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anova: ANOVA testΒΆ

Docstring:

Usage: qiime longitudinal anova [OPTIONS]

  Perform an ANOVA test on any factors present in a metadata file and/or
  metadata-transformable artifacts. This is followed by pairwise t-tests to
  examine pairwise differences between categorical sample groups.

Parameters:
  --m-metadata-file METADATA...
    (multiple          Sample metadata containing formula terms.
     arguments will
     be merged)                                                     [required]
  --p-formula TEXT     R-style formula specifying the model. All terms must
                       be present in the sample metadata or
                       metadata-transformable artifacts and can be continuous
                       or categorical metadata columns. Formulae will be in
                       the format "a ~ b + c", where "a" is the metric
                       (dependent variable) and "b" and "c" are independent
                       covariates. Use "+" to add a variable; "+ a:b" to add
                       an interaction between variables a and b; "*" to
                       include a variable and all interactions; and "-" to
                       subtract a particular term (e.g., an interaction term).
                       See
                       https://patsy.readthedocs.io/en/latest/formulas.html
                       for full documentation of valid formula operators.
                       Always enclose formulae in quotes to avoid unpleasant
                       surprises.                                   [required]
  --p-sstype TEXT Choices('I', 'II', 'III')
                       Type of sum of squares calculation to perform (I, II,
                       or III).                                [default: 'II']
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.longitudinal.visualizers import anova

Docstring:

ANOVA test

Perform an ANOVA test on any factors present in a metadata file and/or
metadata-transformable artifacts. This is followed by pairwise t-tests to
examine pairwise differences between categorical sample groups.

Parameters
----------
metadata : Metadata
    Sample metadata containing formula terms.
formula : Str
    R-style formula specifying the model. All terms must be present in the
    sample metadata or metadata-transformable artifacts and can be
    continuous or categorical metadata columns. Formulae will be in the
    format "a ~ b + c", where "a" is the metric (dependent variable) and
    "b" and "c" are independent covariates. Use "+" to add a variable; "+
    a:b" to add an interaction between variables a and b; "*" to include a
    variable and all interactions; and "-" to subtract a particular term
    (e.g., an interaction term). See
    https://patsy.readthedocs.io/en/latest/formulas.html for full
    documentation of valid formula operators. Always enclose formulae in
    quotes to avoid unpleasant surprises.
sstype : Str % Choices('I', 'II', 'III'), optional
    Type of sum of squares calculation to perform (I, II, or III).

Returns
-------
visualization : Visualization