songlab-cal / forward-equivalent-trees Goto Github PK

Here are some next steps:

• Outline the workflow in the readme, e.g. "run notebook x to generate data y then run notebook z, ...".
• Some code looks like non-functional stubs, e.g. draw_tree.ipynb. Consider what might be removed or migrated.
• gcdyn is still imported in one notebook
• There are several unused imports, which could be removed.

As of BDMS v4.0, the parameter

birth_mutations: bool

of the bdms.Tree.evolve() method has been replaced with

birth_mutation_prob: float | Callable[[Any, rng], float]

A new install will require a change in notebooks/efficiency.ipynb to replace birth_mutations=False with birth_mutation_prob=0.