alifestd_mark_sample_tips_lineage_asexual

alifestd_mark_sample_tips_lineage_asexual(phylogeny_df: ~pandas.core.frame.DataFrame, n_sample: int, mutate: bool = False, seed: int | None = None, *, criterion_delta: str = 'origin_time', criterion_target: str = 'origin_time', progress_wrap: ~typing.Callable = <function <lambda>>, mark_as: str = 'alifestd_mark_sample_tips_lineage_asexual') → DataFrame

Mark the n_sample leaves closest to the lineage of a target leaf.

Adds a boolean column mark_as indicating retained tips.

Selects a target leaf as the leaf with the largest criterion_target value (ties broken randomly). For each leaf, the most recent common ancestor (MRCA) with the target leaf is identified and the “off-lineage delta” is computed as the absolute difference between the leaf’s criterion_delta value and its MRCA’s criterion_delta value. The n_sample leaves with the smallest off-lineage deltas are marked.

If n_sample is greater than or equal to the number of leaves in the phylogeny, all leaves are marked. Ties in off-lineage delta are broken arbitrarily.

Only supports asexual phylogenies.

Parameters

phylogeny_dfpandas.DataFrame

The phylogeny as a dataframe in alife standard format.

Must represent an asexual phylogeny.

n_sampleint

Number of tips to mark.

mutatebool, default False

Are side effects on the input argument phylogeny_df allowed?

seedint, optional

Random seed for reproducible target-leaf selection when there are ties in criterion_target.

criterion_deltastr, default “origin_time”

Column name used to compute the off-lineage delta for each leaf.

criterion_targetstr, default “origin_time”

Column name used to select the target leaf.

progress_wrapCallable, optional

Pass tqdm or equivalent to display a progress bar.

mark_asstr, default “alifestd_mark_sample_tips_lineage_asexual”

Column name for the boolean mark.

Raises

ValueError

If criterion_delta or criterion_target is not a column in phylogeny_df.

Returns

pandas.DataFrame

The phylogeny with an added boolean mark column.