alifestd_mark_sample_tips_lineage_stratified_asexual

alifestd_mark_sample_tips_lineage_stratified_asexual(phylogeny_df: ~pandas.core.frame.DataFrame, n_sample: int | None = None, mutate: bool = False, seed: int | None = None, *, criterion_delta: str = 'origin_time', criterion_stratify: str = 'origin_time', criterion_target: str = 'origin_time', n_tips_per_stratum: int = 1, progress_wrap: ~typing.Callable = <function <lambda>>, mark_as: str = 'alifestd_mark_sample_tips_lineage_stratified_asexual') → DataFrame

Mark leaves per stratified group, chosen by proximity to the lineage of a target leaf.

Adds a boolean column mark_as indicating retained tips.

Only supports asexual phylogenies.

Parameters

phylogeny_dfpandas.DataFrame

The phylogeny as a dataframe in alife standard format.

Must represent an asexual phylogeny.

n_sampleint, optional

Desired number of retained tips. If None, every distinct criterion_stratify value forms its own group.

mutatebool, default False

Are side effects on the input argument phylogeny_df allowed?

seedint, optional

Random seed for reproducible target-leaf selection.

criterion_deltastr, default “origin_time”

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

criterion_stratifystr, default “origin_time”

Column name used to stratify leaves into groups.

criterion_targetstr, default “origin_time”

Column name used to select the target leaf.

n_tips_per_stratumint, default 1

Number of tips to retain per stratified group.

progress_wrapCallable, optional

Pass tqdm or equivalent to display a progress bar.

mark_asstr, default “alifestd_mark_sample_tips_lineage_stratified_asexual”

Column name for the boolean mark.

Raises

ValueError

If criterion_delta, criterion_stratify, or criterion_target is not a column in phylogeny_df.

ValueError

If n_sample is not None and n_tips_per_stratum does not evenly divide n_sample.

Returns

pandas.DataFrame

The phylogeny with an added boolean mark column.