first-distances: Compute first distances or distance from baseline between sequential states¶

Docstring:

Usage: qiime longitudinal first-distances [OPTIONS]

  Calculates first distances between sequential states for samples collected
  from individual subjects sampled repeatedly at two or more states. This
  method is similar to the "first differences" method, except that it requires
  a distance matrix as input and calculates first differences as distances
  between successive states. Outputs a data series of first distances for each
  individual subject at each sequential pair of states, labeled by the
  SampleID of the second state (e.g., paired distances 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 distances across time or among groups of
  subjects. Also supports distance from baseline (or other static comparison
  state) by setting the "baseline" parameter.

Inputs:
  --i-distance-matrix ARTIFACT
    DistanceMatrix       Matrix of distances between pairs of samples.
                                                                    [required]
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-baseline NUMBER    A value listed in the state-column metadata column
                         against which all other states should be compared.
                         Toggles calculation of static distances instead of
                         first distances (which are calculated if no value is
                         given for baseline). If a "baseline" value is
                         provided, sample distances at each state are compared
                         against the baseline state, instead of the previous
                         state. Must be a value listed in the state-column.
                                                                    [optional]
  --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']
Outputs:
  --o-first-distances ARTIFACT SampleData[FirstDifferences]
                         Series of first distances.                 [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.