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alpha: Alpha diversityΒΆ

Docstring:

Usage: qiime diversity alpha [OPTIONS]

  Computes a user-specified alpha diversity metric for all samples in a
  feature table.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence]   The feature table containing the samples for which
                       alpha diversity should be computed.          [required]
Parameters:
  --p-metric TEXT Choices('strong', 'menhinick', 'observed_features',
    'esty_ci', 'robbins', 'goods_coverage', 'simpson_e', 'margalef', 'heip_e',
    'chao1_ci', 'singles', 'pielou_e', 'berger_parker_d', 'ace', 'mcintosh_e',
    'gini_index', 'kempton_taylor_q', 'mcintosh_d', 'dominance',
    'fisher_alpha', 'lladser_pe', 'doubles', 'osd', 'shannon', 'enspie',
    'brillouin_d', 'chao1', 'simpson', 'michaelis_menten_fit')
                       The alpha diversity metric to be computed. Information
                       about specific metrics is available at
                       https://data.qiime2.org/a_diversity_metrics  [required]
Outputs:
  --o-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
                       Vector containing per-sample alpha diversities.
                                                                    [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).
  --example-data PATH  Write example data and exit.
  --citations          Show citations and exit.
  --help               Show this message and exit.

Import:

from qiime2.plugins.diversity.pipelines import alpha

Docstring:

Alpha diversity

Computes a user-specified alpha diversity metric for all samples in a
feature table.

Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
    The feature table containing the samples for which alpha diversity
    should be computed.
metric : Str % Choices('michaelis_menten_fit', 'fisher_alpha', 'strong', 'esty_ci', 'chao1', 'simpson_e', 'goods_coverage', 'berger_parker_d', 'lladser_pe', 'mcintosh_d', 'brillouin_d', 'shannon', 'ace', 'observed_features', 'menhinick', 'singles', 'mcintosh_e', 'kempton_taylor_q', 'margalef', 'pielou_e', 'enspie', 'gini_index', 'dominance', 'chao1_ci', 'osd', 'doubles', 'robbins', 'simpson', 'heip_e')
    The alpha diversity metric to be computed. Information about specific
    metrics is available at https://data.qiime2.org/a_diversity_metrics

Returns
-------
alpha_diversity : SampleData[AlphaDiversity]
    Vector containing per-sample alpha diversities.