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nmit: Nonparametric microbial interdependence test¶
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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 arguments will be individual-id-column. 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). --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.
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.