java.lang.Object
- gov.nih.mipav.model.algorithms.StochasticForests.Forest
- - gov.nih.mipav.model.algorithms.StochasticForests.ForestClassification

Enclosing class:: StochasticForests

private class StochasticForests.ForestClassification
extends StochasticForests.Forest

Nested Class Summary
- Nested classes/interfaces inherited from class gov.nih.mipav.model.algorithms.StochasticForests.Forest
  StochasticForests.Forest.computeTreePermutationImportanceInThread, StochasticForests.Forest.growTreesInThread, StochasticForests.Forest.predictInternalInThread, StochasticForests.Forest.predictTreesInThread, StochasticForests.Forest.showProgress

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) java.util.HashMap<StochasticForests.ValuePair<java.lang.Double,java.lang.Double>,java.lang.Integer>`	`classification_table`
`(package private) java.util.Vector<java.lang.Integer>`	`response_classIDs`
`(package private) java.util.Vector<java.util.Vector<java.lang.Integer>>`	`sampleIDs_per_class`

Fields inherited from class gov.nih.mipav.model.algorithms.StochasticForests.Forest
alpha, case_weights, data, dependent_varID, deterministic_varIDs, holdout, importance_mode, keep_inbag, memory_mode, memory_saving_splitting, min_node_size, minprop, mtry, mutex, num_independent_variables, num_random_splits, num_samples, num_threads, num_trees, num_variables, output_prefix, overall_prediction_error, predict_all, prediction_mode, prediction_type, predictions, progress, random, sample_fraction, sample_with_replacement, seed, split_select_varIDs, split_select_weights, splitrule, thread_ranges, trees, variable_importance, verbose_out

Constructor Summary

Constructors
Constructor Description

ForestClassification()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`allocatePredictMemory()`
`void`	`computePredictionErrorInternal()`
`java.util.Vector<java.lang.Double>`	`getClassValues()`
`void`	`growInternal()`
`void`	`initInternal(java.lang.String status_variable_name)`
`void`	`loadForest(int dependent_varID, int num_trees, java.util.Vector<java.util.Vector<java.util.Vector<java.lang.Integer>>> forest_child_nodeIDs, java.util.Vector<java.util.Vector<java.lang.Integer>> forest_split_varIDs, java.util.Vector<java.util.Vector<java.lang.Double>> forest_split_values, java.util.Vector<java.lang.Double> class_values, java.util.Vector<java.lang.Boolean> is_ordered_variable)`
`void`	`loadFromFileInternal(java.io.BufferedReader br)`
`void`	`predictInternal(int sample_idx)`
`void`	`saveToFileInternal(java.io.BufferedWriter bw)`
`void`	`setClassWeights(java.util.Vector<java.lang.Double> class_weights)`
`void`	`writeConfusionFile()`
`void`	`writeOutputInternal()`
`void`	`writePredictionFile()`

Methods inherited from class gov.nih.mipav.model.algorithms.StochasticForests.Forest
computePermutationImportance, computePredictionError, dispose, getChildNodeIDs, getDependentVarId, getInbagCounts, getIsOrderedVariable, getMinNodeSize, getMtry, getNumIndependentVariables, getNumTrees, getOverallPredictionError, getPredictions, getSplitValues, getSplitVarIDs, getVariableImportance, grow, init, initCpp, initR, loadFromFile, predict, run, saveToFile, setAlwaysSplitVariables, setSplitWeightVector, writeImportanceFile, writeOutput

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

class_weights

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

classification_table

java.util.HashMap<StochasticForests.ValuePair<java.lang.Double,java.lang.Double>,java.lang.Integer> classification_table

Constructor Detail
- ForestClassification
```
public ForestClassification()
```

Method Detail

getClassValues

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

setClassWeights

public void setClassWeights(java.util.Vector<java.lang.Double> class_weights)

loadForest

public void loadForest(int dependent_varID,
                       int num_trees,
                       java.util.Vector<java.util.Vector<java.util.Vector<java.lang.Integer>>> forest_child_nodeIDs,
                       java.util.Vector<java.util.Vector<java.lang.Integer>> forest_split_varIDs,
                       java.util.Vector<java.util.Vector<java.lang.Double>> forest_split_values,
                       java.util.Vector<java.lang.Double> class_values,
                       java.util.Vector<java.lang.Boolean> is_ordered_variable)

initInternal

public void initInternal(java.lang.String status_variable_name)

Specified by:: initInternal in class StochasticForests.Forest

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

growInternal in class StochasticForests.Forest

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

allocatePredictMemory in class StochasticForests.Forest

predictInternal
```
public void predictInternal(int sample_idx)
```
Specified by:

predictInternal in class StochasticForests.Forest

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

computePredictionErrorInternal in class StochasticForests.Forest

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

writeOutputInternal in class StochasticForests.Forest

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

writeConfusionFile in class StochasticForests.Forest

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

writePredictionFile in class StochasticForests.Forest

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

saveToFileInternal in class StochasticForests.Forest

loadFromFileInternal
```
public void loadFromFileInternal(java.io.BufferedReader br)
```
Specified by:

loadFromFileInternal in class StochasticForests.Forest

Class StochasticForests.ForestClassification

Nested Class Summary

Nested classes/interfaces inherited from class gov.nih.mipav.model.algorithms.StochasticForests.Forest

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

class_values

response_classIDs

sampleIDs_per_class

class_weights

classification_table

Constructor Detail

ForestClassification

Method Detail

getClassValues

setClassWeights

loadForest

initInternal

growInternal

allocatePredictMemory

predictInternal

computePredictionErrorInternal

writeOutputInternal

writeConfusionFile

writePredictionFile

saveToFileInternal

loadFromFileInternal