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anova: ANOVA test¶
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