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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.

Options:
  --i-table ARTIFACT PATH FeatureTable[Frequency]
                                  The feature table containing the samples for
                                  which alpha diversity should be computed.
                                  [required]
  --p-metric [heip_e|kempton_taylor_q|dominance|enspie|osd|mcintosh_e|chao1_ci|singles|chao1|goods_coverage|berger_parker_d|robbins|lladser_ci|michaelis_menten_fit|menhinick|pielou_e|fisher_alpha|ace|gini_index|mcintosh_d|simpson_e|shannon|observed_otus|esty_ci|lladser_pe|strong|doubles|brillouin_d|margalef|simpson]
                                  The alpha diversity metric to be computed.
                                  [required]
  --o-alpha-diversity ARTIFACT PATH SampleData[AlphaDiversity]
                                  Vector containing per-sample alpha
                                  diversities.  [required if not passing
                                  --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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({'ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_ci', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'observed_otus', 'osd', 'pielou_e', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles', 'strong'})
    The alpha diversity metric to be computed.

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