Package gov.nih.mipav.model.algorithms

Class StochasticForests.TreeSurvival

java.lang.Object

gov.nih.mipav.model.algorithms.StochasticForests.Tree

gov.nih.mipav.model.algorithms.StochasticForests.TreeSurvival

Enclosing class:

StochasticForests

private class StochasticForests.TreeSurvival
extends StochasticForests.Tree

Field Summary

Fields

Modifier and Type	Field	Description
private java.util.Vector<java.util.Vector<java.lang.Double>>	chf
private int[]	num_deaths
private int[]	num_samples_at_risk
private int	num_timepoints
private java.util.Vector<java.lang.Integer>	response_timepointIDs
private int	status_varID
private java.util.Vector<java.lang.Double>	unique_timepoints

Fields inherited from class gov.nih.mipav.model.algorithms.StochasticForests.Tree

alpha, case_weights, child_nodeIDs, data, dependent_varID, deterministic_varIDs, holdout, importance_mode, inbag_counts, keep_inbag, memory_saving_splitting, min_node_size, minprop, mtry, num_random_splits, num_samples, num_samples_oob, oob_sampleIDs, prediction_terminal_nodeIDs, random, sample_fraction, sample_with_replacement, sampleIDs, split_select_varIDs, split_select_weights, split_values, split_varIDs, splitrule, variable_importance

Constructor Summary

Constructors

Constructor	Description
TreeSurvival(java.util.Vector<java.lang.Double> unique_timepoints, int status_varID, java.util.Vector<java.lang.Integer> response_timepoints)
TreeSurvival(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, java.util.Vector<java.util.Vector<java.lang.Double>> chf, java.util.Vector<java.lang.Double> unique_timepoints, java.util.Vector<java.lang.Integer> response_timepointIDs)

Method Summary

Modifier and Type	Method	Description
void	addImpurityImportance(int nodeID, int varID, double decrease)
void	allocateMemory()
void	appendToFileInternal(java.io.BufferedWriter bw)
void	bootstrapClassWise()
void	bootstrapWithoutReplacementClassWise()
void	cleanUpInternal()
void	computeAucSplit(double time_k, double time_l, double status_k, double status_l, double value_k, double value_l, int num_splits, java.util.Vector<java.lang.Double> possible_split_values, double[] num_count, double[] num_total)
void	computeChildDeathCounts(int nodeID, int varID, java.util.Vector<java.lang.Double> possible_split_values, int[] num_samples_right_child, int[] delta_samples_at_risk_right_child, int[] num_deaths_right_child, int num_splits)
void	computeDeathCounts(int nodeID)
double	computePredictionAccuracyInternal()
void	computeSurvival(int nodeID)
void	createEmptyNodeInternal()
boolean	findBestSplit(int nodeID, java.util.Vector<java.lang.Integer> possible_split_varIDs)
boolean	findBestSplitExtraTrees(int nodeID, java.util.Vector<java.lang.Integer> possible_split_varIDs)
boolean	findBestSplitMaxstat(int nodeID, java.util.Vector<java.lang.Integer> possible_split_varIDs)
void	findBestSplitValueAUC(int nodeID, int varID, double[] best_value, int[] best_varID, double[] best_auc)
void	findBestSplitValueExtraTrees(int nodeID, int varID, double[] best_value, int[] best_varID, double[] best_logrank)
void	findBestSplitValueExtraTreesUnordered(int nodeID, int varID, double[] best_value, int[] best_varID, double[] best_logrank)
void	findBestSplitValueLogRank(int nodeID, int varID, double[] best_value, int[] best_varID, double[] best_logrank)
void	findBestSplitValueLogRankUnordered(int nodeID, int varID, double[] best_value, int[] best_varID, double[] best_logrank)
java.util.Vector<java.util.Vector<java.lang.Double>>	getChf()
java.util.Vector<java.lang.Double>	getPrediction(int sampleID)
int	getPredictionTerminalNodeID(int sampleID)
boolean	splitNodeInternal(int nodeID, java.util.Vector<java.lang.Integer> possible_split_varIDs)

Methods inherited from class gov.nih.mipav.model.algorithms.StochasticForests.Tree

appendToFile, bootstrap, bootstrapWeighted, bootstrapWithoutReplacement, bootstrapWithoutReplacementWeighted, computePermutationImportance, createEmptyNode, createPossibleSplitVarSubset, dispose, dropDownSamplePermuted, getChildNodeIDs, getInbagCounts, getNumSamplesOob, getOobSampleIDs, getSplitValues, getSplitVarIDs, grow, init, permuteAndPredictOobSamples, predict, splitNode

