qdiv.diversity.dissimilarity_by_feature

qdiv.diversity.dissimilarity_by_feature(obj, *, by=None, q=1, div_type='naive', index='regional', use_values_in_tab=False)[source]

Compute the contribution of individual taxa (or phylogenetic nodes) to the overall dissimilarity between multiple samples, following Chao & Ricotta (2019, Ecology 100:e02852).

Supports:

  • naive (taxonomic) dissimilarity

  • phylogenetic dissimilarity

Parameters:

  • obj (DataFrame | MicrobiomeData-like | dict) –

    Must contain:

    • ’tab’ : abundance table (features × samples)

    • ’meta’ : metadata table (optional if by=None)

    • ’tree’ : phylogenetic tree (required if divType=’phyl’)

  • by (str or None, default=None) – Metadata column defining sample groups. If None, all samples are treated as one group.

  • q (float, default=1) – Diversity order.

  • div_type ({'naive','phyl'}, default='naive') – Type of dissimilarity measure.

  • index ({'local','regional','CR1','CR2'}, default='regional') – Evenness/dissimilarity index.

  • use_values_in_tab (bool, default=False) – If False, convert abundances to relative abundances.

Returns:

Rows:

  • ’dis’ : total dissimilarity

  • ’N’ : number of samples in group

  • one row per taxon (naive) or per node (phylogenetic)

Columns:

  • one column per category in by

Return type:

pandas.DataFrame