Field Detail

• mask

  static final int[] mask

• offset

  static final int[] offset

• DEFAULT_NUM_TREE

  final int DEFAULT_NUM_TREE

  See Also:

  Constant Field Values

• DEFAULT_NUM_THREADS

  final int DEFAULT_NUM_THREADS

  See Also:

  Constant Field Values

• DEFAULT_IMPORTANCE_MODE

  final StochasticForests.ImportanceMode DEFAULT_IMPORTANCE_MODE

• DEFAULT_MIN_NODE_SIZE_CLASSIFICATION

  final int DEFAULT_MIN_NODE_SIZE_CLASSIFICATION

  See Also:

  Constant Field Values

• DEFAULT_MIN_NODE_SIZE_REGRESSION

  final int DEFAULT_MIN_NODE_SIZE_REGRESSION

  See Also:

  Constant Field Values

• DEFAULT_MIN_NODE_SIZE_SURVIVAL

  final int DEFAULT_MIN_NODE_SIZE_SURVIVAL

  See Also:

  Constant Field Values

• DEFAULT_MIN_NODE_SIZE_PROBABILITY

  final int DEFAULT_MIN_NODE_SIZE_PROBABILITY

  See Also:

  Constant Field Values

• DEFAULT_SPLITRULE

  final StochasticForests.SplitRule DEFAULT_SPLITRULE

• DEFAULT_ALPHA

  final double DEFAULT_ALPHA

  See Also:

  Constant Field Values

• DEFAULT_MINPROP

  final double DEFAULT_MINPROP

  See Also:

  Constant Field Values

• DEFAULT_PREDICTIONTYPE

  final StochasticForests.PredictionType DEFAULT_PREDICTIONTYPE

• DEFAULT_NUM_RANDOM_SPLITS

  final int DEFAULT_NUM_RANDOM_SPLITS

  See Also:

  Constant Field Values

• STATUS_INTERVAL

  final double STATUS_INTERVAL

  See Also:

  Constant Field Values

• Q_THRESHOLD

  final double Q_THRESHOLD

  See Also:

  Constant Field Values

• RAND_MAX

  public static int RAND_MAX

• logprop

  public static double logprop

• testUtility

  private boolean testUtility

• testMain

  private boolean testMain

• treetype

  private StochasticForests.TreeType treetype

• probability

  private boolean probability

• verbose_out

  private boolean verbose_out

• dependent_variable_name

  private java.lang.String dependent_variable_name

• memory_mode

  private StochasticForests.MemoryMode memory_mode

• input_file

  private java.lang.String input_file

• mtry

  private int mtry

• output_prefix

  private java.lang.String output_prefix

• num_trees

  private int num_trees

• seed

  private long seed

• num_threads

  private int num_threads

• load_forest_filename

  private java.lang.String load_forest_filename

• importance_mode

  private StochasticForests.ImportanceMode importance_mode

• min_node_size

  private int min_node_size

• split_select_weights_file

  private java.lang.String split_select_weights_file

• always_split_variable_names

  private java.util.Vector<java.lang.String> always_split_variable_names

• status_variable_name

  private java.lang.String status_variable_name

• sample_with_replacement

  private boolean sample_with_replacement

• unordered_variable_names

  private java.util.Vector<java.lang.String> unordered_variable_names

• memory_saving_splitting

  private boolean memory_saving_splitting

• splitrule

  private StochasticForests.SplitRule splitrule

• case_weights_file

  private java.lang.String case_weights_file

• predict_all

  private boolean predict_all

• sample_fraction

  private double sample_fraction

• alpha

  private double alpha

• minprop

  private double minprop

• holdout

  private boolean holdout

• prediction_type

  private StochasticForests.PredictionType prediction_type

• num_random_splits

  private int num_random_splits

• write

  private boolean write

Constructor Detail

• StochasticForests

  public StochasticForests()

