def test_cdf_coal_cond_counts(self):
# test coalescent pdf when conditioned on future lineage counts
outdir = 'test/tmp/test_coal/Coal_test_cdf_coal_cond_counts/'
make_clean_dir(outdir)
a = 5
for b in xrange(2, a):
t = 500
n = 1000
p = Gnuplot()
p.enableOutput(False)
p.plotfunc(lambda x: coal.cdf_coal_cond_counts(
x, a, b, t, n), 0, t, 10)
# draw single coal samples using rejection sampling
s = []
for i in xrange(1000):
while True:
times = coal.sample_coal_times(a, n)
if times[a-b-1] < t and (b == 1 or times[a-b] > t):
break
s.append(times[0])
x2, y2 = stats.cdf(s)
p.plot(x2, y2, style='lines')
p.enableOutput(True)
p.save(outdir + 'plot-%d.png' % b)
eq_sample_pdf(
x2, lambda x: coal.prob_coal_cond_counts(x, a, b, t, n), 40)
def test_prob_coal_cond_counts2(self):
# test coalescent pdf when conditioned on future lineage counts
a = 5
for b in xrange(2, a):
t = 500
n = 1000
# draw single coal samples using rejection sampling
x2 = []
for i in xrange(1000):
while True:
times = coal.sample_coal_times(a, n)
if times[a-b-1] < t and (b == 1 or times[a-b]) > t:
break
x2.append(times[0])
eq_sample_pdf(x2, lambda x: coal.prob_coal_cond_counts(
x, a, b, t, n), 40)
def test_prob_mrca(self):
n = 1000
k = 50
x = [coal.sample_coal_times(k, n)[-1] for i in xrange(10000)]
eq_sample_pdf(x, lambda t: coal.prob_mrca(t, k, n), 40)