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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).

Options:
  --i-table ARTIFACT PATH FeatureTable[Balance]
                                  The feature table containing the samples in
                                  which simplicial regression with mixed
                                  effect will be performed.  [required]
  --i-tree ARTIFACT PATH 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.  [required]
  --m-metadata-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata. Metadata
                                  information that contains the covariates of
                                  interest.  [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.html  [required]
  --p-groups TEXT                 [required]
  --o-visualization VISUALIZATION PATH
                                  [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.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