__init__.py

High-level description

This file serves as the top-level module for the cassiopeia critique package. It imports and exposes two key functions, robinson_foulds and triplets_correct, from the compare module, which are used for comparing phylogenetic trees.

Symbols

robinson_foulds

Description

This function computes the Robinson-Foulds distance between two phylogenetic trees. It is imported from the compare module.

Inputs

Name	Type	Description
tree1	CassiopeiaTree	The first tree to compare
tree2	CassiopeiaTree	The second tree to compare

Outputs

Name	Type	Description
rf	float	The Robinson-Foulds distance between the two trees
rf_max	float	The maximum possible Robinson-Foulds distance for normalization

triplets_correct

Description

This function calculates the triplets correct accuracy between two phylogenetic trees. It samples triplets at different depths and compares their structure between the two trees.

Inputs

Name	Type	Description
tree1	CassiopeiaTree	The first tree to compare
tree2	CassiopeiaTree	The second tree to compare
number_of_trials	int	Number of triplets to sample at each depth (default: 1000)
min_triplets_at_depth	int	Minimum number of triplets needed at a depth for inclusion (default: 1)

Outputs

Name	Type	Description
all_triplets_correct	Dict[int, float]	Total triplets correct at each depth
resolvable_triplets_correct	Dict[int, float]	Triplets correct for resolvable triplets at each depth
unresolved_triplets_correct	Dict[int, float]	Triplets correct for unresolvable triplets at each depth
proportion_resolvable	Dict[int, float]	Proportion of unresolvable triplets per depth

Dependencies

Dependency	Purpose
cassiopeia.critique.compare	Source of the imported functions for tree comparison

This file acts as an interface to the tree comparison functionality in the cassiopeia critique module, making it easier for users to access these functions without having to import from deeper within the package structure.