API reference

Docstrings are defined once per module below. Import everything from the top level as usual (import phypanda as pp); this page maps names to the detailed sections—there is no separate duplicate “package” autodoc page.

Where to find what

Topic	Page
diversity, marginal_diversities, greedy_max_diversity, solve_max_diversity	Base helpers
DiversityMeasure protocol	Measure protocol
all_paths, AllPathsDiversity	All-paths (MAPD) measure
solve_esw_fpt, solve_nsw_fpt_budget (low-level solvers)	All-paths solvers
max_tree, MaxTreeDiversity	Max-tree PD
min_tree, MinTreeDiversity, prune_to_taxa, adapt_tree_extension_for_pruned_network	Min-tree PD
tree, network, average_tree stubs	Tree diversity (stub), Network diversity (stub), Average-tree diversity (stub)

Modules

• Base helpers
  • diversity()
  • greedy_max_diversity()
  • marginal_diversities()
  • solve_max_diversity()
• Measure protocol
  • DiversityMeasure
• All-paths (MAPD) measure
  • AllPathsDiversity
• All-paths solvers
  • solve_esw_fpt()
  • solve_nsw_fpt_budget()
• Max-tree PD
  • MaxTreeDiversity
• Min-tree PD
  • MinTreeDiversity
  • adapt_tree_extension_for_pruned_network()
  • prune_to_taxa()
• Tree diversity (stub)
  • TreeDiversity
• Network diversity (stub)
  • NetworkDiversity
• Average-tree diversity (stub)
  • AverageTreeDiversity