alifestd_mask_monomorphic_clades_asexual

alifestd_mask_monomorphic_clades_asexual(phylogeny_df: DataFrame, mutate: bool = False, *, trait_mask: ndarray, trait_values: ndarray) → DataFrame

Compute a mask marking “monomorphic” clades where all members with a trait defined value share the same trait value.

Clades containing no members with a defined trait value are considered monomorphic. All leaf nodes are considered monomorphic.

Parameters

phylogeny_dfpd.DataFrame

DataFrame containing the phylogeny, including an ancestor_id column.

mutatebool, default=False

If False, operates on a copy of phylogeny_df; if True, modifies phylogeny_df in place (but still returns it).

trait_masknp.ndarray

Boolean array marking the nodes that have a defined trait value, aligned with phylogeny_df.index.

trait_valuesnp.ndarray

Array of trait values aligned with phylogeny_df.index.

Returns

pd.DataFrame