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ols-regression: Simplicial Ordinary Least Squares RegressionΒΆ

Docstring:

Usage: qiime gneiss ols-regression [OPTIONS]

  Perform linear regression on balances. This will tell youhow much
  variability is explained by metadata categories in your formula.

Options:
  --i-table ARTIFACT PATH FeatureTable[Balance]
                                  The feature table containing the samples in
                                  which simplicial regression will be
                                  performed.  [required]
  --i-tree ARTIFACT PATH Hierarchy
                                  A hierarchy of feature identifiers where
                                  each tipcorresponds 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                Formula specifying the statistical model. In
                                  other words, a list of the metadata
                                  categories that will be used in the
                                  regression model, typically separated by
                                  "+". For more information see
                                  https://patsy.readthedocs.io/en/latest/API-
                                  reference.html  [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 ols_regression

Docstring:

Simplicial Ordinary Least Squares Regression

Perform linear regression on balances. This will tell youhow much
variability is explained by metadata categories in your formula.

Parameters
----------
table : FeatureTable[Balance]
    The feature table containing the samples in which simplicial regression
    will be performed.
tree : Hierarchy
    A hierarchy of feature identifiers where each tipcorresponds 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
    Formula specifying the statistical model. In other words, a list of the
    metadata categories that will be used in the regression model,
    typically separated by "+". For more information see
    https://patsy.readthedocs.io/en/latest/API-reference.html

Returns
-------
visualization : Visualization