PLSFilter

java.lang.Object
- weka.filters.Filter
- - weka.filters.SimpleFilter
  - - weka.filters.SimpleBatchFilter
    - - weka.filters.supervised.attribute.PLSFilter

All Implemented Interfaces:: java.io.Serializable, CapabilitiesHandler, OptionHandler, RevisionHandler, TechnicalInformationHandler, SupervisedFilter

public class PLSFilter
extends SimpleBatchFilter
implements SupervisedFilter, TechnicalInformationHandler

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.

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: 5541 $
Author:: FracPete (fracpete at waikato dot ac dot nz)
See Also:: Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`ALGORITHM_PLS1` the type of algorithm: PLS1
`static int`	`ALGORITHM_SIMPLS` the type of algorithm: SIMPLS
`static int`	`PREPROCESSING_CENTER` the type of preprocessing: Center
`static int`	`PREPROCESSING_NONE` the type of preprocessing: None
`static int`	`PREPROCESSING_STANDARDIZE` the type of preprocessing: Standardize
`static Tag[]`	`TAGS_ALGORITHM` the types of algorithm
`static Tag[]`	`TAGS_PREPROCESSING` the types of preprocessing

Constructor Summary

Constructors
Constructor and Description

PLSFilter()
default constructor

Constructors
Constructor and Description
`PLSFilter()` default constructor

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.lang.String`	`algorithmTipText()` Returns the tip text for this property
`SelectedTag`	`getAlgorithm()` Gets the type of algorithm to use
`Capabilities`	`getCapabilities()` Returns the Capabilities of this filter.
`int`	`getNumComponents()` returns the maximum number of attributes to use.
`java.lang.String[]`	`getOptions()` returns the options of the current setup
`boolean`	`getPerformPrediction()` Gets whether the class attribute is updated with the predicted value.
`SelectedTag`	`getPreprocessing()` Gets the type of preprocessing to use
`boolean`	`getReplaceMissing()` Gets whether missing values are replace.
`java.lang.String`	`getRevision()` Returns the revision string.
`TechnicalInformation`	`getTechnicalInformation()` Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
`java.lang.String`	`globalInfo()` Returns a string describing this classifier.
`java.util.Enumeration`	`listOptions()` Gets an enumeration describing the available options.
`static void`	`main(java.lang.String[] args)` runs the filter with the given arguments.
`java.lang.String`	`numComponentsTipText()` Returns the tip text for this property
`java.lang.String`	`performPredictionTipText()` Returns the tip text for this property
`java.lang.String`	`preprocessingTipText()` Returns the tip text for this property
`java.lang.String`	`replaceMissingTipText()` Returns the tip text for this property
`void`	`setAlgorithm(SelectedTag value)` Sets the type of algorithm to use
`void`	`setNumComponents(int value)` sets the maximum number of attributes to use.
`void`	`setOptions(java.lang.String[] options)` Parses the options for this object.
`void`	`setPerformPrediction(boolean value)` Sets whether to update the class attribute with the predicted value.
`void`	`setPreprocessing(SelectedTag value)` Sets the type of preprocessing to use
`void`	`setReplaceMissing(boolean value)` Sets whether to replace missing values.

Methods inherited from class weka.filters.SimpleBatchFilter
batchFinished, input

Methods inherited from class weka.filters.SimpleFilter
debugTipText, getDebug, setDebug, setInputFormat

Methods inherited from class weka.filters.Filter
batchFilterFile, filterFile, getCapabilities, getOutputFormat, isFirstBatchDone, isNewBatch, isOutputFormatDefined, makeCopies, makeCopy, numPendingOutput, output, outputPeek, toString, useFilter, wekaStaticWrapper

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - ALGORITHM_SIMPLS
```
public static final int ALGORITHM_SIMPLS
```
    the type of algorithm: SIMPLS
    
    See Also:
    
    Constant Field Values
  - ALGORITHM_PLS1
```
public static final int ALGORITHM_PLS1
```
    the type of algorithm: PLS1
    
    See Also:
    
    Constant Field Values
  - TAGS_ALGORITHM
```
public static final Tag[] TAGS_ALGORITHM
```
    the types of algorithm
  - PREPROCESSING_NONE
```
public static final int PREPROCESSING_NONE
```
    the type of preprocessing: None
    
    See Also:
    
    Constant Field Values
  - PREPROCESSING_CENTER
```
public static final int PREPROCESSING_CENTER
```
    the type of preprocessing: Center
    
    See Also:
    
    Constant Field Values
  - PREPROCESSING_STANDARDIZE
```
public static final int PREPROCESSING_STANDARDIZE
```
    the type of preprocessing: Standardize
    
    See Also:
    
    Constant Field Values
  - TAGS_PREPROCESSING
```
public static final Tag[] TAGS_PREPROCESSING
```
    the types of preprocessing
- Constructor Detail
  - PLSFilter
```
public PLSFilter()
```
    default constructor
- Method Detail
  - globalInfo
```
public java.lang.String globalInfo()
```
    Returns a string describing this classifier.
    
