skbio.stats.distance.DistanceMatrix.from_iterable¶

classmethod DistanceMatrix.from_iterable(iterable, metric, key=None, keys=None)[source]

Create DistanceMatrix from all pairs in an iterable given a metric.

State: Experimental as of 0.4.1.

Parameters: iterable : iterable Iterable containing objects to compute pairwise distances on. metric : callable A function that takes two arguments and returns a float representing the distance between the two arguments. key : callable or metadata key, optional A function that takes one argument and returns a string representing the id of the element in the distance matrix. Alternatively, a key to a metadata property if it exists for each element in the iterable. If None, then default ids will be used. keys : iterable, optional An iterable of the same length as iterable. Each element will be used as the respective key. DistanceMatrix The metric applied to all pairwise elements in the iterable. ValueError If key and keys are both provided.

Notes

Symmetry and hollowness are assumed when calculating the distances via metric. Therefore, distances are only computed for the strictly upper/lower triangle.