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]
Parameters:
--p-threads VALUE Int % Range(1, None) | Str % Choices('auto')
The number of CPU threads to use in performing this
calculation. May not exceed the number of available
physical cores. If threads = 'auto', one thread will
be created for each identified CPU core on the host.
[default: 1]
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).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Examples:
# ### example: basic
qiime diversity-lib faith-pd \
--i-table feature-table.qza \
--i-phylogeny phylogeny.qza \
--o-vector faith-pd-vector.qza
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.
threads : Int % Range(1, None) | Str % Choices('auto'), optional
The number of CPU threads to use in performing this calculation. May
not exceed the number of available physical cores. If threads = 'auto',
one thread will be created for each identified CPU core on the host.
Returns
-------
vector : SampleData[AlphaDiversity]
Vector containing per-sample values for Faith's Phylogenetic Diversity.