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

status_varID

private int status_varID

unique_timepoints

private java.util.Vector<java.lang.Double> unique_timepoints

num_timepoints

private int num_timepoints

response_timepointIDs

private java.util.Vector<java.lang.Integer> response_timepointIDs

chf

private java.util.Vector<java.util.Vector<java.lang.Double>> chf

num_deaths

private int[] num_deaths

num_samples_at_risk

private int[] num_samples_at_risk

Constructor Detail

TreeSurvival

public TreeSurvival(java.util.Vector<java.lang.Double> unique_timepoints,
                    int status_varID,
                    java.util.Vector<java.lang.Integer> response_timepoints)

TreeSurvival

public TreeSurvival(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,
                    java.util.Vector<java.util.Vector<java.lang.Double>> chf,
                    java.util.Vector<java.lang.Double> unique_timepoints,
                    java.util.Vector<java.lang.Integer> response_timepointIDs)

Method Detail

getChf

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

getPrediction

public java.util.Vector<java.lang.Double> getPrediction(int sampleID)

getPredictionTerminalNodeID

public int getPredictionTerminalNodeID(int sampleID)

allocateMemory

public void allocateMemory()

Specified by:

allocateMemory in class StochasticForests.Tree

appendToFileInternal

public void appendToFileInternal(java.io.BufferedWriter bw)

Specified by:

appendToFileInternal in class StochasticForests.Tree

createEmptyNodeInternal

public void createEmptyNodeInternal()

Specified by:

createEmptyNodeInternal in class StochasticForests.Tree

computeSurvival

public void computeSurvival(int nodeID)

computePredictionAccuracyInternal

public double computePredictionAccuracyInternal()

Specified by:

computePredictionAccuracyInternal in class StochasticForests.Tree

splitNodeInternal

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

Specified by:

splitNodeInternal in class StochasticForests.Tree

findBestSplit

public boolean findBestSplit(int nodeID,
                             java.util.Vector<java.lang.Integer> possible_split_varIDs)

findBestSplitMaxstat

public boolean findBestSplitMaxstat(int nodeID,
                                    java.util.Vector<java.lang.Integer> possible_split_varIDs)

computeDeathCounts

public void computeDeathCounts(int nodeID)

computeChildDeathCounts

public void computeChildDeathCounts(int nodeID,
                                    int varID,
                                    java.util.Vector<java.lang.Double> possible_split_values,
                                    int[] num_samples_right_child,
                                    int[] delta_samples_at_risk_right_child,
                                    int[] num_deaths_right_child,
                                    int num_splits)

findBestSplitValueLogRank

public void findBestSplitValueLogRank(int nodeID,
                                      int varID,
                                      double[] best_value,
                                      int[] best_varID,
                                      double[] best_logrank)

findBestSplitValueLogRankUnordered

public void findBestSplitValueLogRankUnordered(int nodeID,
                                               int varID,
                                               double[] best_value,
                                               int[] best_varID,
                                               double[] best_logrank)

findBestSplitValueAUC

public void findBestSplitValueAUC(int nodeID,
                                  int varID,
                                  double[] best_value,
                                  int[] best_varID,
                                  double[] best_auc)

computeAucSplit

public void computeAucSplit(double time_k,
                            double time_l,
                            double status_k,
                            double status_l,
                            double value_k,
                            double value_l,
                            int num_splits,
                            java.util.Vector<java.lang.Double> possible_split_values,
                            double[] num_count,
                            double[] num_total)

findBestSplitExtraTrees

public boolean findBestSplitExtraTrees(int nodeID,
                                       java.util.Vector<java.lang.Integer> possible_split_varIDs)

findBestSplitValueExtraTrees

public void findBestSplitValueExtraTrees(int nodeID,
                                         int varID,
                                         double[] best_value,
                                         int[] best_varID,
                                         double[] best_logrank)

findBestSplitValueExtraTreesUnordered

public void findBestSplitValueExtraTreesUnordered(int nodeID,
                                                  int varID,
                                                  double[] best_value,
                                                  int[] best_varID,
                                                  double[] best_logrank)

addImpurityImportance

public void addImpurityImportance(int nodeID,
                                  int varID,
                                  double decrease)

bootstrapClassWise

public void bootstrapClassWise()

Specified by:

bootstrapClassWise in class StochasticForests.Tree

bootstrapWithoutReplacementClassWise

public void bootstrapWithoutReplacementClassWise()

Specified by:

bootstrapWithoutReplacementClassWise in class StochasticForests.Tree

cleanUpInternal

public void cleanUpInternal()

Specified by:

cleanUpInternal in class StochasticForests.Tree