wilcoxon-srt: Wilcoxon Signed Rank Test¶

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