def _test_bounded_multicoal_tree(stree, n, T, nsamples):
"""test multicoal_tree"""
tops = {}
for i in xrange(nsamples):
# use rejection sampling
#tree, recon = coal.sample_bounded_multicoal_tree_reject(
# stree, n, T, namefunc=lambda x: x)
# sample tree
tree, recon = coal.sample_bounded_multicoal_tree(
stree, n, T, namefunc=lambda x: x)
top = phylo.hash_tree(tree)
tops.setdefault(top, [0, tree, recon])[0] += 1
tab = Table(headers=["top", "simple_top", "percent", "prob"])
for top, (num, tree, recon) in tops.items():
tree2 = tree.copy()
treelib.remove_single_children(tree2)
tab.add(top=top,
simple_top=phylo.hash_tree(tree2),
percent=num/float(nsamples),
prob=exp(coal.prob_bounded_multicoal_recon_topology(
tree, recon, stree, n, T)))
tab.sort(col="prob", reverse=True)
return tab, tops
def test_top(self):
outdir = 'test/tmp/test_coal/BMC_test_top/'
make_clean_dir(outdir)
stree = treelib.parse_newick(
"(((A:200, E:200):800, B:1000):500, (C:700, D:700):800);")
n = 500
T = 2000
nsamples = 4000
# compare top hist with simpler rejection sampling
tops = {}
tops2 = {}
for i in xrange(nsamples):
# use rejection sampling
tree, recon = coal.sample_bounded_multicoal_tree_reject(
stree, n, T, namefunc=lambda x: x)
# sample tree
tree2, recon2 = coal.sample_bounded_multicoal_tree(
stree, n, T, namefunc=lambda x: x)
top = phylo.hash_tree(tree)
top2 = phylo.hash_tree(tree2)
tops.setdefault(top, [0, tree, recon])[0] += 1
tops.setdefault(top2, [0, tree2, recon2])
tops2.setdefault(top2, [0, tree2, recon2])[0] += 1
tops2.setdefault(top, [0, tree, recon])
keys = tops.keys()
x = [safelog(tops[i][0], default=0) for i in keys]
y = [safelog(tops2[i][0], default=0) for i in keys]
self.assertTrue(stats.corr(x, y) > .9)
p = Gnuplot()
p.enableOutput(False)
p.plot(x, y)
p.plot([min(x), max(x)], [min(x), max(x)], style="lines")
p.enableOutput(True)
p.save(outdir + 'plot.png')