• StochasticForests

  public StochasticForests​(StochasticForests.TreeType treetype,
                           boolean probability,
                           boolean verbose_out,
                           java.lang.String dependent_variable_name,
                           StochasticForests.MemoryMode memory_mode,
                           java.lang.String input_file,
                           int mtry,
                           java.lang.String output_prefix,
                           int num_trees,
                           long seed,
                           int num_threads,
                           java.lang.String load_forest_filename,
                           StochasticForests.ImportanceMode importance_mode,
                           int min_node_size,
                           java.lang.String split_select_weights_file,
                           java.util.Vector<java.lang.String> always_split_variable_names,
                           java.lang.String status_variable_name,
                           boolean sample_with_replacement,
                           java.util.Vector<java.lang.String> unordered_variable_names,
                           boolean memory_saving_splitting,
                           StochasticForests.SplitRule splitrule,
                           java.lang.String case_weights_file,
                           boolean predict_all,
                           double sample_fraction,
                           double alpha,
                           double minprop,
                           boolean holdout,
                           StochasticForests.PredictionType prediction_type,
                           int num_random_splits,
                           boolean write)

Method Detail

• order

  private java.util.Vector<java.lang.Integer> order​(java.util.Vector<java.lang.Double> x,
                                                    boolean decreasing)

• rank

  java.util.Vector<java.lang.Double> rank​(java.util.Vector<java.lang.Double> values)

  Sample ranks starting from 1. Ties are given the average rank.

  Parameters:

  values - Values to rank

  Returns:

  Ranks of input values

• roundToNextMultiple

  private int roundToNextMultiple​(int value,
                                  int multiple)

• shuffle

  private void shuffle​(java.util.Vector<java.lang.Integer> v,
                       java.util.Random random)

• equalSplit

  private void equalSplit​(java.util.Vector<java.lang.Integer> result,
                          int start,
                          int end,
                          int num_parts)

• loadDoubleVectorFromFile

  void loadDoubleVectorFromFile​(java.util.Vector<java.lang.Double> result,
                                java.lang.String filename)

• drawWithoutReplacementSkip

  private void drawWithoutReplacementSkip​(java.util.Vector<java.lang.Integer> result,
                                          java.util.Random random,
                                          int max,
                                          java.util.Vector<java.lang.Integer> skip,
                                          int num_samples)

• drawWithoutReplacementSimple

  private void drawWithoutReplacementSimple​(java.util.Vector<java.lang.Integer> result,
                                            java.util.Random random,
                                            int max,
                                            java.util.Vector<java.lang.Integer> skip,
                                            int num_samples)

• drawWithoutReplacementFisherYates

  private void drawWithoutReplacementFisherYates​(java.util.Vector<java.lang.Integer> result,
                                                 java.util.Random random,
                                                 int max,
                                                 java.util.Vector<java.lang.Integer> skip,
                                                 int num_samples)

• drawWithoutReplacementWeighted

  private void drawWithoutReplacementWeighted​(java.util.Vector<java.lang.Integer> result,
                                              java.util.Random random,
                                              java.util.Vector<java.lang.Integer> indices,
                                              int num_samples,
                                              java.util.Vector<java.lang.Double> weights)

• drawWithoutReplacementWeighted

  private void drawWithoutReplacementWeighted​(java.util.Vector<java.lang.Integer> result,
                                              java.util.Random random,
                                              int max_index,
                                              int num_samples,
                                              java.util.Vector<java.lang.Double> weights)

• mostFrequentClass

  private int mostFrequentClass​(java.util.Vector<java.lang.Integer> class_count,
                                java.util.Random random)

  Returns the most frequent class index of a vector with counts for the classes. Returns a random class if counts are equal.

  Parameters:

  class_count - Vector with class counts

  random_number_generator - Random number generator

  Returns:

  Most frequent class index. Out of range index if all 0.

