Warning
This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2. You can still access the content from the “old docs” here for the QIIME 2 2024.10 and earlier releases, but we recommend that you transition to the new documentation at https://amplicon-docs.qiime2.org. Content on this site is no longer updated and may be out of date.
Are you looking for:
the QIIME 2 homepage? That’s https://qiime2.org.
learning resources for microbiome marker gene (i.e., amplicon) analysis? See the QIIME 2 amplicon distribution documentation.
learning resources for microbiome metagenome analysis? See the MOSHPIT documentation.
installation instructions, plugins, books, videos, workshops, or resources? See the QIIME 2 Library.
general help? See the QIIME 2 Forum.
Old content beyond this point… 👴👵
prep-alpha-distribution: Alpha diversity to Dist1D¶
Docstring:
Usage: qiime stats prep-alpha-distribution [OPTIONS]
Alpha diversity to Dist1D
WARNING:
This command is deprecated and will be removed in a future version of this
plugin.
Inputs:
--i-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
Alpha diversity which will become the "measure"
[required]
Parameters:
--m-metadata-file METADATA...
(multiple Sample metadata to use
arguments will be
merged) [required]
--p-columns TEXT... Columns to include as group information
List[Str] [required]
--p-subject VALUE Str % Choices('')¹'³ | Str²'⁴
If provided, will cause the Dist1D to be matched for
repeated measures. [default: '']
--p-timepoint VALUE Str % Choices('')¹'² | Str³'⁴
If provided, will cause the Dist1D to be stratified
by timepoint. Required if using ``subject``.
[default: '']
Outputs:
--o-distribution ARTIFACT Dist1D[Multi, Independent]¹ | Dist1D[Multi,
Matched]² | Dist1D[NestedOrdered, Independent]³ | Dist1D[NestedOrdered,
Matched]⁴ The resulting Dist1D. [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.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible to
all nodes in the cluster.
--help Show this message and exit.
Import:
from qiime2.plugins.stats.methods import prep_alpha_distribution
Docstring:
Alpha diversity to Dist1D
.. deprecated::
This Method is deprecated and will be removed in a future version of
this plugin.
Alpha diversity to Dist1D
Parameters
----------
alpha_diversity : SampleData[AlphaDiversity]
Alpha diversity which will become the "measure"
metadata : Metadata
Sample metadata to use
columns : List[Str]
Columns to include as group information
subject : Str % Choices('')¹'³ | Str²'⁴, optional
If provided, will cause the Dist1D to be matched for repeated measures.
timepoint : Str % Choices('')¹'² | Str³'⁴, optional
If provided, will cause the Dist1D to be stratified by timepoint.
Required if using ``subject``.
Returns
-------
distribution : Dist1D[Multi, Independent]¹ | Dist1D[Multi, Matched]² | Dist1D[NestedOrdered, Independent]³ | Dist1D[NestedOrdered, Matched]⁴
The resulting Dist1D.