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_significance in that it accepts R formulae to
perform multi-way ADONIS tests; beta_group_signficance only performs one-way
tests. For more details, consult the reference manual available on the CRAN
vegan page: https://CRAN.R-project.org/package=vegan
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 NTHREADS Number of parallel processes to run. [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).
--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.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_significance in that it accepts R formulae
to perform multi-way ADONIS tests; beta_group_signficance only performs
one-way tests. For more details, consult the reference manual available on
the CRAN vegan page: https://CRAN.R-project.org/package=vegan
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 : Threads, optional
Number of parallel processes to run.
Returns
-------
visualization : Visualization
