java.lang.Object
- gov.nih.mipav.model.algorithms.StochasticForests.Tree
- - gov.nih.mipav.model.algorithms.StochasticForests.TreeProbability

Enclosing class:: StochasticForests

private class StochasticForests.TreeProbability
extends StochasticForests.Tree

Field Summary

Fields
Modifier and Type	Field	Description
`(package private) java.util.Vector<java.lang.Double>`	`class_values`
`(package private) java.util.Vector<java.lang.Double>`	`class_weights`
`(package private) int[]`	`counter`
`(package private) int[]`	`counter_per_class`
`(package private) java.util.Vector<java.lang.Integer>`	`response_classIDs`
`(package private) java.util.Vector<java.util.Vector<java.lang.Integer>>`	`sampleIDs_per_class`
`(package private) java.util.Vector<java.util.Vector<java.lang.Double>>`	`terminal_class_counts`

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
`TreeProbability(java.util.Vector<java.lang.Double> class_values, java.util.Vector<java.lang.Integer> response_classIDs, java.util.Vector<java.util.Vector<java.lang.Integer>> sampleIDs_per_class, java.util.Vector<java.lang.Double> class_weights)`
`TreeProbability(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.lang.Double> class_values, java.util.Vector<java.lang.Integer> response_classIDs, java.util.Vector<java.util.Vector<java.lang.Double>> terminal_class_counts)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addImpurityImportance(int nodeID, int varID, double decrease)`
`void`	`addToTerminalNodes(int nodeID)`
`void`	`allocateMemory()`
`void`	`appendToFileInternal(java.io.BufferedWriter bw)`
`void`	`bootstrapClassWise()`
`void`	`bootstrapWithoutReplacementClassWise()`
`void`	`cleanUpInternal()`
`double`	`computePredictionAccuracyInternal()`
`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)`
`void`	`findBestSplitValueExtraTrees(int nodeID, int varID, int num_classes, int[] class_counts, int num_samples_node, double[] best_value, int[] best_varID, double[] best_decrease)`
`void`	`findBestSplitValueExtraTreesUnordered(int nodeID, int varID, int num_classes, int[] class_counts, int num_samples_node, double[] best_value, int[] best_varID, double[] best_decrease)`
`void`	`findBestSplitValueLargeQ(int nodeID, int varID, int num_classes, int[] class_counts, int num_samples_node, double[] best_value, int[] best_varID, double[] best_decrease)`
`void`	`findBestSplitValueSmallQ(int nodeID, int varID, int num_classes, int[] class_counts, int num_samples_node, double[] best_value, int[] best_varID, double[] best_decrease)`
`void`	`findBestSplitValueUnordered(int nodeID, int varID, int num_classes, int[] class_counts, int num_samples_node, double[] best_value, int[] best_varID, double[] best_decrease)`
`java.util.Vector<java.lang.Double>`	`getPrediction(int sampleID)`
`int`	`getPredictionTerminalNodeID(int sampleID)`
`java.util.Vector<java.util.Vector<java.lang.Double>>`	`getTerminalClassCounts()`
`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

class_values

java.util.Vector<java.lang.Double> class_values

response_classIDs

java.util.Vector<java.lang.Integer> response_classIDs

sampleIDs_per_class

java.util.Vector<java.util.Vector<java.lang.Integer>> sampleIDs_per_class

terminal_class_counts

java.util.Vector<java.util.Vector<java.lang.Double>> terminal_class_counts

class_weights

java.util.Vector<java.lang.Double> class_weights

counter
```
int[] counter
```

counter_per_class
```
int[] counter_per_class
```

Constructor Detail

TreeProbability

public TreeProbability(java.util.Vector<java.lang.Double> class_values,
                       java.util.Vector<java.lang.Integer> response_classIDs,
                       java.util.Vector<java.util.Vector<java.lang.Integer>> sampleIDs_per_class,
                       java.util.Vector<java.lang.Double> class_weights)

TreeProbability

public TreeProbability(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.lang.Double> class_values,
                       java.util.Vector<java.lang.Integer> response_classIDs,
                       java.util.Vector<java.util.Vector<java.lang.Double>> terminal_class_counts)

Method Detail

cleanUpInternal
```
public void cleanUpInternal()
```
Specified by:

cleanUpInternal in class StochasticForests.Tree

getPrediction

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

getPredictionTerminalNodeID

public int getPredictionTerminalNodeID(int sampleID)

getTerminalClassCounts

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

allocateMemory
```
public void allocateMemory()
```
Specified by:

allocateMemory in class StochasticForests.Tree

addToTerminalNodes

public void addToTerminalNodes(int nodeID)

appendToFileInternal
```
public void appendToFileInternal(java.io.BufferedWriter bw)
```
Specified by:

appendToFileInternal 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

createEmptyNodeInternal
```
public void createEmptyNodeInternal()
```
Specified by:

createEmptyNodeInternal in class StochasticForests.Tree

computePredictionAccuracyInternal
```
public double computePredictionAccuracyInternal()
```
Specified by:

computePredictionAccuracyInternal in class StochasticForests.Tree

findBestSplit

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

findBestSplitValueSmallQ

public void findBestSplitValueSmallQ(int nodeID,
                                     int varID,
                                     int num_classes,
                                     int[] class_counts,
                                     int num_samples_node,
                                     double[] best_value,
                                     int[] best_varID,
                                     double[] best_decrease)

findBestSplitValueLargeQ

public void findBestSplitValueLargeQ(int nodeID,
                                     int varID,
                                     int num_classes,
                                     int[] class_counts,
                                     int num_samples_node,
                                     double[] best_value,
                                     int[] best_varID,
                                     double[] best_decrease)

findBestSplitValueUnordered

public void findBestSplitValueUnordered(int nodeID,
                                        int varID,
                                        int num_classes,
                                        int[] class_counts,
                                        int num_samples_node,
                                        double[] best_value,
                                        int[] best_varID,
                                        double[] best_decrease)

findBestSplitExtraTrees

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

findBestSplitValueExtraTrees

public void findBestSplitValueExtraTrees(int nodeID,
                                         int varID,
                                         int num_classes,
                                         int[] class_counts,
                                         int num_samples_node,
                                         double[] best_value,
                                         int[] best_varID,
                                         double[] best_decrease)

findBestSplitValueExtraTreesUnordered

public void findBestSplitValueExtraTreesUnordered(int nodeID,
                                                  int varID,
                                                  int num_classes,
                                                  int[] class_counts,
                                                  int num_samples_node,
                                                  double[] best_value,
                                                  int[] best_varID,
                                                  double[] best_decrease)

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

Class StochasticForests.TreeProbability

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

class_values

response_classIDs

sampleIDs_per_class

terminal_class_counts

class_weights

counter

counter_per_class

Constructor Detail

TreeProbability

TreeProbability

Method Detail

cleanUpInternal

getPrediction

getPredictionTerminalNodeID

getTerminalClassCounts

allocateMemory

addToTerminalNodes

appendToFileInternal

splitNodeInternal

createEmptyNodeInternal

computePredictionAccuracyInternal

findBestSplit

findBestSplitValueSmallQ

findBestSplitValueLargeQ

findBestSplitValueUnordered

findBestSplitExtraTrees

findBestSplitValueExtraTrees

findBestSplitValueExtraTreesUnordered

addImpurityImportance

bootstrapClassWise

bootstrapWithoutReplacementClassWise