• mostFrequentDClass

  private int mostFrequentDClass​(java.util.Vector<java.lang.Double> class_count,
                                 java.util.Random random)

  Returns the most frequent class index of a vector with counts for the classes. Returns a random class if counts are equal.

  Parameters:

  class_count - Vector with class counts

  random_number_generator - Random number generator

  Returns:

  Most frequent class index. Out of range index if all 0.

• mostFrequentValue

  private double mostFrequentValue​(java.util.HashMap<java.lang.Double,​java.lang.Integer> class_count,
                                   java.util.Random random)

• computeConcordanceIndex

  private double computeConcordanceIndex​(StochasticForests.Data data,
                                         java.util.Vector<java.lang.Double> sum_chf,
                                         int dependent_varID,
                                         int status_varID,
                                         java.util.Vector<java.lang.Integer> sample_IDs)

• uintToString

  private java.lang.String uintToString​(int number)

• beautifyTime

  private java.lang.String beautifyTime​(int seconds)

• splitString

  private void splitString​(java.util.Vector<java.lang.String> result,
                           java.lang.String input,
                           java.lang.String split_string)

• shuffleAndSplit

  private void shuffleAndSplit​(java.util.Vector<java.lang.Integer> first_part,
                               java.util.Vector<java.lang.Integer> second_part,
                               int n_all,
                               int n_first,
                               java.util.Random random)

• shuffleAndSplitAppend

  private void shuffleAndSplitAppend​(java.util.Vector<java.lang.Integer> first_part,
                                     java.util.Vector<java.lang.Integer> second_part,
                                     int n_all,
                                     int n_first,
                                     java.util.Vector<java.lang.Integer> mapping,
                                     java.util.Random random)

• checkUnorderedVariables

  private java.lang.String checkUnorderedVariables​(StochasticForests.Data data,
                                                   java.util.Vector<java.lang.String> unordered_variable_names)

• checkPositiveIntegers

  private boolean checkPositiveIntegers​(java.util.Vector<java.lang.Double> all_values)

• maxstatPValueLau92

  private double maxstatPValueLau92​(double b,
                                    double minprop,
                                    double maxprop)

• maxstatPValueLau94

  private double maxstatPValueLau94​(double b,
                                    double minprop,
                                    double maxprop,
                                    int N,
                                    java.util.Vector<java.lang.Integer> m)

• maxstatPValueUnadjusted

  private double maxstatPValueUnadjusted​(double b)

• dstdnorm

  private double dstdnorm​(double x)

• pstdnorm

  private double pstdnorm​(double x)

• erf

  private double erf​(double x)

• adjustPvalues

  private java.util.Vector<java.lang.Double> adjustPvalues​(java.util.Vector<java.lang.Double> unadjusted_pvalues)

• logrankScores

  private java.util.Vector<java.lang.Double> logrankScores​(java.util.Vector<java.lang.Double> time,
                                                           java.util.Vector<java.lang.Double> status)

• maxstat

  private void maxstat​(java.util.Vector<java.lang.Double> scores,
                       java.util.Vector<java.lang.Double> x,
                       java.util.Vector<java.lang.Integer> indices,
                       double[] best_maxstat,
                       double[] best_split_value,
                       double minprop,
                       double maxprop)

• numSamplesLeftOfCutpoint

  private java.util.Vector<java.lang.Integer> numSamplesLeftOfCutpoint​(java.util.Vector<java.lang.Double> x,
                                                                       java.util.Vector<java.lang.Integer> indices)

• saveVector1D

  private void saveVector1D​(java.util.Vector<java.lang.Integer> vector,
                            java.io.BufferedWriter bw)

  Write a 1d vector to filestream. First the size is written, then all vector elements.

  Parameters:

  vector - Vector of type T to save

  file - ofstream object to write to.

• saveBVector1D

  private void saveBVector1D​(java.util.Vector<java.lang.Boolean> vector,
                             java.io.BufferedWriter bw)

  Write a 1d vector to filestream. First the size is written, then all vector elements.

