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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']
  --p-repeated-measures / --p-no-repeated-measures
                         Perform ANOVA as a repeated measures ANOVA.
                         Implemented via statsmodels, which has the following
                         limitations: Currently, only fully balanced
                         within-subject designs are supported. Calculation of
                         between-subject effects and corrections for violation
                         of sphericity are not yet implemented.
                                                              [default: False]
  --p-individual-id-column TEXT
                         The column containing individual ID with repeated
                         measures to account for.This should not be included
                         in the formula.                            [optional]
  --p-rm-aggregate / --p-no-rm-aggregate
                         If the data set contains more than a single
                         observation per individual id and cell of the
                         specified model, this function will be used to
                         aggregate the data by the mean before running the
                         ANOVA. Only applicable for repeated measures ANOVA.
                                                              [default: False]
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).
  --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.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).
repeated_measures : Bool, optional
    Perform ANOVA as a repeated measures ANOVA. Implemented via
    statsmodels, which has the following limitations: Currently, only fully
    balanced within-subject designs are supported. Calculation of between-
    subject effects and corrections for violation of sphericity are not yet
    implemented.
individual_id_column : Str, optional
    The column containing individual ID with repeated measures to account
    for.This should not be included in the formula.
rm_aggregate : Bool, optional
    If the data set contains more than a single observation per individual
    id and cell of the specified model, this function will be used to
    aggregate the data by the mean before running the ANOVA. Only
    applicable for repeated measures ANOVA.

Returns
-------
visualization : Visualization