first-differences: Compute first differences or difference from baseline between sequential states¶

Docstring:

Usage: qiime longitudinal first-differences [OPTIONS]

  Calculates first differences in "metric" between sequential states for
  samples collected from individual subjects sampled repeatedly at two or more
  states. First differences can be performed on a metadata column (including
  artifacts that can be input as metadata) or a feature in a feature table.
  Outputs a data series of first differences for each individual subject at
  each sequential pair of states, labeled by the SampleID of the second state
  (e.g., paired differences between time 0 and time 1 would be labeled by the
  SampleIDs at time 1). This file can be used as input to linear mixed effects
  models or other longitudinal or diversity methods to compare changes in
  first differences across time or among groups of subjects. Also supports
  differences from baseline (or other static comparison state) by setting the
  "baseline" parameter.

Inputs:
  --i-table ARTIFACT FeatureTable[RelativeFrequency]
                         Feature table to optionally use for computing first
                         differences.                               [optional]
Parameters:
  --m-metadata-file METADATA...
    (multiple            Sample metadata file containing
     arguments will be   individual-id-column.
     merged)                                                        [required]
  --p-state-column TEXT  Metadata column containing state (time) variable
                         information.                               [required]
  --p-individual-id-column TEXT
                         Metadata column containing IDs for individual
                         subjects.                                  [required]
  --p-metric TEXT        Numerical metadata or artifact column to test.
                                                                    [required]
  --p-replicate-handling TEXT Choices('error', 'random', 'drop')
                         Choose how replicate samples are handled. If
                         replicates are detected, "error" causes method to
                         fail; "drop" will discard all replicated samples;
                         "random" chooses one representative at random from
                         among replicates.                  [default: 'error']
  --p-baseline NUMBER    A value listed in the state-column metadata column
                         against which all other states should be compared.
                         Toggles calculation of static differences instead of
                         first differences (which are calculated if no value
                         is given for baseline). If a "baseline" value is
                         provided, sample differences at each state are
                         compared against the baseline state, instead of the
                         previous state. Must be a value listed in the
                         state-column.                              [optional]
Outputs:
  --o-first-differences ARTIFACT SampleData[FirstDifferences]
                         Series of first differences.               [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.