skbio.diversity.
block_beta_diversity
(metric, counts, ids, validate=True, k=64, reduce_f=None, map_f=None, **kwargs)[source]¶Perform a block-decomposition beta diversity calculation
State: Experimental as of 0.5.1.
Parameters: | metric : str or callable
counts : 2D array_like of ints or floats
ids : iterable of strs
validate : bool, optional
reduce_f : function, optional
map_f: function, optional
k : int, optional
kwargs : kwargs, optional
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Returns: | DistanceMatrix
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Notes
This method is designed to facilitate computing beta diversity in parallel. In general, if you are processing a few hundred samples or less, then it is likely the case that skbio.diversity.beta_diversity will be faster. The original need which motivated the development of this method was processing the Earth Microbiome Project [R311311] dataset which at the time spanned over 25,000 samples and 7.5 million open reference OTUs.
References
[R311311] | (1, 2) http://www.earthmicrobiome.org/ |