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.
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
of ids
.
validate (bool, optional) – See skbio.diversity.beta_diversity
for details.
kwargs (kwargs, optional) – Metric-specific parameters.
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.
skbio.DistanceMatrix
ValueError – If ids
are not specified.
If id_pairs
are not a subset of ids
.
If metric
is not a callable or is unresolvable string by
scikit-bio.
If duplicates are observed in id_pairs
.