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_sample_bounded_coal(self):
n = 1000
k = 5
T = 500
d = [coal.sample_bounded_coal(k, n, T) for i in xrange(2000)]
p = plotdistrib(d, 40)
p.plotfunc(lambda t: coal.prob_bounded_coal(t, k, n, T), 0, T, T/200)
eq_sample_pdf(d, lambda t: coal.prob_bounded_coal(t, k, n, T), 40)
def test_sample_coal_cond_counts(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
s = [coal.sample_coal_cond_counts(a, b, t, n)
for i in xrange(1000)]
eq_sample_pdf(s, lambda x: coal.prob_coal_cond_counts(
x, a, b, t, n), 40)
def test_prob_coal2(self):
outdir = 'test/tmp/test_coal/Coal_test_prob_coal2/'
make_clean_dir(outdir)
k = 2
n = 1000
p = Gnuplot()
p.enableOutput(False)
p.plotfunc(lambda t: coal.prob_coal(t, k, n), 0, 4000, 10,
ymin=0)
# draw single coal samples
x = [coal.sample_coal(k, n) for i in xrange(200)]
plotdistrib(x, 40, plot=p)
p.enableOutput(True)
p.save(outdir + 'plot.png')
eq_sample_pdf(x, lambda t: coal.prob_coal(t, k, 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_cdf_mrca(self):
outdir = 'test/tmp/test_coal/Coal_test_cdf_mrca/'
make_clean_dir(outdir)
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]
p = Gnuplot()
p.enableOutput(False)
p.plot(x, y2, style="lines")
p.plot(x, y3, style="lines")
p.enableOutput(True)
p.save(outdir + 'plot.png')
eq_sample_pdf(x, lambda t: coal.cdf_mrca(t, k, 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)
