Package weka.filters.supervised.attribute

Class SIMPLSMatrixFilter

  • All Implemented Interfaces:
    Serializable, weka.core.CapabilitiesHandler, weka.core.CapabilitiesIgnorer, weka.core.CommandlineRunnable, weka.core.OptionHandler, weka.core.RevisionHandler, weka.core.TechnicalInformationHandler, weka.filters.SupervisedFilter
    public class SIMPLSMatrixFilter
extends weka.filters.supervised.attribute.PLSFilter
    Runs Partial Least Square Regression over the given instances and computes the resulting beta matrix for prediction.
    By default it replaces missing values and centers the data.

    Allows access to the internal matrices.

    For more information see:

    Tormod Naes, Tomas Isaksson, Tom Fearn, Tony Davies (2002). A User Friendly Guide to Multivariate Calibration and Classification. NIR Publications.

    StatSoft, Inc.. Partial Least Squares (PLS).

    Bent Jorgensen, Yuri Goegebeur. Module 7: Partial least squares regression I.

    S. de Jong (1993). SIMPLS: an alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems. 18:251-263.

    BibTeX: 
     @book{Naes2002,
    author = {Tormod Naes and Tomas Isaksson and Tom Fearn and Tony Davies},
    publisher = {NIR Publications},
    title = {A User Friendly Guide to Multivariate Calibration and Classification},
    year = {2002},
    ISBN = {0-9528666-2-5}
 }
 
 @misc{missing_id,
    author = {StatSoft, Inc.},
    booktitle = {Electronic Textbook StatSoft},
    title = {Partial Least Squares (PLS)},
    HTTP = {http://www.statsoft.com/textbook/stpls.html}
 }
 
 @misc{missing_id,
    author = {Bent Jorgensen and Yuri Goegebeur},
    booktitle = {ST02: Multivariate Data Analysis and Chemometrics},
    title = {Module 7: Partial least squares regression I},
    HTTP = {http://statmaster.sdu.dk/courses/ST02/module07/}
 }
 
 @article{Jong1993,
    author = {S. de Jong},
    journal = {Chemometrics and Intelligent Laboratory Systems},
    pages = {251-263},
    title = {SIMPLS: an alternative approach to partial least squares regression},
    volume = {18},
    year = {1993}
 }


    Valid options are: 

     -D
  Turns on output of debugging information.
     -C <num>
  The number of components to compute.
  (default: 20)
     -U
  Updates the class attribute as well.
  (default: off)
     -M
  Turns replacing of missing values on.
  (default: off)
     -A <SIMPLS|PLS1>
  The algorithm to use.
  (default: PLS1)
     -P <none|center|standardize>
  The type of preprocessing that is applied to the data.
  (default: center)
    Version:
    $Revision: 10824 $
    Author:
    FracPete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected weka.core.matrix.Matrix m_SIMPLS_MATRIX_LOCAL  

      • Fields inherited from class weka.filters.supervised.attribute.PLSFilter

        ALGORITHM_PLS1, ALGORITHM_SIMPLS, m_Algorithm, m_ClassMean, m_ClassStdDev, m_Filter, m_Missing, m_NumComponents, m_PerformPrediction, m_PLS1_b_hat, m_PLS1_P, m_PLS1_RegVector, m_PLS1_W, m_Preprocessing, m_ReplaceMissing, m_SIMPLS_B, m_SIMPLS_W, PREPROCESSING_CENTER, PREPROCESSING_NONE, PREPROCESSING_STANDARDIZE, TAGS_ALGORITHM, TAGS_PREPROCESSING

      • Fields inherited from class weka.filters.Filter

        m_Debug, m_DoNotCheckCapabilities, m_FirstBatchDone, m_InputRelAtts, m_InputStringAtts, m_NewBatch, m_OutputRelAtts, m_OutputStringAtts

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      weka.core.matrix.Matrix getMatrix()  
      String globalInfo()
      Returns a string describing this classifier.
      void initialiseW​(weka.core.Instances ins)  
      void initialiseWeights()  
      static void main​(String[] args)
      runs the filter with the given arguments.
      protected weka.core.Instances processSIMPLS​(weka.core.Instances instances)  
      void setMatrix​(weka.core.matrix.Matrix m)  

      • Methods inherited from class weka.filters.supervised.attribute.PLSFilter

        algorithmTipText, columnAsVector, determineOutputFormat, getAlgorithm, getCapabilities, getDominantEigenVector, getNumComponents, getOptions, getPerformPrediction, getPreprocessing, getReplaceMissing, getRevision, getTechnicalInformation, getVector, getX, getX, getY, getY, listOptions, normalizeVector, numComponentsTipText, performPredictionTipText, preprocessingTipText, process, processPLS1, replaceMissingTipText, setAlgorithm, setNumComponents, setOptions, setPerformPrediction, setPreprocessing, setReplaceMissing, setVector, toInstances

      • Methods inherited from class weka.filters.SimpleBatchFilter

        allowAccessToFullInputFormat, batchFinished, hasImmediateOutputFormat, input

      • Methods inherited from class weka.filters.SimpleFilter

        reset, setInputFormat

      • Methods inherited from class weka.filters.Filter

        batchFilterFile, bufferInput, copyValues, copyValues, debugTipText, doNotCheckCapabilitiesTipText, filterFile, flushInput, getCapabilities, getDebug, getDoNotCheckCapabilities, getInputFormat, getOutputFormat, initInputLocators, initOutputLocators, inputFormatPeek, isFirstBatchDone, isNewBatch, isOutputFormatDefined, makeCopies, makeCopy, mayRemoveInstanceAfterFirstBatchDone, numPendingOutput, output, outputFormatPeek, outputPeek, postExecution, preExecution, push, push, resetQueue, run, runFilter, setDebug, setDoNotCheckCapabilities, setOutputFormat, testInputFormat, toString, useFilter, wekaStaticWrapper

    • Field Detail

      • m_SIMPLS_MATRIX_LOCAL

        protected weka.core.matrix.Matrix m_SIMPLS_MATRIX_LOCAL

    • Constructor Detail

      • SIMPLSMatrixFilter

        public SIMPLSMatrixFilter()

    • Method Detail

      • initialiseWeights

        public void initialiseWeights()

      • initialiseW

        public void initialiseW​(weka.core.Instances ins)
                 throws Exception
        Throws:
        Exception

      • setMatrix

        public void setMatrix​(weka.core.matrix.Matrix m)

      • getMatrix

        public weka.core.matrix.Matrix getMatrix()

      • processSIMPLS

        protected weka.core.Instances processSIMPLS​(weka.core.Instances instances)
                                     throws Exception
        Overrides:
        processSIMPLS in class weka.filters.supervised.attribute.PLSFilter
        Throws:
        Exception

      • globalInfo

        public String globalInfo()
        Returns a string describing this classifier.
        Overrides:
        globalInfo in class weka.filters.supervised.attribute.PLSFilter
        Returns:
        a description of the classifier suitable for displaying in the explorer/experimenter gui

      • main

        public static void main​(String[] args)
        runs the filter with the given arguments.
        Parameters:
        args - the commandline arguments