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alpha-phylogenetic: Alpha diversity (phylogenetic)

Citations

[diversity:alpha-phylogenetic:Fai92]Daniel P Faith. Conservation evaluation and phylogenetic diversity. Biological conservation, 61(1):1–10, 1992. doi:https://doi.org/10.1016/0006-3207(92)91201-3.

Docstring:

Usage: qiime diversity alpha-phylogenetic [OPTIONS]

  Computes a user-specified phylogenetic 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]
  --i-phylogeny ARTIFACT PATH 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.  [required]
  --p-metric [faith_pd]           The alpha diversity metric to be computed.
                                  [required]
  --o-alpha-diversity ARTIFACT PATH SampleData[AlphaDiversity] % Properties(['phylogenetic'])
                                  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_phylogenetic

Docstring:

Alpha diversity (phylogenetic)

Computes a user-specified phylogenetic 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.
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.