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: |
|
---|---|
Returns: | A distance matrix relating all samples represented by counts to each other. |
Return type: |
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 [1] dataset which at the time spanned over 25,000 samples and 7.5 million open reference OTUs.
References
[1] | http://www.earthmicrobiome.org/ |