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fit-classifier-naive-bayes: Train the naive_bayes classifier

Citations

[feature-classifier:fit-classifier-naive-bayes:PVG+11]Fabian Pedregosa, Gaël Varoquaux, Alexandre Gramfort, Vincent Michel, Bertrand Thirion, Olivier Grisel, Mathieu Blondel, Peter Prettenhofer, Ron Weiss, Vincent Dubourg, Jake Vanderplas, Alexandre Passos, David Cournapeau, Matthieu Brucher, Matthieu Perrot, and Édouard Duchesnay. Scikit-learn: machine learning in python. Journal of machine learning research, 12(Oct):2825–2830, 2011.

Docstring:

Usage: qiime feature-classifier fit-classifier-naive-bayes
           [OPTIONS]

  Create a scikit-learn naive_bayes classifier for reads

Options:
  --i-reference-reads ARTIFACT PATH FeatureData[Sequence]
                                  [required]
  --i-reference-taxonomy ARTIFACT PATH FeatureData[Taxonomy]
                                  [required]
  --i-class-weight ARTIFACT PATH FeatureTable[RelativeFrequency]
                                  [optional]
  --p-classify--alpha FLOAT       [default: 0.001]
  --p-classify--chunk-size INTEGER
                                  [default: 20000]
  --p-classify--class-prior TEXT  [default: null]
  --p-classify--fit-prior / --p-no-classify--fit-prior
                                  [default: False]
  --p-feat-ext--alternate-sign / --p-no-feat-ext--alternate-sign
                                  [default: False]
  --p-feat-ext--analyzer TEXT     [default: char_wb]
  --p-feat-ext--binary / --p-no-feat-ext--binary
                                  [default: False]
  --p-feat-ext--decode-error TEXT
                                  [default: strict]
  --p-feat-ext--encoding TEXT     [default: utf-8]
  --p-feat-ext--input TEXT        [default: content]
  --p-feat-ext--lowercase / --p-no-feat-ext--lowercase
                                  [default: True]
  --p-feat-ext--n-features INTEGER
                                  [default: 8192]
  --p-feat-ext--ngram-range TEXT  [default: [7, 7]]
  --p-feat-ext--non-negative / --p-no-feat-ext--non-negative
                                  [default: False]
  --p-feat-ext--norm TEXT         [default: l2]
  --p-feat-ext--preprocessor TEXT
                                  [default: null]
  --p-feat-ext--stop-words TEXT   [default: null]
  --p-feat-ext--strip-accents TEXT
                                  [default: null]
  --p-feat-ext--token-pattern TEXT
                                  [default: (?u)\b\w\w+\b]
  --p-feat-ext--tokenizer TEXT    [default: null]
  --o-classifier ARTIFACT PATH TaxonomicClassifier
                                  [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.feature_classifier.methods import fit_classifier_naive_bayes

Docstring:

Train the naive_bayes classifier

Create a scikit-learn naive_bayes classifier for reads

Parameters
----------
reference_reads : FeatureData[Sequence]
reference_taxonomy : FeatureData[Taxonomy]
class_weight : FeatureTable[RelativeFrequency], optional
classify__alpha : Float, optional
classify__chunk_size : Int, optional
classify__class_prior : Str, optional
classify__fit_prior : Bool, optional
feat_ext__alternate_sign : Bool, optional
feat_ext__analyzer : Str, optional
feat_ext__binary : Bool, optional
feat_ext__decode_error : Str, optional
feat_ext__encoding : Str, optional
feat_ext__input : Str, optional
feat_ext__lowercase : Bool, optional
feat_ext__n_features : Int, optional
feat_ext__ngram_range : Str, optional
feat_ext__non_negative : Bool, optional
feat_ext__norm : Str, optional
feat_ext__preprocessor : Str, optional
feat_ext__stop_words : Str, optional
feat_ext__strip_accents : Str, optional
feat_ext__token_pattern : Str, optional
feat_ext__tokenizer : Str, optional

Returns
-------
classifier : TaxonomicClassifier