Docstring:
Usage: qiime stats wilcoxon-srt [OPTIONS]
Inputs:
--i-distribution ARTIFACT Dist1D[Ordered, Matched]
[required]
Parameters:
--p-compare TEXT Choices('baseline', 'consecutive')
The type of comparison that will be used to analyze
the input `distribution`. The "baseline" comparison
defines Group A as the timepoint provided to
`baseline-group` (sourced from `time_column`), and
Group B as all other timepoints contained in
`time_column`. The "consecutive" comparison defines
Group A as "timepoint n", and Group B as "timepoint
n+1" (both sourced from `time_column`). [required]
--p-baseline-group TEXT
If "baseline" is the selected comparison, this is
the column that will be used to compare all other
groups against. [optional]
--p-alternative TEXT Choices('two-sided', 'greater', 'less')
The "two-sided" alternative hypothesis is that the
median of Group A does not equal the median of Group
B. The "greater" alternative hypothesis is that the
median of group A is greater than the median of Group
B. The "less" alternative hypothesis is that the
median of group A is less than the median of Group B.
[default: 'two-sided']
--p-p-val-approx TEXT Choices('auto', 'exact', 'asymptotic')
"exact" will calculate an exact p-value for
distributions of up to 25 (inclusive) measurements,
"asymptotic" will use a normal distribution, and
"auto" will use either "exact" or "approx" depending
on size. [default: 'auto']
--p-ignore-empty-comparator / --p-no-ignore-empty-comparator
Ignore any group that does not have any overlapping
subjects with comparison group. These groups will
have NaNs in the stats table output [default: False]
Outputs:
--o-stats ARTIFACT StatsTable[Pairwise]
The Wilcoxon SRT table for either the "baseline" or
"consecutive" comparison. [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.
Examples:
# ### example: wilcoxon baseline0
qiime stats wilcoxon-srt \
--i-distribution timedist.qza \
--p-compare baseline \
--p-baseline-group 0 \
--p-p-val-approx asymptotic \
--o-stats stats.qza
Import:
from qiime2.plugins.stats.methods import wilcoxon_srt
Docstring:
Wilcoxon Signed Rank Test
Parameters
----------
distribution : Dist1D[Ordered, Matched]
compare : Str % Choices('baseline', 'consecutive')
The type of comparison that will be used to analyze the input
`distribution`. The "baseline" comparison defines Group A as the
timepoint provided to `baseline_group` (sourced from `time_column`),
and Group B as all other timepoints contained in `time_column`. The
"consecutive" comparison defines Group A as "timepoint n", and Group B
as "timepoint n+1" (both sourced from `time_column`).
baseline_group : Str, optional
If "baseline" is the selected comparison, this is the column that will
be used to compare all other groups against.
alternative : Str % Choices('two-sided', 'greater', 'less'), optional
The "two-sided" alternative hypothesis is that the median of Group A
does not equal the median of Group B. The "greater" alternative
hypothesis is that the median of group A is greater than the median of
Group B. The "less" alternative hypothesis is that the median of group
A is less than the median of Group B.
p_val_approx : Str % Choices('auto', 'exact', 'asymptotic'), optional
"exact" will calculate an exact p-value for distributions of up to 25
(inclusive) measurements, "asymptotic" will use a normal distribution,
and "auto" will use either "exact" or "approx" depending on size.
ignore_empty_comparator : Bool, optional
Ignore any group that does not have any overlapping subjects with
comparison group. These groups will have NaNs in the stats table output
Returns
-------
stats : StatsTable[Pairwise]
The Wilcoxon SRT table for either the "baseline" or "consecutive"
comparison.
