Package gov.nih.mipav.model.algorithms

Class StochasticForests.Tree

    • Field Detail

      • random

        protected java.util.Random random

      • dependent_varID

        protected int dependent_varID

      • mtry

        protected int mtry

      • num_samples

        protected int num_samples

      • num_samples_oob

        protected int num_samples_oob

      • min_node_size

        protected int min_node_size

      • deterministic_varIDs

        protected java.util.Vector<java.lang.Integer> deterministic_varIDs

      • split_select_varIDs

        protected java.util.Vector<java.lang.Integer> split_select_varIDs

      • split_select_weights

        protected java.util.Vector<java.lang.Double> split_select_weights

      • case_weights

        protected java.util.Vector<java.lang.Double> case_weights

      • split_varIDs

        protected java.util.Vector<java.lang.Integer> split_varIDs

      • split_values

        protected java.util.Vector<java.lang.Double> split_values

      • child_nodeIDs

        protected java.util.Vector<java.util.Vector<java.lang.Integer>> child_nodeIDs

      • sampleIDs

        protected java.util.Vector<java.util.Vector<java.lang.Integer>> sampleIDs

      • oob_sampleIDs

        protected java.util.Vector<java.lang.Integer> oob_sampleIDs

      • holdout

        protected boolean holdout

      • keep_inbag

        protected boolean keep_inbag

      • inbag_counts

        protected java.util.Vector<java.lang.Integer> inbag_counts

      • variable_importance

        protected java.util.Vector<java.lang.Double> variable_importance

      • prediction_terminal_nodeIDs

        protected java.util.Vector<java.lang.Integer> prediction_terminal_nodeIDs

      • sample_with_replacement

        protected boolean sample_with_replacement

      • sample_fraction

        protected java.util.Vector<java.lang.Double> sample_fraction

      • memory_saving_splitting

        protected boolean memory_saving_splitting

      • alpha

        protected double alpha

      • minprop

        protected double minprop

      • num_random_splits

        protected int num_random_splits

    • Constructor Detail

      • Tree

        public Tree()

      • Tree

        public Tree​(java.util.Vector<java.util.Vector<java.lang.Integer>> child_nodeIDs,
            java.util.Vector<java.lang.Integer> split_varIDs,
            java.util.Vector<java.lang.Double> split_values)

    • Method Detail

      • dispose

        public void dispose()

      • init

        public void init​(StochasticForests.Data data,
                 int mtry,
                 int dependent_varID,
                 int num_samples,
                 long seed,
                 java.util.Vector<java.lang.Integer> deterministic_varIDs,
                 java.util.Vector<java.lang.Integer> split_select_varIDs,
                 java.util.Vector<java.lang.Double> split_select_weights,
                 StochasticForests.ImportanceMode importance_mode,
                 int min_node_size,
                 boolean sample_with_replacement,
                 boolean memory_saving_splitting,
                 StochasticForests.SplitRule splitrule,
                 java.util.Vector<java.lang.Double> case_weights,
                 boolean keep_inbag,
                 java.util.Vector<java.lang.Double> sample_fraction,
                 double alpha,
                 double minprop,
                 boolean holdout,
                 int num_random_splits)

      • grow

        public void grow​(java.util.Vector<java.lang.Double> variable_importance)

      • computePermutationImportance

        public void computePermutationImportance​(java.util.Vector<java.lang.Double> forest_importance,
                                         java.util.Vector<java.lang.Double> forest_variance)

      • appendToFile

        public void appendToFile​(java.io.BufferedWriter bw)

      • createPossibleSplitVarSubset

        public void createPossibleSplitVarSubset​(java.util.Vector<java.lang.Integer> result)

      • splitNode

        public boolean splitNode​(int nodeID)

      • createEmptyNode

        public void createEmptyNode()

      • dropDownSamplePermuted

        public int dropDownSamplePermuted​(int permuted_varID,
                                  int sampleID,
                                  int permuted_sampleID)

      • permuteAndPredictOobSamples

        public void permuteAndPredictOobSamples​(int permuted_varID,
                                        java.util.Vector<java.lang.Integer> permutations)

      • bootstrap

        public void bootstrap()

      • bootstrapWeighted

        public void bootstrapWeighted()

      • bootstrapWithoutReplacement

        public void bootstrapWithoutReplacement()

      • bootstrapWithoutReplacementWeighted

        public void bootstrapWithoutReplacementWeighted()

      • allocateMemory

        public abstract void allocateMemory()

      • appendToFileInternal

        public abstract void appendToFileInternal​(java.io.BufferedWriter bw)

      • getChildNodeIDs

        public java.util.Vector<java.util.Vector<java.lang.Integer>> getChildNodeIDs()

      • getSplitValues

        public java.util.Vector<java.lang.Double> getSplitValues()

      • getSplitVarIDs

        public java.util.Vector<java.lang.Integer> getSplitVarIDs()

      • getOobSampleIDs

        public java.util.Vector<java.lang.Integer> getOobSampleIDs()

      • getNumSamplesOob

        public int getNumSamplesOob()

      • getInbagCounts

        public java.util.Vector<java.lang.Integer> getInbagCounts()

      • splitNodeInternal

        protected abstract boolean splitNodeInternal​(int nodeID,
                                             java.util.Vector<java.lang.Integer> possible_split_varIDs)

      • createEmptyNodeInternal

        protected abstract void createEmptyNodeInternal()

      • computePredictionAccuracyInternal

        protected abstract double computePredictionAccuracyInternal()

      • bootstrapClassWise

        protected abstract void bootstrapClassWise()

      • bootstrapWithoutReplacementClassWise

        protected abstract void bootstrapWithoutReplacementClassWise()

      • cleanUpInternal

        protected abstract void cleanUpInternal()