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

All Methods Instance Methods Concrete Methods
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

Class StochasticForests.TreeSurvival

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

status_varID

unique_timepoints

num_timepoints

response_timepointIDs

chf

num_deaths

num_samples_at_risk

Constructor Detail

TreeSurvival

TreeSurvival

Method Detail

getChf

getPrediction

getPredictionTerminalNodeID

allocateMemory

appendToFileInternal

createEmptyNodeInternal

computeSurvival

computePredictionAccuracyInternal

splitNodeInternal

findBestSplit

findBestSplitMaxstat

computeDeathCounts

computeChildDeathCounts

findBestSplitValueLogRank

findBestSplitValueLogRankUnordered

findBestSplitValueAUC

computeAucSplit

findBestSplitExtraTrees

findBestSplitValueExtraTrees

findBestSplitValueExtraTreesUnordered

addImpurityImportance

bootstrapClassWise

bootstrapWithoutReplacementClassWise

cleanUpInternal