skbio.tree.TreeNode.depth#

TreeNode.depth(ancestor=None, include_root=False, use_length=True, missing_as_zero=False)[source]#

Calculate the depth of the current node.

Changed in version 0.6.3: Renamed from accumulate_to_ancestor. The old name is kept as an alias.

The depth of a node is the sum of branch lengths from it to the root of the tree.

Parameters:
ancestorTreeNode, optional

An ancestral node of self. If provided, the distance from self to this node instead of the root node will be calculated.

Changed in version 0.6.3: Becomes optional.

include_rootbool, optional

If True, the distance will include the length of the root node, or the given ancestral node if ancestor is provided. Default is False.

Added in version 0.6.3.

use_lengthbool, optional

Whether to return the sum of branch lengths (True, default) or the number of branches (False) from self to root.

Added in version 0.6.3.

missing_as_zerobool, optional

When a node without an associated branch length is encountered, raise an error (False, default) or use 0 (True). Applicable when use_length is True.

Added in version 0.6.3.

Returns:
float

The depth of self.

Raises:
NoParentError

If the given ancestral node is not an ancestor of self.

NoLengthError

If nodes without branch length are encountered, but missing_as_zero is False.

See also

height
distance

Examples

>>> from skbio import TreeNode
>>> tree = TreeNode.read(["((a:1,b:2)c:3,(d:4,e:5)f:6)root;"])
>>> tree.find('a').depth()
4.0
>>> tree.find('a').depth(tree.find('c'))
1.0
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