def runTest(self):
rng = MockRandom()
newick = "((t5:1611.75,t6:1611.75):3922.93,((t4:1043.81,(t2:754.11,t1:754.11):2896.9):6584.0,t3:1702.21):3832.47);"
tree = dendropy.Tree.get_from_string(newick, "newick")
root = tree.seed_node
root.mutation_rate = 1e-5
root.mean_edge_rate = root.mutation_rate
continuous.evolve_continuous_char(root, rng, roeotroe=0.01,
min_rate=1.0e-6, max_rate=1.0e-3, model='KTB',
time_attr='edge_length', val_attr='mutation_rate',
mean_val_attr='mean_edge_rate',
constrain_rate_mode="linear_bounce")
for i in tree.preorder_node_iter():
if i.edge_length is not None:
i.edge_length *= i.mean_edge_rate
def simulate_continuous(node, rng=None, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.continuous' module has moved to 'dendropy.model.continuous', and this function has been renamed 'evolve_continuous_char()'.",
old_construct="from dendropy import continuous\ncontinuous.simulate_continuous(...)",
new_construct="from dendropy.model import continuous\ncontinuous.evolve_continuous_char(...)",
epilog="Note that this function is also available through 'dendropy.simulate.charsim.evolve_continuous_char(...)'.")
return continuous.evolve_continuous_char(node, rng, **kwargs)
def runTest(self):
rng = MockRandom()
newick = "((t5:1611.75,t6:1611.75):3922.93,((t4:1043.81,(t2:754.11,t1:754.11):2896.9):6584.0,t3:1702.21):3832.47);"
tree = dendropy.Tree.get_from_string(newick, "newick")
root = tree.seed_node
root.mutation_rate = 1e-5
root.mean_edge_rate = root.mutation_rate
continuous.evolve_continuous_char(root,
rng,
roeotroe=0.01,
min_rate=1.0e-6,
max_rate=1.0e-3,
model='KTB',
time_attr='edge_length',
val_attr='mutation_rate',
mean_val_attr='mean_edge_rate',
constrain_rate_mode="linear_bounce")
for i in tree.preorder_node_iter():
if i.edge_length is not None:
i.edge_length *= i.mean_edge_rate
