def test_plot_prob_bounded_coal(self):
n = 1000
k = 4
t = 800
alltimes = []
# sample times
for i in xrange(5000):
while True:
times = [0]
for j in xrange(k, 1, -1):
times.append(times[-1] + coal.sample_coal(j, n))
if times[-1] >= t:
break
if times[-1] < t:
break
alltimes.append(times)
p = Gnuplot()
for i in range(1, 2):
x, y = distrib([q[i] - q[i-1] for q in alltimes], width=20)
p.plot(x, y, style="lines", xmax=500)
x = list(frange(0, 500, 10))
#for i in range(1, 2): #k):
y2 = [coal.prob_bounded_coal(j, k, n, t) for j in x]
p.plot(x, y2, style="lines", xmax=500)
fequals(y, y2, rel=.05, eabs=.01)
def test_1(self):
"""Test multicoal_tree on simple 4 species tree"""
stree = treelib.parse_newick(
"((A:1000, B:1000):500, (C:700, D:700):800);")
n = 500
nsamples = 1000
tab, tops = _test_multicoal_tree(stree, n, nsamples)
print repr(tab[:20].get(cols=["simple_top", "percent", "prob"]))
a, b = tab[:20].cget("percent", "prob")
fequals(a, b, eabs=.05)
def test_cdf_mrca2(self):
n = 1000
k = 6
step = 10
x = list(frange(0, 5000, step))
y = [coal.prob_mrca(i, k, n) * step for i in x]
y2 = cumsum(y)
y3 = [coal.cdf_mrca(t, k, n) for t in x]
y4 = [coal.prob_coal_counts(k, 1, t, n) for t in x]
fequals(y2, y3, eabs=.01)
fequals(y3, y4)
def _test_recon(self):
# test multicoal_tree on simple 4 species tree
stree = treelib.parse_newick(
"((A:1000, B:1000):500, (C:700, D:700):800);")
n = 500
T = 2000
nsamples = 10000
tab, tops = _test_bounded_multicoal_tree(stree, n, T, nsamples)
print repr(tab[:20].get(cols=["simple_top", "percent", "prob"]))
a, b = tab[:20].cget("percent", "prob")
fequals(a, b, rel=.05, eabs=.005)
def test_cdf_coal_bounded(self):
n = 1000
k = 4
t = 500
step = .1
x = list(frange(0, 500, step))
y = [coal.prob_bounded_coal(i, k, n, t) * step for i in x]
y2 = cumsum(y)
y3 = [coal.cdf_bounded_coal(i, k, n, t) for i in x]
p = plot(x, y2, style="lines")
p.plot(x, y3, style="lines")
p.plot([0, 500], [1, 1], style="lines")
fequals(y2, y3, eabs=.01)
def test_flies(self):
stree = treelib.parse_newick("""(
(
(
(
(
(
dmel:5.32,
(
dsec:1.89,
dsim:1.89
):3.43
):5.91,
(
dere:8.57,
dyak:8.57
):2.66
):42.17,
dana:53.40
):2.40,
(
dpse:1.37,
dper:1.37
):54.43
):6.69,
dwil:62.49
):1.02,
(
(
dmoj:32.74,
dvir:32.74
):4.37,
dgri:37.11
):26.40
);""")
for node in stree:
node.dist *= 1e6 * 10
n = 10e6
nsamples = 5000
tab, tops = _test_multicoal_tree(stree, n, nsamples)
print repr(tab[:20].get(cols=["simple_top", "percent", "prob"]))
a, b = tab[:20].cget("percent", "prob")
fequals(a, b, eabs=.05)