alifestd_mark_colless_like_index_var_asexual

alifestd_mark_colless_like_index_var_asexual(phylogeny_df: DataFrame, mutate: bool = False, *, mark_as: str = 'colless_like_index_var') → DataFrame

Add column colless_like_index_var with Colless-like index using sample variance as dissimilarity.

The output column name can be changed via the mark_as parameter.

Computes the Colless-like balance index from Mir, Rossello, and Rotger (2018) that supports polytomies. Uses weight function f(k) = ln(k + e) and variance dissimilarity.

For each internal node v with children v_1, …, v_k:

bal(v) = var(delta_f(T_v1), …, delta_f(T_vk))

where delta_f(T) is the f-size of subtree T, defined as the sum of f(deg(u)) over all nodes u in T, and

var(x_1, …, x_k) = (1/(k-1)) * sum (x_i - mean(x))^2

The Colless-like index at a node is the sum of balance values across all internal nodes in its subtree.

Leaf nodes will have Colless-like index 0. The root node contains the Colless-like index for the entire tree.

A topological sort will be applied if phylogeny_df is not topologically sorted. Dataframe reindexing (e.g., df.index) may be applied.

Input dataframe is not mutated by this operation unless mutate set True. If mutate set True, operation does not occur in place; still use return value to get transformed phylogeny dataframe.

Parameters

phylogeny_dfpd.DataFrame

Alife standard DataFrame containing the phylogenetic relationships.

mutatebool, optional

If True, modify the input DataFrame in place. Default is False.

Returns

pd.DataFrame

Phylogeny DataFrame with an additional column “colless_like_index_var” containing the Colless-like imbalance index for the subtree rooted at each node.

References

Mir, A., Rossello, F., & Rotger, L. (2018). Sound Colless-like balance indices for multifurcating trees. PLOS ONE, 13(9), e0203401. https://doi.org/10.1371/journal.pone.0203401

See Also

alifestd_mark_colless_like_index_mdm_asexual :

Colless-like index using MDM dissimilarity.

alifestd_mark_colless_like_index_sd_asexual :

Colless-like index using standard deviation dissimilarity.

alifestd_mark_colless_index_asexual :

Classic Colless index for strictly bifurcating trees.