Docstring:
Usage: qiime diversity adonis [OPTIONS]
Determine whether groups of samples are significantly different from one
another using the ADONIS permutation-based statistical test in vegan-R.
The function partitions sums of squares of a multivariate data set, and is
directly analogous to MANOVA (multivariate analysis of variance). This
action differs from beta_group_signficance in that it accepts R formulae
to perform multi-way ADONIS tests; beta_group_signficance only performs
one-way tests. For more details see
http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html
Inputs:
--i-distance-matrix ARTIFACT
DistanceMatrix Matrix of distances between pairs of samples.
[required]
Parameters:
--m-metadata-file METADATA...
(multiple Sample metadata containing formula terms.
arguments will
be merged) [required]
--p-formula TEXT Model formula containing only independent terms
contained in the sample metadata. These can be
continuous variables or factors, and they can have
interactions as in a typical R formula. E.g., the
formula "treatment+block" would test whether the input
distance matrix partitions based on "treatment" and
"block" sample metadata. The formula "treatment*block"
would test both of those effects as well as their
interaction. Enclose formulae in quotes to avoid
unpleasant surprises. [required]
--p-permutations INTEGER
Range(1, None) The number of permutations to be run when computing
p-values. [default: 999]
--p-n-jobs INTEGER Number of parallel processes to run.
Range(1, None) [default: 1]
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.diversity.visualizers import adonis
Docstring:
adonis PERMANOVA test for beta group significance
Determine whether groups of samples are significantly different from one
another using the ADONIS permutation-based statistical test in vegan-R. The
function partitions sums of squares of a multivariate data set, and is
directly analogous to MANOVA (multivariate analysis of variance). This
action differs from beta_group_signficance in that it accepts R formulae to
perform multi-way ADONIS tests; beta_group_signficance only performs one-
way tests. For more details see
http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html
Parameters
----------
distance_matrix : DistanceMatrix
Matrix of distances between pairs of samples.
metadata : Metadata
Sample metadata containing formula terms.
formula : Str
Model formula containing only independent terms contained in the sample
metadata. These can be continuous variables or factors, and they can
have interactions as in a typical R formula. E.g., the formula
"treatment+block" would test whether the input distance matrix
partitions based on "treatment" and "block" sample metadata. The
formula "treatment*block" would test both of those effects as well as
their interaction. Enclose formulae in quotes to avoid unpleasant
surprises.
permutations : Int % Range(1, None), optional
The number of permutations to be run when computing p-values.
n_jobs : Int % Range(1, None), optional
Number of parallel processes to run.
Returns
-------
visualization : Visualization