:py:mod:`biotaphy.analyses.anc_dp`
==================================

.. py:module:: biotaphy.analyses.anc_dp

.. autoapi-nested-parse::

   Module containing code for calculating ancestral states.



Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   biotaphy.analyses.anc_dp._get_node_label
   biotaphy.analyses.anc_dp.calculate_ancestral_distributions
   biotaphy.analyses.anc_dp.calculate_continuous_ancestral_states



.. py:function:: _get_node_label(node)

   Returns the node label or taxon label if node is a tip.

   :param node: A tree node to get the label for.
   :type node: Node

   :returns: The node label or taxon label.
   :rtype: str


.. py:function:: calculate_ancestral_distributions(tree, char_mtx)

   Calculates ancestral distributions.

   :param tree: A dendropy tree or TreeWrapper object.
   :type tree: Tree
   :param char_mtx: A Matrix object with character information.  Each
                    row should represent a tip in the tree and each column should be a
                    bin to calculate ancestral distribution.
   :type char_mtx: Matrix

   :returns:     * rows: nodes / tips in the tree
                 * columns: character variables
                 * depth: first is the calculated value, second layer is standard
                     error if desired
   :rtype: A matrix of character data with the following dimensions


.. py:function:: calculate_continuous_ancestral_states(tree, char_mtx, sum_to_one=False, calc_std_err=False)

   Calculates the continuous ancestral states for the nodes in a tree.

   :param tree: A dendropy tree or TreeWrapper object.
   :type tree: Tree
   :param char_mtx: A Matrix object with character information.  Each
                    row should represent a tip in the tree and each column should be a
                    variable to calculate ancestral state for.
   :type char_mtx: Matrix
   :param calc_std_err: If True, calculate standard error
                        for each variable.  Defaults to False.
   :type calc_std_err: :obj:`bool`, optional
   :param sum_to_one: If True, standardize the character
                      matrix so that the values in a row sum to one. Defaults to False.
   :type sum_to_one: :obj:`bool`, optional

   :raises ValueError: Raised if none of the tree tips were found in the character data.

   :returns:     * rows: nodes / tips in the tree
                 * columns: character variables
                 * depth: first is the calculated value, second layer is standard
                     error if desired
   :rtype: A matrix of character data with the following dimensions

   .. todo:: * Add function for consistent label handling.