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jaccard: Jaccard Distance

Citations
  • P Jaccard. Nouvelles recherches sur la distribution floral. Bull. Soc. Vard. Sci. Nat, 44:223–270, 1908.

Docstring:

Usage: qiime diversity-lib jaccard [OPTIONS]

  Compute Jaccard distance for each sample in a feature table. Jaccard is
  calculated usingpresence/absence data. Data of type FeatureTable[Frequency
  | Relative Frequency] is reducedto presence/absence prior to calculation.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence]   The feature table containing the samples for which
                       Jaccard distance should be computed.         [required]
Parameters:
  --p-n-jobs VALUE Int % Range(1, None) | Str % Choices('auto')
                       The number of concurrent jobs to use in performing
                       this calculation. May not exceed the number of
                       available physical cores. If n-jobs = 'auto', one job
                       will be launched for each identified CPU core on the
                       host.                                      [default: 1]
Outputs:
  --o-distance-matrix ARTIFACT
    DistanceMatrix     Distance matrix for Jaccard index            [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).
  --examples           Show usage examples and exit.
  --citations          Show citations and exit.
  --help               Show this message and exit.

Import:

from qiime2.plugins.diversity_lib.methods import jaccard

Docstring:

Jaccard Distance

Compute Jaccard distance for each sample in a feature table. Jaccard is
calculated usingpresence/absence data. Data of type FeatureTable[Frequency
| Relative Frequency] is reducedto presence/absence prior to calculation.

Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
    The feature table containing the samples for which Jaccard distance
    should be computed.
n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of concurrent jobs to use in performing this calculation.
    May not exceed the number of available physical cores. If n_jobs =
    'auto', one job will be launched for each identified CPU core on the
    host.

Returns
-------
distance_matrix : DistanceMatrix
    Distance matrix for Jaccard index