def test_prob_coal_cond_counts(self):
# match against a simpler slower implementation
a = 5
b = 3
t = 2000
n = 1000
for x in frange(0, 2000, 10):
y = coal.prob_coal_cond_counts(x, a, b, t, n)
y2 = coal.prob_coal_cond_counts_simple(x, a, b, t, n)
self.assertAlmostEqual(y, y2)
def test_prob_coal_cond_counts_simple(self):
# when we condition on b=1, it is the same as the bounded coal
# PDF.
# prob_coal_cond_counts is actually a more general version of
# prob_bounded_coal
outdir = 'test/tmp/test_coal/Coal_test_prob_coal_counys_simple/'
make_clean_dir(outdir)
a = 5
b = 1
t = 2000
n = 1000
p = Gnuplot()
p.enableOutput(False)
for x in frange(0, 2000, 10):
y = coal.prob_coal_cond_counts_simple(x, a, b, t, n)
y2 = coal.prob_bounded_coal(x, a, n, t)
self.assertAlmostEqual(y, y2)
def test_prob_coal_cond_counts2_simple(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_simple(
x, a, b, t, n), 40)