1 files changed, 0 insertions, 117 deletions
diff --git a/lib/crossvalidation.rb b/lib/crossvalidation.rb
deleted file mode 100644
index e1761bc..0000000
--- a/lib/crossvalidation.rb
+++ /dev/null
@@ -1,117 +0,0 @@
-module OpenTox
-
-  module Validation
-
-    # Crossvalidation
-    class CrossValidation < Validation
-      field :validation_ids, type: Array, default: []
-      field :folds, type: Integer, default: 10
-
-      # Create a crossvalidation
-      # @param [OpenTox::Model::Lazar]
-      # @param [Fixnum] number of folds
-      # @return [OpenTox::Validation::CrossValidation]
-      def self.create model, n=10
-        $logger.debug model.algorithms
-        klass = ClassificationCrossValidation if model.is_a? Model::LazarClassification
-        klass = RegressionCrossValidation if model.is_a? Model::LazarRegression
-        raise ArgumentError, "Unknown model class #{model.class}." unless klass
-
-        cv = klass.new(
-          name: model.name,
-          model_id: model.id,
-          folds: n
-        )
-        cv.save # set created_at
-
-        training_dataset = model.training_dataset
-        training_dataset.folds(n).each_with_index do |fold,fold_nr|
-          #fork do # parallel execution of validations can lead to Rserve and memory problems
-          $logger.debug "Dataset #{training_dataset.name}: Fold #{fold_nr} started"
-          t = Time.now
-          validation = TrainTest.create(model, fold[0], fold[1])
-          cv.validation_ids << validation.id
-          $logger.debug "Dataset #{training_dataset.name}, Fold #{fold_nr}:  #{Time.now-t} seconds"
-        end
-        cv.save
-        cv.statistics
-        cv.update_attributes(finished_at: Time.now)
-        cv
-      end
-
-      # Get execution time
-      # @return [Fixnum]
-      def time
-        finished_at - created_at
-      end
-
-      # Get individual validations
-      # @return [Array<OpenTox::Validation>]
-      def validations
-        validation_ids.collect{|vid| TrainTest.find vid}
-      end
-
-      # Get predictions for all compounds
-      # @return [Array<Hash>]
-      def predictions
-        predictions = {}
-        validations.each{|v| predictions.merge!(v.predictions)}
-        predictions
-      end
-    end
-
-    # Crossvalidation of classification models
-    class ClassificationCrossValidation < CrossValidation
-      include ClassificationStatistics
-      field :accept_values, type: Array
-      field :confusion_matrix, type: Hash
-      field :accuracy, type: Hash
-      field :true_rate, type: Hash
-      field :predictivity, type: Hash
-      field :nr_predictions, type: Hash
-      field :probability_plot_id, type: BSON::ObjectId
-    end
-
-    # Crossvalidation of regression models
-    class RegressionCrossValidation < CrossValidation
-      include RegressionStatistics
-      field :rmse, type: Hash
-      field :mae, type: Hash
-      field :r_squared, type: Hash
-      field :within_prediction_interval, type: Hash
-      field :out_of_prediction_interval, type: Hash
-      field :nr_predictions, type: Hash
-      field :warnings, type: Array
-      field :correlation_plot_id, type: BSON::ObjectId
-    end
-
-    # Independent repeated crossvalidations
-    class RepeatedCrossValidation < Validation
-      field :crossvalidation_ids, type: Array, default: []
-      field :correlation_plot_id, type: BSON::ObjectId
-
-      # Create repeated crossvalidations
-      # @param [OpenTox::Model::Lazar]
-      # @param [Fixnum] number of folds
-      # @param [Fixnum] number of repeats
-      # @return [OpenTox::Validation::RepeatedCrossValidation]
-      def self.create model, folds=10, repeats=5
-        repeated_cross_validation = self.new
-        repeats.times do |n|
-          $logger.debug "Crossvalidation #{n+1} for #{model.name}"
-          repeated_cross_validation.crossvalidation_ids << CrossValidation.create(model, folds).id
-        end
-        repeated_cross_validation.save
-        repeated_cross_validation
-      end
-
-      # Get crossvalidations
-      # @return [OpenTox::Validation::CrossValidation]
-      def crossvalidations
-        crossvalidation_ids.collect{|id| CrossValidation.find(id)}
-      end
-
-    end
-  end
-
-end