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first-differences: Compute first differences or difference from baseline between sequential statesΒΆ

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.

Options:
  --m-metadata-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata. Sample
                                  metadata file containing
                                  individual_id_column.  [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 [drop|random|error]
                                  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 FLOAT              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]
  --i-table ARTIFACT PATH FeatureTable[RelativeFrequency]
                                  Feature table to optionally use for
                                  computing first differences.  [optional]
  --o-first-differences ARTIFACT PATH SampleData[FirstDifferences]
                                  Series of first differences.  [required if
                                  not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --citations                     Show citations and exit.
  --help                          Show this message and exit.

Import:

from qiime2.plugins.longitudinal.methods import first_differences

Docstring:

Compute first differences or difference from baseline between sequential
states

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.

Parameters
----------
metadata : Metadata
    Sample metadata file containing individual_id_column.
state_column : Str
    Metadata column containing state (time) variable information.
individual_id_column : Str
    Metadata column containing IDs for individual subjects.
metric : Str
    Numerical metadata or artifact column to test.
replicate_handling : Str % Choices({'drop', 'error', 'random'}), optional
    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.
baseline : Float, optional
    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.
table : FeatureTable[RelativeFrequency], optional
    Feature table to optionally use for computing first differences.

Returns
-------
first_differences : SampleData[FirstDifferences]
    Series of first differences.