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alpha-phylogenetic-alt: Alpha diversity (phylogenetic) - alternative implementation

Citations

Docstring:

Usage: qiime diversity alpha-phylogenetic-alt [OPTIONS]

  Computes a user-specified phylogenetic alpha diversity metric for all
  samples in a feature table. This implementation is recommended for large
  datasets, otherwise the results are identical to alpha_phylogenetic.

  This method is an implementation of the Stacked Faith Algorithm
  (manuscript in preparation).

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                          The feature table containing the samples for which
                          alpha diversity should be computed.       [required]
  --i-phylogeny ARTIFACT  Phylogenetic tree containing tip identifiers that
    Phylogeny[Rooted]     correspond to the feature identifiers in the table.
                          This tree can contain tip ids that are not present
                          in the table, but all feature ids in the table must
                          be present in this tree.                  [required]
Parameters:
  --p-metric TEXT         The alpha diversity metric to be computed.
    Choices('faith_pd')                                             [required]
Outputs:
  --o-alpha-diversity ARTIFACT SampleData[AlphaDiversity] %
    Properties('phylogenetic')
                          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_phylogenetic_alt

Docstring:

Alpha diversity (phylogenetic) - alternative implementation

Computes a user-specified phylogenetic alpha diversity metric for all
samples in a feature table. This implementation is recommended for large
datasets, otherwise the results are identical to alpha_phylogenetic.   This
method is an implementation of the Stacked Faith Algorithm (manuscript in
preparation).

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples for which alpha diversity
    should be computed.
phylogeny : Phylogeny[Rooted]
    Phylogenetic tree containing tip identifiers that correspond to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree.
metric : Str % Choices('faith_pd')
    The alpha diversity metric to be computed.

Returns
-------
alpha_diversity : SampleData[AlphaDiversity] % Properties('phylogenetic')
    Vector containing per-sample alpha diversities.