    Specified by:
    
    globalInfo in class SimpleFilter
    
    Returns:
    
    a description of the classifier suitable for displaying in the explorer/experimenter gui
  - getTechnicalInformation
```
public TechnicalInformation getTechnicalInformation()
```
    Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
    
    Specified by:
    
    getTechnicalInformation in interface TechnicalInformationHandler
    
    Returns:
    
    the technical information about this class
  - listOptions
```
public java.util.Enumeration listOptions()
```
    Gets an enumeration describing the available options.
    
    Specified by:
    
    listOptions in interface OptionHandler
    
    Overrides:
    
    listOptions in class SimpleFilter
    
    Returns:
    
    an enumeration of all the available options.
  - getOptions
```
public java.lang.String[] getOptions()
```
    returns the options of the current setup
    
    Specified by:
    
    getOptions in interface OptionHandler
    
    Overrides:
    
    getOptions in class SimpleFilter
    
    Returns:
    
    the current options
  - setOptions
```
public void setOptions(java.lang.String[] options)
                throws java.lang.Exception
```
    Parses the options for this object.
    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)
```
    Specified by:
    
    setOptions in interface OptionHandler
    
    Overrides:
    
    setOptions in class SimpleFilter
    
    Parameters:
    
    options - the options to use
    
    Throws:
    
    java.lang.Exception - if the option setting fails
    
    See Also:
    
    SimpleFilter.reset()
  - numComponentsTipText
```
public java.lang.String numComponentsTipText()
```
    Returns the tip text for this property
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - setNumComponents
```
public void setNumComponents(int value)
```
    sets the maximum number of attributes to use.
    
    Parameters:
    
    value - the maximum number of attributes
  - getNumComponents
```
public int getNumComponents()
```
    returns the maximum number of attributes to use.
    
    Returns:
    
    the current maximum number of attributes
  - performPredictionTipText
```
public java.lang.String performPredictionTipText()
```
    Returns the tip text for this property
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - setPerformPrediction
```
public void setPerformPrediction(boolean value)
```
    Sets whether to update the class attribute with the predicted value.
    
    Parameters:
    
    value - if true the class value will be replaced by the predicted value.
  - getPerformPrediction
```
public boolean getPerformPrediction()
```
    Gets whether the class attribute is updated with the predicted value.
    
    Returns:
    
    true if the class attribute is updated
  - algorithmTipText
```
public java.lang.String algorithmTipText()
```
    Returns the tip text for this property
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - setAlgorithm
```
public void setAlgorithm(SelectedTag value)
```
    Sets the type of algorithm to use
    
    Parameters:
    
    value - the algorithm type
  - getAlgorithm
```
public SelectedTag getAlgorithm()
```
    Gets the type of algorithm to use
    
    Returns:
    
    the current algorithm type.
  - replaceMissingTipText
```
public java.lang.String replaceMissingTipText()
```
    Returns the tip text for this property
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - setReplaceMissing
```
public void setReplaceMissing(boolean value)
```
    Sets whether to replace missing values.
    
    Parameters:
    
    value - if true missing values are replaced with the ReplaceMissingValues filter.
  - getReplaceMissing
```
public boolean getReplaceMissing()
```
    Gets whether missing values are replace.
    
    Returns:
    
    true if missing values are replaced with the ReplaceMissingValues filter
  - preprocessingTipText
```
public java.lang.String preprocessingTipText()
```
    Returns the tip text for this property
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - setPreprocessing
```
public void setPreprocessing(SelectedTag value)
```
    Sets the type of preprocessing to use
    
    Parameters:
    
    value - the preprocessing type
  - getPreprocessing
```
public SelectedTag getPreprocessing()
```
    Gets the type of preprocessing to use
    
    Returns:
    
    the current preprocessing type.
  - getCapabilities
```
public Capabilities getCapabilities()
```
    Returns the Capabilities of this filter.
    
    Specified by:
    
    getCapabilities in interface CapabilitiesHandler
    
    Overrides:
    
    getCapabilities in class Filter
    
    Returns:
    
    the capabilities of this object
    
    See Also:
    
    Capabilities
  - getRevision
```
public java.lang.String getRevision()
```
    Returns the revision string.
    
    Specified by:
    
    getRevision in interface RevisionHandler
    
    Overrides:
    
    getRevision in class Filter
    
    Returns:
    
    the revision
  - main
```
public static void main(java.lang.String[] args)
```
    runs the filter with the given arguments.
    
    Parameters:
    
    args - the commandline arguments

Class PLSFilter

Field Summary

Constructor Summary

Method Summary

Methods inherited from class weka.filters.SimpleBatchFilter

Methods inherited from class weka.filters.SimpleFilter

Methods inherited from class weka.filters.Filter

Methods inherited from class java.lang.Object

Field Detail

ALGORITHM_SIMPLS

ALGORITHM_PLS1

TAGS_ALGORITHM

PREPROCESSING_NONE

PREPROCESSING_CENTER

PREPROCESSING_STANDARDIZE

TAGS_PREPROCESSING

Constructor Detail

PLSFilter

Method Detail

globalInfo

getTechnicalInformation

listOptions

getOptions

setOptions

numComponentsTipText

setNumComponents

getNumComponents

performPredictionTipText

setPerformPrediction

getPerformPrediction

algorithmTipText

setAlgorithm

getAlgorithm

replaceMissingTipText

setReplaceMissing

getReplaceMissing

preprocessingTipText

setPreprocessing

getPreprocessing

getCapabilities

getRevision

main