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lme-regression: Simplicial Linear mixed effects regressionΒΆ

Docstring:

Usage: qiime gneiss lme-regression [OPTIONS]

  Build and run linear mixed effects model on balances. Use LME over OLS
  when you have repeated measurements such as (timeseries).

Inputs:
  --i-table ARTIFACT FeatureTable[Balance]
                       The feature table containing the samples in which
                       simplicial regression with mixed effect will be
                       performed.                                   [required]
  --i-tree ARTIFACT    A hierarchy of feature identifiers where each tip
    Hierarchy          corresponds 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:
  --m-metadata-file METADATA...
    (multiple          Metadata information that contains the covariates of
     arguments will    interest.
     be merged)                                                     [required]
  --p-formula TEXT     Statistical formula specifying the statistical model.
                       In other words, a list of the metadata categories that
                       will be used in the linear mixed effect model,
                       typically separated by "+". For more information see
                       https://patsy.readthedocs.io/en/latest/API-reference.ht
                       ml                                           [required]
  --p-groups TEXT                                                   [required]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [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.gneiss.visualizers import lme_regression

Docstring:

Simplicial Linear mixed effects regression

Build and run linear mixed effects model on balances. Use LME over OLS when
you have repeated measurements such as (timeseries).

Parameters
----------
table : FeatureTable[Balance]
    The feature table containing the samples in which simplicial regression
    with mixed effect will be performed.
tree : Hierarchy
    A hierarchy of feature identifiers where each tip corresponds 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.
metadata : Metadata
    Metadata information that contains the covariates of interest.
formula : Str
    Statistical formula specifying the statistical model. In other words, a
    list of the metadata categories that will be used in the linear mixed
    effect model, typically separated by "+". For more information see
    https://patsy.readthedocs.io/en/latest/API-reference.html
groups : Str

Returns
-------
visualization : Visualization