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# skbio.diversity.block_beta_diversity

`skbio.diversity.``block_beta_diversity`(metric, counts, ids, validate=True, k=64, reduce_f=None, map_f=None, **kwargs)

  Perform a block-decomposition beta diversity calculation

  State: Experimental as of 0.5.1.

  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`.

  validate : bool, optional

  > See `skbio.diversity.beta_diversity` for details.

  reduce_f : function, optional

  > A method to reduce PartialDistanceMatrix objects into a single DistanceMatrix. The expected signature is:

  > > f(Iterable of DistanceMatrix) -> DistanceMatrix

  > Note, this is the reduce within a map/reduce.

  map_f: function, optional

  > A method that accepts a _block_compute. The expected signature is:

  > > f(**kwargs) -> DistanceMatrix

  > NOTE: ipyparallel’s map_async will not work here as we need to be able to pass around **kwargs`.

  k : int, optional

  > The blocksize used when computing distances

  kwargs : kwargs, optional

  > Metric-specific parameters.

  Returns:

  DistanceMatrix

  > A distance matrix relating all samples represented by counts to each other.

  See also

  `skbio.diversity.beta_diversity`, `skbio.diversity.partial_beta_diversity`

  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/