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bray-curtis: Bray-Curtis Dissimilarity

Citations
  • Thorvald Sørensen. A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on danish commons. Biol. Skr., 5:1–34, 1948.

Docstring:

Usage: qiime diversity-lib bray-curtis [OPTIONS]

  Compute Bray-Curtis dissimilarity for each sample in a feature table.
  Note: Frequency and relative frequency data produce different results
  unless overall sample sizes are identical. Please consider the impact on
  your results if you use Bray-Curtis with count data that has not been
  adjusted (normalized).

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                       The feature table containing the samples for which
                       Bray-Curtis dissimilarity 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 Bray-Curtis dissimilarity
                                                                    [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 bray_curtis

Docstring:

Bray-Curtis Dissimilarity

Compute Bray-Curtis dissimilarity for each sample in a feature table. Note:
Frequency and relative frequency data produce different results unless
overall sample sizes are identical. Please consider the impact on your
results if you use Bray-Curtis with count data that has not been adjusted
(normalized).

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples for which Bray-Curtis
    dissimilarity 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 Bray-Curtis dissimilarity