def _test_multicoal_tree(stree, n, nsamples):
"""test multicoal_tree"""
tops = {}
for i in xrange(nsamples):
tree, recon = coal.sample_multicoal_tree(stree, n,
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)
print phylo.hash_tree(tree2)
print phylo.hash_tree(stree)
tab.add(top=top,
simple_top=phylo.hash_tree(tree2),
percent=num/float(nsamples),
prob=exp(coal.prob_multicoal_recon_topology(
tree, recon, stree, n)))
tab.sort(col="prob", reverse=True)
return tab, tops
pretime=None, premean=None,
maxdoom=20, nsamples=100,
add_spec=True))
if 0:
draw_tree_names(coal_tree, scale=.5e-7, minlen=8)
draw_tree_names(ex["locus_tree"], scale=.5e-7, minlen=8)
print exp(dlcoal.prob_multicoal_recon_topology(
coal_tree, ex["coal_recon"], ex["locus_tree"], n, ex["daughters"]))
print exp(dlcoal.prob_multicoal_recon_topology2(
coal_tree, ex["coal_recon"], ex["locus_tree"], n, ex["daughters"]))
if 0:
draw_tree_names(coal_tree, scale=1e-7)
print exp(coal.prob_multicoal_recon_topology(
coal_tree, ex["coal_recon"], ex["locus_tree"], n))
print exp(coal.prob_multicoal_recon_topology_old(
coal_tree, ex["coal_recon"], ex["locus_tree"], n))
if 0:
pd(coal.count_lineages_per_branch(
coal_tree, ex["coal_recon"], ex["locus_tree"]))
#=============================================================================
show_plots = False
def show_plot():
if show_plots:
