def test_setDescendantTipProperty(self):
"""setDescendantTipProperty should set correct property and value"""
leaf_dict = {'d':2, 'e':1, 'g':6, 'h':7}
means_dict = leaf_dict.copy()
means_dict.update({'f':6, 'c':3, 'b':3, 'a':4})
stdevs_dict = {'d':0, 'e':0, 'g':0, 'f':0, 'c':stdev([2,1,6]), \
'b':stdev([2,1,6]), 'h':0, 'a':stdev([2,1,6,7])}
def set_leaf_f(node):
return leaf_dict[node.Data]
r = self.TreeRoot
r.setDescendantTipProperty(set_leaf_f, 'x')
for node in r.traverse():
self.assertEqual(node.xMean, means_dict[node.Data])
self.assertFloatEqual(node.xStdev, stdevs_dict[node.Data])
def setDescendantTipProperty(self,f,prop_name='Trait',force_recalc=False):
"""Sets n.propMean, n.propStdev) of f(node) for all nodes in self.
These correspond to T_i and S_i respectively in AOT, Ackerley 2004.
Example usage:
(a) You have a dict mapping leaf -> property:
leaf_f = lambda node: d[node.Data]
(b) You have the property stored in leaf.prop_xyz:
leaf_f = lambda node: node.prop_xyz
tree.setDescendantTipProperty(leaf_f, 'MyProp') will set on each node
n.MyPropMean and n.MyPropStdev.
"""
for node in self.traverse(self_before=False, self_after=True):
if force_recalc or not hasattr(node, 'DescendantTips'):
node.setDescendantTips()
values = map(f, node.DescendantTips)
setattr(node, prop_name+'Mean', mean(values))
if len(values) > 1:
std = stdev(values)
else:
std = 0
setattr(node, prop_name+'Stdev', std)
