Class: OpenTox::Validation

Inherits:
Object
  • Object
show all
Includes:
OpenTox
Defined in:
lib/validation.rb

Instance Attribute Summary

Attributes included from OpenTox

#metadata, #uri

Class Method Summary collapse

Instance Method Summary collapse

Methods included from OpenTox

#add_metadata, all, #delete, #initialize, login, text_to_html, #to_rdfxml

Class Method Details

.find(uri, subjectid = nil) ⇒ OpenTox::Validation

find validation, raises error if not found

Parameters:

  • uri (String)
  • subjectid (String, optional) (defaults to: nil)

Returns:



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# File 'lib/validation.rb', line 9

def self.find( uri, subjectid=nil )
  val = Validation.new(uri)
  val.load_metadata( subjectid )
  val
end

.from_cv_statistics(crossvalidation_uri, subjectid = nil) ⇒ OpenTox::Validation

creates a validation object from crossvaldiation statistics, raise error if not found (as crossvaldiation statistics are returned as an average valdidation over all folds)

Parameters:

  • crossvalidation (String) —

    uri

  • subjectid (String, optional) (defaults to: nil)

Returns:



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# File 'lib/validation.rb', line 20

def self.from_cv_statistics( crossvalidation_uri, subjectid=nil )
  find( File.join(crossvalidation_uri, 'statistics'),subjectid )
end

Instance Method Details

#load_metadata(subjectid = nil) ⇒ Object

loads metadata via yaml from validation object fields (like for example the validated model) can be acces via validation.metadata



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# File 'lib/validation.rb', line 26

def load_metadata( subjectid=nil )
  @metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid, :accept => "application/x-yaml"}))
end

#summary ⇒ Object

PENDING: creates summary as used for ToxCreate



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# File 'lib/validation.rb', line 31

def summary
  if @metadata[OT.classificationStatistics]
    res = {
      :nr_predictions => @metadata[OT.numInstances] - @metadata[OT.numUnpredicted],
      :correct_predictions => @metadata[OT.classificationStatistics][OT.percentCorrect],
      :weighted_area_under_roc => @metadata[OT.classificationStatistics][OT.weightedAreaUnderRoc],
    }
    @metadata[OT.classificationStatistics][OT.classValueStatistics].each do |s|
      if s[OT.classValue].to_s=="true"
        res[:true_positives] = s[OT.numTruePositives]
        res[:false_positives] = s[OT.numFalsePositives]
        res[:true_negatives] = s[OT.numTrueNegatives]
        res[:false_negatives] = s[OT.numFalseNegatives]
        res[:sensitivity] = s[OT.truePositiveRate]
        res[:specificity] = s[OT.falsePositiveRate]
        break
      end
    end
    res
  elsif @metadata[OT.regressionStatistics]
    {
      :nr_predictions => @metadata[OT.numInstances] - @metadata[OT.numUnpredicted],
      :r_square => @metadata[OT.regressionStatistics][OT.rSquare],
      :root_mean_squared_error => @metadata[OT.regressionStatistics][OT.rootMeanSquaredError],
      :mean_absolute_error => @metadata[OT.regressionStatistics][OT.meanAbsoluteError],
    }
  end
end