Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs, and Helene Wagner. vegan: Community Ecology Package. 2018. R package version 2.5-3. URL: https://CRAN.R-project.org/package=vegan.
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.
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
