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nmit: Nonparametric microbial interdependence test

Citations

[longitudinal:nmit:ZHCL17]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:https://doi.org/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

Options:
  --i-table ARTIFACT PATH FeatureTable[RelativeFrequency]
                                  Feature table to use for microbial
                                  interdependence test.  [required]
  --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-individual-id-column TEXT   Metadata column containing IDs for
                                  individual subjects.  [required]
  --p-corr-method [kendall|spearman|pearson]
                                  The temporal correlation test to be applied.
                                  [default: kendall]
  --p-dist-method [fro|nuc]       Temporal distance method, see
                                  numpy.linalg.norm for details.  [default:
                                  fro]
  --o-distance-matrix ARTIFACT PATH DistanceMatrix
                                  The resulting distance matrix.  [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 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.