linear-mixed-effects: Linear mixed effects modeling¶

Docstring:

Usage: qiime longitudinal linear-mixed-effects [OPTIONS]

  Linear mixed effects models evaluate the contribution of exogenous
  covariates "group_columns" and "random_effects" to a single dependent
  variable, "metric". Perform LME and plot line plots of each group column. A
  feature table artifact is required input, though whether "metric" is derived
  from the feature table or metadata is optional.

Inputs:
  --i-table ARTIFACT FeatureTable[RelativeFrequency]
                          Feature table containing metric.          [optional]
Parameters:
  --m-metadata-file METADATA...
    (multiple arguments   Sample metadata file containing
     will be merged)      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         Dependent variable column name. Must be a column
                          name located in the metadata or feature table files.
                                                                    [optional]
  --p-group-columns TEXT  Comma-separated list (without spaces) of metadata
                          columns to use as independent covariates used to
                          determine mean structure of "metric".     [optional]
  --p-random-effects TEXT Comma-separated list (without spaces) of metadata
                          columns to use as independent covariates used to
                          determine the variance and covariance structure
                          (random effects) of "metric". To add a random slope,
                          the same value passed to "state-column" should be
                          passed here. A random intercept for each individual
                          is set by default and does not need to be passed
                          here.                                     [optional]
  --p-palette TEXT Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2',
    'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c',
    'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis')
                          Color palette to use for generating boxplots.
                                                             [default: 'Set1']
  --p-lowess / --p-no-lowess
                          Estimate locally weighted scatterplot smoothing.
                          Note that this will eliminate confidence interval
                          plotting.                           [default: False]
  --p-ci NUMBER           Size of the confidence interval for the regression
    Range(0, 100)         estimate.                              [default: 95]
  --p-formula TEXT        R-style formula to use for model specification. A
                          formula must be used if the "metric" parameter is
                          None. Note that the metric and group columns
                          specified in the formula will override metric and
                          group columns that are passed separately as
                          parameters to this method. Formulae will be in the
                          format "a ~ b + c", where "a" is the metric
                          (dependent variable) and "b" and "c" are independent
                          covariates. Use "+" to add a variable; "+ a:b" to
                          add an interaction between variables a and b; "*" to
                          include a variable and all interactions; and "-" to
                          subtract a particular term (e.g., an interaction
                          term). See
                          https://patsy.readthedocs.io/en/latest/formulas.html
                          for full documentation of valid formula operators.
                          Always enclose formulae in quotes to avoid
                          unpleasant surprises.                     [optional]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [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.