def test_cdf_bmc_simple(self):
# test cdf mrca BMC
stree = treelib.parse_newick("((A:1000, B:1000):500, C:1500);")
n = 1000
gene_counts = dict.fromkeys(stree.leaf_names(), 1)
T = 2000
self.assertAlmostEqual(
exp(coal.cdf_mrca_bounded_multicoal(gene_counts, T, stree, n)),
0.27719726132)
def test_cdf_bmc(self):
# test cdf mrca BMC
stree = treelib.parse_newick(
"((A:1000, B:1000):500, (C:700, D:700):800);")
n = 1000
gene_counts = dict.fromkeys(stree.leaf_names(), 1)
T = 2000
p = exp(coal.cdf_mrca_bounded_multicoal(gene_counts, T, stree, n))
nsamples = 5000
c = 0
for i in xrange(nsamples):
tree, recon = coal.sample_multicoal_tree(stree, n)
if treelib.get_tree_timestamps(tree)[tree.root] < T:
c += 1
p2 = c / float(nsamples)
fequal(p, p2, .05)
