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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 [osd|chao1_ci|mcintosh_e|michaelis_menten_fit|shannon|menhinick|margalef|simpson_e|esty_ci|dominance|lladser_pe|ace|kempton_taylor_q|enspie|brillouin_d|singles|observed_otus|pielou_e|berger_parker_d|gini_index|chao1|doubles|goods_coverage|mcintosh_d|strong|lladser_ci|simpson|heip_e|robbins|fisher_alpha]
                                  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.