
counts = list(range(1, 10))
birth = 0.01
death = 0.02
t = 1.0
for a in range(1, 10):
for b in range(0, 10):
l = spidir.birthDeathCounts(a, b, t, birth, death)
#l2 = spidir.birthDeathCounts2(a, b, t, birth, death)
l2 = l
l3 = birthdeath.prob_birth_death(a, b, t, birth, death)
print a, b, l, l2, l3
#fequal(l, l2, .1)
fequal(l, l3, .01)
fequal(sum(spidir.birthDeathCounts(a, b, t, birth, death)
for b in xrange(0, 20)),
1.0, .001)
def test_birthDeathCounts2(self):
"""birthDeathCounts"""
l = 3.0
u = .5
t = 1.0
for s in range(1, 40):
for e in range(0, 40):
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_birthDeathCounts2(self):
"""birthDeathCounts"""
l = 3.0
u = .5
t = 1.0
for s in range(1, 40):
for e in range(0, 40):
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_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_birth_death(self):
counts = list(range(1, 10))
birth = 0.01
death = 0.02
t = 1.0
for a in range(1, 10):
for b in range(0, 10):
l = spidir.birthDeathCounts(a, b, t, birth, death)
#l2 = spidir.birthDeathCounts2(a, b, t, birth, death)
l2 = l
l3 = birthdeath.prob_birth_death(a, b, t, birth, death)
print a, b, l, l2, l3
#fequal(l, l2, .1)
fequal(l, l3, .01)
fequal(
sum(
spidir.birthDeathCounts(a, b, t, birth, death)
for b in xrange(0, 20)), 1.0, .001)
def test_birth_death_same(self):
counts = list(range(1, 10))
birth = .2
death = .1
lam = birth
t = 10.4
for a in range(1, 10):
for b in range(0, 10):
l = spidir.birthDeathCounts(a, b, t, birth, death)
#l2 = spidir.birthDeathCounts2(a, b, t, birth, death*.999)
#l2 = prob_birth_death_same(a, b, t, lam)
l2 = l
l3 = birthdeath.prob_birth_death(a, b, t, birth, death)
print a, b, l, l2, l3
#fequal(l, l2, .01)
fequal(l, l3, .01)
def test_birth_death_same(self):
counts = list(range(1, 10))
birth = .2
death = .1
lam = birth
t = 10.4
for a in range(1, 10):
for b in range(0, 10):
l = spidir.birthDeathCounts(a, b, t, birth, death)
#l2 = spidir.birthDeathCounts2(a, b, t, birth, death*.999)
#l2 = prob_birth_death_same(a, b, t, lam)
l2 = l
l3 = birthdeath.prob_birth_death(a, b, t, birth, death)
print a, b, l, l2, l3
#fequal(l, l2, .01)
fequal(l, l3, .01)
def test_birth_death_large(self):
t = 0.0392320007
birth = 0.400400013
death = 0.400000006
print "large"
print birthdeath.prob_birth_death(60, 71, t, birth, death)
print spidir.birthDeathCounts2(60, 71, t, birth, death)
print spidir.birthDeathCounts(60, 71, t, birth, death)
t = 0.067008
birth = 0.010100
death = 0.010000
print spidir.birthDeathCounts(51, 51, t, birth, death)
print spidir.birthDeathCounts2(51, 51, t, birth, death)
print spidir.birthDeathCounts(51, 51, t, birth, death)
def test_birth_death_large(self):
t = 0.0392320007
birth = 0.400400013
death = 0.400000006
print "large"
print birthdeath.prob_birth_death(60, 71, t, birth, death)
print spidir.birthDeathCounts2(60, 71, t, birth, death)
print spidir.birthDeathCounts(60, 71, t, birth, death)
t = 0.067008
birth = 0.010100
death = 0.010000
print spidir.birthDeathCounts(51, 51, t, birth, death)
print spidir.birthDeathCounts2(51, 51, t, birth, death)
print spidir.birthDeathCounts(51, 51, t, birth, death)
def test_birthDeathCounts3(self):
"""birthDeathCounts"""
print spidir.birthDeathCounts(30, 33, .05, 173.2958, 171.58002)
print spidir.birthDeathCounts(26, 27, 0.068190, 173.2958, 171.58002)
def test_birthDeathCounts3(self):
"""birthDeathCounts"""
print spidir.birthDeathCounts(30, 33, .05, 173.2958, 171.58002)
print spidir.birthDeathCounts(26, 27, 0.068190, 173.2958, 171.58002)
