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nmit: Nonparametric microbial interdependence test

Citations
  • Yilong Zhang, Sung Won Han, Laura M Cox, and Huilin Li. A multivariate distance-based analytic framework for microbial interdependence association test in longitudinal study. Genetic epidemiology, 41(8):769–778, 2017. doi:10.1002/gepi.22065.

Docstring:

Usage: qiime longitudinal nmit [OPTIONS]

  Perform nonparametric microbial interdependence test to determine
  longitudinal sample similarity as a function of temporal microbial
  composition. For more details and citation, please see
  doi.org/10.1002/gepi.22065

Inputs:
  --i-table ARTIFACT FeatureTable[RelativeFrequency]
                        Feature table to use for microbial interdependence
                        test.                                       [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple           Sample metadata file containing individual-id-column.
     arguments will be
     merged)                                                        [required]
  --p-individual-id-column TEXT
                        Metadata column containing IDs for individual
                        subjects.                                   [required]
  --p-corr-method TEXT Choices('kendall', 'pearson', 'spearman')
                        The temporal correlation test to be applied.
                                                          [default: 'kendall']
  --p-dist-method TEXT Choices('fro', 'nuc')
                        Temporal distance method, see numpy.linalg.norm for
                        details.                              [default: 'fro']
Outputs:
  --o-distance-matrix ARTIFACT
    DistanceMatrix      The resulting distance matrix.              [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).
  --citations           Show citations and exit.
  --help                Show this message and exit.

Import:

from qiime2.plugins.longitudinal.methods import nmit

Docstring:

Nonparametric microbial interdependence test

Perform nonparametric microbial interdependence test to determine
longitudinal sample similarity as a function of temporal microbial
composition. For more details and citation, please see
doi.org/10.1002/gepi.22065

Parameters
----------
table : FeatureTable[RelativeFrequency]
    Feature table to use for microbial interdependence test.
metadata : Metadata
    Sample metadata file containing individual_id_column.
individual_id_column : Str
    Metadata column containing IDs for individual subjects.
corr_method : Str % Choices('kendall', 'pearson', 'spearman'), optional
    The temporal correlation test to be applied.
dist_method : Str % Choices('fro', 'nuc'), optional
    Temporal distance method, see numpy.linalg.norm for details.

Returns
-------
distance_matrix : DistanceMatrix
    The resulting distance matrix.