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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]
                       The feature table containing the samples for which
                       alpha diversity should be computed.          [required]
Parameters:
  --p-metric TEXT Choices('margalef', 'singles', 'chao1', 'heip_e',
    'doubles', 'osd', 'shannon', 'mcintosh_e', 'pielou_e', 'berger_parker_d',
    'goods_coverage', 'menhinick', 'chao1_ci', 'enspie', 'simpson_e',
    'michaelis_menten_fit', 'lladser_ci', 'simpson', 'esty_ci',
    'kempton_taylor_q', 'mcintosh_d', 'ace', 'fisher_alpha', 'observed_otus',
    'lladser_pe', 'robbins', 'brillouin_d', 'gini_index', 'strong',
    'dominance')       The alpha diversity metric to be computed.   [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).
  --citations          Show citations and exit.
  --help               Show this message and exit.

Import:

from qiime2.plugins.diversity.methods import alpha

Docstring:

Alpha diversity

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

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples for which alpha diversity
    should be computed.
metric : Str % Choices('dominance', 'goods_coverage', 'doubles', 'shannon', 'chao1', 'simpson', 'ace', 'lladser_ci', 'simpson_e', 'esty_ci', 'michaelis_menten_fit', 'chao1_ci', 'observed_otus', 'osd', 'fisher_alpha', 'lladser_pe', 'kempton_taylor_q', 'mcintosh_d', 'pielou_e', 'gini_index', 'strong', 'heip_e', 'berger_parker_d', 'margalef', 'mcintosh_e', 'menhinick', 'robbins', 'singles', 'brillouin_d', 'enspie')
    The alpha diversity metric to be computed.

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