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

.. py:module:: biotaphy.analyses.site_statistics

.. autoapi-nested-parse::

   Module containing functions for computing site statistics.



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


Functions
~~~~~~~~~

.. autoapisummary::

   biotaphy.analyses.site_statistics.calculate_tree_site_statistics
   biotaphy.analyses.site_statistics.get_tip_lengths
   biotaphy.analyses.site_statistics.mean_node_height
   biotaphy.analyses.site_statistics.mean_tip_length
   biotaphy.analyses.site_statistics.median_node_height
   biotaphy.analyses.site_statistics.median_tip_length
   biotaphy.analyses.site_statistics.node_height_percentile_25
   biotaphy.analyses.site_statistics.node_height_percentile_2_5
   biotaphy.analyses.site_statistics.node_height_percentile_75
   biotaphy.analyses.site_statistics.node_height_percentile_97_5
   biotaphy.analyses.site_statistics.tip_length_percentile_25
   biotaphy.analyses.site_statistics.tip_length_percentile_2_5
   biotaphy.analyses.site_statistics.tip_length_percentile_75
   biotaphy.analyses.site_statistics.tip_length_percentile_97_5



Attributes
~~~~~~~~~~

.. autoapisummary::

   biotaphy.analyses.site_statistics.TOLERANCE


.. py:data:: TOLERANCE
   :annotation: = 0.005

   

.. py:function:: calculate_tree_site_statistics(pam, tree)

   Calculate tree statistics for each site in a PAM.

   :param pam: A PAM to compute statistics for.
   :type pam: Matrix
   :param tree: A corresponding tree to use for statistics.
   :type tree: TreeWrapper

   :returns: Matrix - A site by statistic matrix of tree pam statistics.


.. py:function:: get_tip_lengths(tree)

   Get the tip lengths in a tree.

   :param tree: A tree object to get tip lengths from.
   :type tree: Tree

   :returns: A list of tip lengths in the tree.
   :rtype: list


.. py:function:: mean_node_height(tree)

   Get the mean node height for the tree.

   :param tree: A tree object used to measure node heights.
   :type tree: Tree

   :returns: The mean height of the nodes in the tree.
   :rtype: float


.. py:function:: mean_tip_length(tree)

   Determine the mean tip length for the tips in a tree.

   :param tree: A tree object used to retrieve tip lengths.
   :type tree: Tree

   :returns: The mean tip length for the tips in the tree.
   :rtype: float


.. py:function:: median_node_height(tree)

   Get the median node height for the tree.

   :param tree: A tree object used to measure node heights.
   :type tree: Tree

   :returns: The median height of the nodes in the tree.
   :rtype: float


.. py:function:: median_tip_length(tree)

   Determine the median tip length for the tips in a tree.

   :param tree: A tree object used to retrieve tip lengths.
   :type tree: Tree

   :returns: The median tip length for the tips in the tree.
   :rtype: float


.. py:function:: node_height_percentile_25(tree)

   Determine the 25 percentile node height for a tree.

   :param tree: A tree object used to measure node heights.
   :type tree: Tree

   :returns: The 25 percentile node height for the tree.
   :rtype: float


.. py:function:: node_height_percentile_2_5(tree)

   Determine the 2.5 percentile node height for a tree.

   :param tree: A tree object used to measure node heights.
   :type tree: Tree

   :returns: The 2.5 percentile node height for the tree.
   :rtype: float


.. py:function:: node_height_percentile_75(tree)

   Determine the 75 percentile node height for a tree.

   :param tree: A tree object used to measure node heights.
   :type tree: Tree

   :returns: The 75 percentile node height for the tree.
   :rtype: float


.. py:function:: node_height_percentile_97_5(tree)

   Determine the 97.5 percentile node height for a tree.

   :param tree: A tree object used to measure node heights.
   :type tree: Tree

   :returns: The 97.5 percentile node height for the tree.
   :rtype: float


.. py:function:: tip_length_percentile_25(tree)

   Determine the 25 percentile for tip length for the tips of the tree.

   :param tree: A tree object used to retrieve tip lengths.
   :type tree: Tree

   :returns: The 25 percentile tip length for the tips in the tree.
   :rtype: float


.. py:function:: tip_length_percentile_2_5(tree)

   Determine the 2.5 percentile for tip length for the tips of the tree.

   :param tree: A tree object used to retrieve tip lengths.
   :type tree: Tree

   :returns: The 2.5 percentile tip length for the tips in the tree.
   :rtype: float


.. py:function:: tip_length_percentile_75(tree)

   Determine the 75 percentile for tip length for the tips of the tree.

   :param tree: A tree object used to retrieve tip lengths.
   :type tree: Tree

   :returns: The 75 percentile tip length for the tips in the tree.
   :rtype: float


.. py:function:: tip_length_percentile_97_5(tree)

   Determine the 97.5 percentile for tip length for the tips of the tree.

   :param tree: A tree object used to retrieve tip lengths.
   :type tree: Tree

   :returns: The 97.5 percentile tip length for the tips in the tree.
   :rtype: float