biotaphy.analyses.anc_dp

Module containing code for calculating ancestral states.

Module Contents

Functions

_get_node_label(node)	Returns the node label or taxon label if node is a tip.
calculate_ancestral_distributions(tree, char_mtx)	Calculates ancestral distributions.
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.

biotaphy.analyses.anc_dp._get_node_label(node)

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

Parameters

node (Node) – A tree node to get the label for.

Returns

The node label or taxon label.

Return type

str

biotaphy.analyses.anc_dp.calculate_ancestral_distributions(tree, char_mtx)

Calculates ancestral distributions.

Parameters

• tree (Tree) – A dendropy tree or TreeWrapper object.

• char_mtx (Matrix) – 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.

Returns

• rows: nodes / tips in the tree

• columns: character variables

• depth: first is the calculated value, second layer is standard

  error if desired

Return type

A matrix of character data with the following dimensions

biotaphy.analyses.anc_dp.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.

Parameters

• tree (Tree) – A dendropy tree or TreeWrapper object.

• char_mtx (Matrix) – 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.

• calc_std_err (bool, optional) – If True, calculate standard error for each variable. Defaults to False.

• sum_to_one (bool, optional) – If True, standardize the character matrix so that the values in a row sum to one. Defaults to False.

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

Return type

A matrix of character data with the following dimensions