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beta: Beta diversityΒΆ

Docstring:

Usage: qiime diversity beta [OPTIONS]

  Computes a user-specified beta diversity metric for all pairs of samples
  in a feature table.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence]   The feature table containing the samples over which
                       beta diversity should be computed.           [required]
Parameters:
  --p-metric TEXT Choices('minkowski', 'sokalmichener', 'aitchison',
    'sqeuclidean', 'canberra', 'correlation', 'braycurtis', 'jensenshannon',
    'euclidean', 'kulsinski', 'cosine', 'dice', 'cityblock', 'yule',
    'rogerstanimoto', 'canberra_adkins', 'jaccard', 'hamming', 'chebyshev',
    'sokalsneath', 'russellrao', 'seuclidean', 'matching')
                       The beta diversity metric to be computed.    [required]
  --p-pseudocount INTEGER
    Range(1, None)     A pseudocount to handle zeros for compositional
                       metrics.  This is ignored for other metrics.
                                                                  [default: 1]
  --p-n-jobs VALUE Int % Range(1, None) | Str % Choices('auto')
                       The number of concurrent jobs to use in performing
                       this calculation. May not exceed the number of
                       available physical cores. If n-jobs = 'auto', one job
                       will be launched for each identified CPU core on the
                       host.                                      [default: 1]
Outputs:
  --o-distance-matrix ARTIFACT
    DistanceMatrix     The resulting distance matrix.               [required]
Miscellaneous:
  --output-dir PATH    Output unspecified results to a directory
  --verbose / --quiet  Display verbose output to stdout and/or stderr during
                       execution of this action. Or silence output if
                       execution is successful (silence is golden).
  --examples           Show usage examples and exit.
  --citations          Show citations and exit.
  --help               Show this message and exit.

Import:

from qiime2.plugins.diversity.pipelines import beta

Docstring:

Beta diversity

Computes a user-specified beta diversity metric for all pairs of samples in
a feature table.

Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
    The feature table containing the samples over which beta diversity
    should be computed.
metric : Str % Choices('yule', 'cityblock', 'matching', 'russellrao', 'seuclidean', 'jaccard', 'braycurtis', 'minkowski', 'sokalmichener', 'aitchison', 'canberra_adkins', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'sokalsneath', 'correlation', 'hamming', 'dice', 'rogerstanimoto', 'canberra', 'chebyshev', 'jensenshannon')
    The beta diversity metric to be computed.
pseudocount : Int % Range(1, None), optional
    A pseudocount to handle zeros for compositional metrics.  This is
    ignored for other metrics.
n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of concurrent jobs to use in performing this calculation.
    May not exceed the number of available physical cores. If n_jobs =
    'auto', one job will be launched for each identified CPU core on the
    host.

Returns
-------
distance_matrix : DistanceMatrix
    The resulting distance matrix.