Class SIMPLSMatrixFilterFromGeneticString
- java.lang.Object
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- weka.filters.Filter
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- weka.filters.SimpleFilter
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- weka.filters.SimpleBatchFilter
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- weka.filters.supervised.attribute.PLSFilter
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- weka.filters.supervised.attribute.SIMPLSMatrixFilterFromGeneticString
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- 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 SIMPLSMatrixFilterFromGeneticString 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
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Field Summary
Fields Modifier and Type Field Description static String
BITSTRING
static String
COLUMNS
protected String
m_BitString
protected int
m_Columns
protected double
m_Max
protected double
m_Min
protected int
m_Rows
protected weka.core.matrix.Matrix
m_SIMPLS_MATRIX_LOCAL
protected int
m_Splits
static String
MAX
static String
MIN
static String
ROWS
static String
SPLITS
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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
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Constructor Summary
Constructors Constructor Description SIMPLSMatrixFilterFromGeneticString()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description String
bitstringTipText()
protected int
calcNumBits()
Calculates the number of bits to use.String
columnsTipText()
String
getBitstring()
int
getColumns()
weka.core.matrix.Matrix
getMatrix()
double
getMax()
double
getMin()
String[]
getOptions()
Gets the current option settings for the OptionHandler.int
getRows()
int
getSplits()
String
globalInfo()
Returns a string describing this classifier.void
initialiseW(weka.core.Instances ins)
void
initialiseWeights()
Enumeration
listOptions()
Returns an enumeration describing the available options.static void
main(String[] args)
runs the filter with the given arguments.String
maxTipText()
String
minTipText()
protected weka.core.Instances
processSIMPLS(weka.core.Instances instances)
protected void
reset()
Resets the cleaner.String
rowsTipText()
void
setBitstring(String bits)
void
setColumns(int columns)
void
setMatrix(weka.core.matrix.Matrix m)
void
setMax(double max)
void
setMin(double min)
void
setOptions(String[] options)
Sets the OptionHandler's options using the given list.void
setRows(int rows)
void
setSplits(int splits)
String
splitsTipText()
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Methods inherited from class weka.filters.supervised.attribute.PLSFilter
algorithmTipText, columnAsVector, determineOutputFormat, getAlgorithm, getCapabilities, getDominantEigenVector, getNumComponents, getPerformPrediction, getPreprocessing, getReplaceMissing, getRevision, getTechnicalInformation, getVector, getX, getX, getY, getY, normalizeVector, numComponentsTipText, performPredictionTipText, preprocessingTipText, process, processPLS1, replaceMissingTipText, setAlgorithm, setNumComponents, setPerformPrediction, setPreprocessing, setReplaceMissing, setVector, toInstances
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Methods inherited from class weka.filters.SimpleBatchFilter
allowAccessToFullInputFormat, batchFinished, hasImmediateOutputFormat, input
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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
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Field Detail
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m_SIMPLS_MATRIX_LOCAL
protected weka.core.matrix.Matrix m_SIMPLS_MATRIX_LOCAL
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BITSTRING
public static final String BITSTRING
- See Also:
- Constant Field Values
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m_BitString
protected String m_BitString
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MIN
public static final String MIN
- See Also:
- Constant Field Values
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m_Min
protected double m_Min
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MAX
public static final String MAX
- See Also:
- Constant Field Values
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m_Max
protected double m_Max
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SPLITS
public static final String SPLITS
- See Also:
- Constant Field Values
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m_Splits
protected int m_Splits
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COLUMNS
public static final String COLUMNS
- See Also:
- Constant Field Values
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m_Columns
protected int m_Columns
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ROWS
public static final String ROWS
- See Also:
- Constant Field Values
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m_Rows
protected int m_Rows
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Method Detail
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setBitstring
public void setBitstring(String bits)
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getBitstring
public String getBitstring()
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bitstringTipText
public String bitstringTipText()
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setMin
public void setMin(double min)
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getMin
public double getMin()
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minTipText
public String minTipText()
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setMax
public void setMax(double max)
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getMax
public double getMax()
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maxTipText
public String maxTipText()
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setSplits
public void setSplits(int splits)
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getSplits
public int getSplits()
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splitsTipText
public String splitsTipText()
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setRows
public void setRows(int rows)
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getRows
public int getRows()
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rowsTipText
public String rowsTipText()
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setColumns
public void setColumns(int columns)
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getColumns
public int getColumns()
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columnsTipText
public String columnsTipText()
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initialiseWeights
public void initialiseWeights()
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calcNumBits
protected int calcNumBits()
Calculates the number of bits to use.- Returns:
- the number of bits
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setMatrix
public void setMatrix(weka.core.matrix.Matrix m)
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getMatrix
public weka.core.matrix.Matrix getMatrix()
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processSIMPLS
protected weka.core.Instances processSIMPLS(weka.core.Instances instances) throws Exception
- Overrides:
processSIMPLS
in classweka.filters.supervised.attribute.PLSFilter
- Throws:
Exception
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listOptions
public Enumeration listOptions()
Returns an enumeration describing the available options.- Specified by:
listOptions
in interfaceweka.core.OptionHandler
- Overrides:
listOptions
in classweka.filters.supervised.attribute.PLSFilter
- Returns:
- an enumeration of all the available options.
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setOptions
public void setOptions(String[] options) throws Exception
Sets the OptionHandler's options using the given list. All options will be set (or reset) during this call (i.e. incremental setting of options is not possible).- Specified by:
setOptions
in interfaceweka.core.OptionHandler
- Overrides:
setOptions
in classweka.filters.supervised.attribute.PLSFilter
- Parameters:
options
- the list of options as an array of strings- Throws:
Exception
- if an option is not supported
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getOptions
public String[] getOptions()
Gets the current option settings for the OptionHandler.- Specified by:
getOptions
in interfaceweka.core.OptionHandler
- Overrides:
getOptions
in classweka.filters.supervised.attribute.PLSFilter
- Returns:
- the list of current option settings as an array of strings
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globalInfo
public String globalInfo()
Returns a string describing this classifier.- Overrides:
globalInfo
in classweka.filters.supervised.attribute.PLSFilter
- Returns:
- a description of the classifier suitable for displaying in the explorer/experimenter gui
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reset
protected void reset()
Resets the cleaner.- Overrides:
reset
in classweka.filters.SimpleFilter
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main
public static void main(String[] args)
runs the filter with the given arguments.- Parameters:
args
- the commandline arguments
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