alifestd_downsample_tips_lineage_asexual

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

Retain the n_downsample leaves closest to the lineage of a target leaf.

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_downsample leaves with the smallest off-lineage deltas are retained.

If n_downsample is greater than or equal to the number of leaves in the phylogeny, the whole phylogeny is returned. 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_downsampleint

Number of tips to retain.

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. The delta is the absolute difference between a leaf’s value and its MRCA’s value in this column.

criterion_targetstr, default “origin_time”

Column name used to select the target leaf. The leaf with the largest value in this column is chosen as the target. Note that ties are broken by random sample, allowing a seed to be provided.

progress_wrapCallable, optional

Pass tqdm or equivalent to display a progress bar.

Raises

ValueError

If criterion_delta or criterion_target is not a column in phylogeny_df.

Returns

pandas.DataFrame

The pruned phylogeny in alife standard format.