  Parameters:

  vector - Vector of type T to save

  file - ofstream object to write to.

• readVector1D

  private void readVector1D​(java.util.Vector<java.lang.Integer> result,
                            java.io.BufferedReader br)

  Read a 1d vector written by saveVector1D() from filestream.

  Parameters:

  result - Result vector with elements of type T.

  file - ifstream object to read from.

• readBVector1D

  private void readBVector1D​(java.util.Vector<java.lang.Boolean> result,
                             java.io.BufferedReader br)

  Read a 1d vector written by saveVector1D() from filestream.

  Parameters:

  result - Result vector with elements of type T.

  file - ifstream object to read from.

• saveDVector1D

  private void saveDVector1D​(java.util.Vector<java.lang.Double> vector,
                             java.io.BufferedWriter bw)

  Write a 1d vector to filestream. First the size is written, then all vector elements.

  Parameters:

  vector - Vector of type T to save

  file - ofstream object to write to.

• readDVector1D

  private void readDVector1D​(java.util.Vector<java.lang.Double> result,
                             java.io.BufferedReader br)

  Read a 1d vector written by saveVector1D() from filestream.

  Parameters:

  result - Result vector with elements of type T.

  file - ifstream object to read from.

• saveVector2D

  private void saveVector2D​(java.util.Vector<java.util.Vector<java.lang.Integer>> vector,
                            java.io.BufferedWriter bw)

  Write a 2d vector to filestream. First the size of the first dim is written as size_t, then for all inner vectors the size and elements.

  Parameters:

  vector - Vector of vectors of type T to write to file.

  file - ofstream object to write to.

• readVector2D

  private void readVector2D​(java.util.Vector<java.util.Vector<java.lang.Integer>> result,
                            java.io.BufferedReader br)

  Read a 2d vector written by saveVector2D() from filestream.

  Parameters:

  result - Result vector of vectors with elements of type T.

  file - ifstream object to read from.

• saveDVector2D

  private void saveDVector2D​(java.util.Vector<java.util.Vector<java.lang.Double>> vector,
                             java.io.BufferedWriter bw)

  Write a 2d vector to filestream. First the size of the first dim is written as size_t, then for all inner vectors the size and elements.

  Parameters:

  vector - Vector of vectors of type T to write to file.

  file - ofstream object to write to.

• readDVector2D

  private void readDVector2D​(java.util.Vector<java.util.Vector<java.lang.Double>> result,
                             java.io.BufferedReader br)

  Read a 2d vector written by saveVector2D() from filestream.

  Parameters:

  result - Result vector of vectors with elements of type T.

  file - ifstream object to read from.

• equalVectorInteger

  private boolean equalVectorInteger​(java.util.Vector<java.lang.Integer> v1,
                                     java.util.Vector<java.lang.Integer> v2,
                                     java.lang.String str)

• equalVectorVectorInteger

  private boolean equalVectorVectorInteger​(java.util.Vector<java.util.Vector<java.lang.Integer>> v1,
                                           java.util.Vector<java.util.Vector<java.lang.Integer>> v2,
                                           java.lang.String str)

• equalVectorDouble

  private boolean equalVectorDouble​(java.util.Vector<java.lang.Double> v1,
                                    java.util.Vector<java.lang.Double> v2,
                                    java.lang.String str)

• equalVectorVectorDouble

  private boolean equalVectorVectorDouble​(java.util.Vector<java.util.Vector<java.lang.Double>> v1,
                                          java.util.Vector<java.util.Vector<java.lang.Double>> v2,
                                          java.lang.String str)

• expectNear

  private boolean expectNear​(double val1,
                             double val2,
                             double error,
                             java.lang.String str)

• runAlgorithm

  public void runAlgorithm()

  Description copied from class: AlgorithmBase
  Actually runs the algorithm. Implemented by inheriting algorithms.

  Specified by:

  runAlgorithm in class AlgorithmBase