alifestd_downsample_tips_canopy_asexual

alifestd_downsample_tips_canopy_asexual(phylogeny_df: DataFrame, n_downsample: int | None = None, mutate: bool = False, criterion: str = 'origin_time') → DataFrame

Retain the n_downsample leaves with the largest criterion values and prune extinct lineages.

If n_downsample is None, it defaults to the number of leaves that share the maximum value of the criterion column. If n_downsample is greater than or equal to the number of leaves in the phylogeny, the whole phylogeny is returned. Ties 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, optional

Number of tips to retain. If None, defaults to the count of leaves with the maximum criterion value.

mutatebool, default False

Are side effects on the input argument phylogeny_df allowed?

criterionstr, default “origin_time”

Column name used to rank leaves. The n_downsample leaves with the largest values in this column are retained. Ties are broken arbitrarily.

Raises

ValueError

If criterion is not a column in phylogeny_df.

Returns

pandas.DataFrame

The pruned phylogeny in alife standard format.