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faith-pd: Faith’s Phylogenetic Diversity

Citations

Docstring:

Usage: qiime diversity-lib faith-pd [OPTIONS]

  Computes Faith's Phylogenetic Diversity for all samples in a feature
  table.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence]      The feature table containing the samples for which
                          Faith's phylogenetic diversity should be computed.
                          Table values will be converted to presence/absence.
                                                                    [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]
Outputs:
  --o-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector containing per-sample values for Faith's
                          Phylogenetic Diversity.                   [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).
  --examples              Show usage examples and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.diversity_lib.methods import faith_pd

Docstring:

Faith's Phylogenetic Diversity

Computes Faith's Phylogenetic Diversity for all samples in a feature table.

Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
    The feature table containing the samples for which Faith's phylogenetic
    diversity should be computed. Table values will be converted to
    presence/absence.
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.

Returns
-------
vector : SampleData[AlphaDiversity]
    Vector containing per-sample values for Faith's Phylogenetic Diversity.