skbio.diversity.partial_beta_diversity¶
-
skbio.diversity.
partial_beta_diversity
(metric, counts, ids, id_pairs, validate=True, **kwargs)[source]¶ Compute distances only between specified ID pairs
Note
Deprecated as of 0.5.0 for removal in 0.6.0. The return type is unstable. Developer caution is advised. The resulting DistanceMatrix object will include zeros when distance has not been calculated, and therefore can be misleading.
- Parameters
metric (str or callable) – The pairwise distance function to apply. If
metric
is a string, it must be resolvable by scikit-bio (e.g., UniFrac methods), or must be callable.counts (2D array_like of ints or floats) – Matrix containing count/abundance data where each row contains counts of OTUs in a given sample.
ids (iterable of strs) – Identifiers for each sample in
counts
.id_pairs (iterable of tuple) – An iterable of tuples of IDs to compare (e.g.,
[('a', 'b'), ('a', 'c'), ...])
. If specified, the set of IDs described must be a subset ofids
.validate (bool, optional) – See
skbio.diversity.beta_diversity
for details.kwargs (kwargs, optional) – Metric-specific parameters.
- Returns
Distances between pairs of samples indicated by id_pairs. Pairwise distances not defined by id_pairs will be 0.0. Use this resulting DistanceMatrix with caution as 0.0 is a valid distance.
- Return type
skbio.DistanceMatrix
- Raises
ValueError – If
ids
are not specified. Ifid_pairs
are not a subset ofids
. Ifmetric
is not a callable or is unresolvable string by scikit-bio. If duplicates are observed inid_pairs
.