Package adams.data.instancesanalysis.pls

Class OPLS

  • All Implemented Interfaces:
    adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.SizeOfHandler, adams.core.TechnicalInformationHandler, Serializable, weka.core.CapabilitiesHandler, GenericPLSMatrixAccess
    public class OPLS
extends AbstractSingleClassPLS
    Orthogonal Projections to latent structures (O-PLS).

    For more informatio see:
    Johan Trygg, Svante Wold (2001). Orthogonal projections to latent structures (O-PLS). JOURNAL OF CHEMOMETRICS. 16:119-128. URL https://onlinelibrary.wiley.com/doi/pdf/10.1002/cem.695 

     @article{Trygg2001,
    author = {Johan Trygg and Svante Wold},
    journal = {JOURNAL OF CHEMOMETRICS},
    pages = {119-128},
    title = {Orthogonal projections to latent structures (O-PLS)},
    volume = {16},
    year = {2001},
    URL = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/cem.695}
 }
 


    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
    min-user-mode: Expert
 
    -preprocessing-type <NONE|CENTER|STANDARDIZE> (property: preprocessingType)
    The type of preprocessing to perform.
    default: CENTER
 
    -replace-missing <boolean> (property: replaceMissing)
    Whether to replace missing values.
    default: false
 
    -num-components <int> (property: numComponents)
    The number of components to compute.
    default: 20
    minimum: 1
 
    -prediction-type <NONE|ALL|EXCEPT_CLASS> (property: predictionType)
    The type of prediction to perform.
    default: NONE
 
    -base <com.github.waikatodatamining.matrix.algorithm.pls.AbstractPLS> (property: base)
    The base PLS algorithm to use.
    default: com.github.waikatodatamining.matrix.algorithm.pls.PLS1 -debug false -num-components 5 -preprocessing-type NONE
    Author:
    FracPete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Detail

      • m_Base

        protected com.github.waikatodatamining.matrix.algorithm.pls.AbstractPLS m_Base
        the base PLS algorithm.

      • m_OPLS

        protected com.github.waikatodatamining.matrix.algorithm.pls.OPLS m_OPLS
        the actual algorithm.

    • Constructor Detail

      • OPLS

        public OPLS()

    • Method Detail

      • globalInfo

        public String globalInfo()
        Returns a string describing the object.
        Specified by:
        globalInfo in interface adams.core.GlobalInfoSupporter
        Specified by:
        globalInfo in class adams.core.option.AbstractOptionHandler
        Returns:
        a description suitable for displaying in the gui

      • getTechnicalInformation

        public adams.core.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 adams.core.TechnicalInformationHandler
        Specified by:
        getTechnicalInformation in class AbstractPLS
        Returns:
        the technical information about this class

      • defineOptions

        public void defineOptions()
        Adds options to the internal list of options.
        Specified by:
        defineOptions in interface adams.core.option.OptionHandler
        Overrides:
        defineOptions in class AbstractPLS

      • setBase

        public void setBase​(com.github.waikatodatamining.matrix.algorithm.pls.AbstractPLS value)
        Sets the base PLS algorithm to use.
        Parameters:
        value - the base algorithm

      • getBase

        public com.github.waikatodatamining.matrix.algorithm.pls.AbstractPLS getBase()
        Sets the base PLS algorithm to use.
        Returns:
        the base algorithm

      • baseTipText

        public String baseTipText()
        Returns the tip text for this property
        Returns:
        tip text for this property suitable for displaying in the explorer/experimenter gui

      • getMatrix

        public weka.core.matrix.Matrix getMatrix​(String name)
        Returns the matrix with the specified name.
        Specified by:
        getMatrix in interface GenericPLSMatrixAccess
        Specified by:
        getMatrix in class AbstractPLS
        Parameters:
        name - the name of the matrix
        Returns:
        the matrix, null if not available

      • determineOutputFormat

        public weka.core.Instances determineOutputFormat​(weka.core.Instances input)
                                          throws Exception
        Determines the output format based on the input format and returns this.
        Overrides:
        determineOutputFormat in class AbstractSingleClassPLS
        Parameters:
        input - the input format to base the output format on
        Returns:
        the output format
        Throws:
        Exception - in case the determination goes wrong

      • doTransform

        protected weka.core.Instances doTransform​(weka.core.Instances data,
                                          Map<String,​Object> params)
                                   throws Exception
        Transforms the data, initializes if necessary.
        Specified by:
        doTransform in class AbstractPLS
        Parameters:
        data - the data to use
        params - additional parameters
        Returns:
        the transformed data
        Throws:
        Exception