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## weka.experiment
Class PairedTTester

    java.lang.Object
      weka.experiment.PairedTTester

All Implemented Interfaces:
  java.io.Serializable, OptionHandler, RevisionHandler, Tester

Direct Known Subclasses:
  PairedCorrectedTTester

    public class PairedTTester

extends java.lang.Object
implements OptionHandler, Tester, RevisionHandler

Calculates T-Test statistics on data stored in a set of instances.

Valid options are:

     -D <index,index2-index4,...>
      Specify list of columns that specify a unique
      dataset.
      First and last are valid indexes. (default none)

     -R <index>
      Set the index of the column containing the run number

     -F <index>
      Set the index of the column containing the fold number

     -G <index1,index2-index4,...>
      Specify list of columns that specify a unique
      'result generator' (eg: classifier name and options).
      First and last are valid indexes. (default none)

     -S <significance level>
      Set the significance level for comparisons (default 0.05)

     -V
      Show standard deviations

     -L
      Produce table comparisons in Latex table format

     -csv
      Produce table comparisons in CSV table format

     -html
      Produce table comparisons in HTML table format

     -significance
      Produce table comparisons with only the significance values

     -gnuplot
      Produce table comparisons output suitable for GNUPlot

Version:
  $Revision: 6431 $
Author:
  Len Trigg (trigg@cs.waikato.ac.nz)
See Also:
  Serialized Form

Constructor Summary
`PairedTTester()`

Method Summary
`void` | `assign(Tester tester)` retrieves all the settings from the given Tester
`PairedStats` | `calculateStatistics(Instance datasetSpecifier, int resultset1Index, int resultset2Index, int comparisonColumn)` Computes a paired t-test comparison for a specified dataset between two resultsets.
`boolean` | `displayResultset(int index)` Checks whether the resultset with the given index shall be displayed.
`Range` | `getDatasetKeyColumns()` Get the value of DatasetKeyColumns.
`int[]` | `getDisplayedResultsets()` Gets the indices of the the datasets that are displayed (if `null` then all are displayed).
`java.lang.String` | `getDisplayName()` returns the name of the tester
`int` | `getFoldColumn()` Get the value of FoldColumn.
`Instances` | `getInstances()` Get the value of Instances.
`int` | `getNumDatasets()` Gets the number of datasets in the resultsets
`int` | `getNumResultsets()` Gets the number of resultsets in the data.
`java.lang.String[]` | `getOptions()` Gets current settings of the PairedTTester.
`ResultMatrix` | `getResultMatrix()` Gets the instance that produces the output.
`Range` | `getResultsetKeyColumns()` Get the value of ResultsetKeyColumns.
`java.lang.String` | `getResultsetName(int index)` Gets a string descriptive of the specified resultset.
`java.lang.String` | `getRevision()` Returns the revision string.
`int` | `getRunColumn()` Get the value of RunColumn.
`boolean` | `getShowStdDevs()` Returns true if standard deviations have been requested.
`double` | `getSignificanceLevel()` Get the value of SignificanceLevel.
`int` | `getSortColumn()` Returns the column to sort on, -1 means the default sorting.
`java.lang.String` | `getSortColumnName()` Returns the name of the column to sort on.
`java.lang.String` | `getToolTipText()` returns a string that is displayed as tooltip on the "perform test" button in the experimenter
`java.lang.String` | `header(int comparisonColumn)` Creates a "header" string describing the current resultsets.
`java.util.Enumeration` | `listOptions()` Lists options understood by this object.
`static void` | `main(java.lang.String[] args)` Test the class from the command line.
`java.lang.String` | `multiResultsetFull(int baseResultset, int comparisonColumn)` Creates a comparison table where a base resultset is compared to the other resultsets.
`java.lang.String` | `multiResultsetRanking(int comparisonColumn)` returns a ranking of the resultsets
`java.lang.String` | `multiResultsetSummary(int comparisonColumn)` Carries out a comparison between all resultsets, counting the number of datsets where one resultset outperforms the other.
`int[][]` | `multiResultsetWins(int comparisonColumn, int[][] nonSigWin)` Carries out a comparison between all resultsets, counting the number of datsets where one resultset outperforms the other.
`java.lang.String` | `resultsetKey()` Creates a key that maps resultset numbers to their descriptions.
`void` | `setDatasetKeyColumns(Range newDatasetKeyColumns)` Set the value of DatasetKeyColumns.
`void` | `setDisplayedResultsets(int[] cols)` Sets the indicies of the datasets to display (`null` means all).
`void` | `setFoldColumn(int newFoldColumn)` Set the value of FoldColumn.
`void` | `setInstances(Instances newInstances)` Set the value of Instances.
`void` | `setOptions(java.lang.String[] options)` Parses a given list of options.
`void` | `setResultMatrix(ResultMatrix matrix)` Sets the matrix to use to produce the output.
`void` | `setResultsetKeyColumns(Range newResultsetKeyColumns)` Set the value of ResultsetKeyColumns.
`void` | `setRunColumn(int newRunColumn)` Set the value of RunColumn.
`void` | `setShowStdDevs(boolean s)` Set whether standard deviations are displayed or not.
`void` | `setSignificanceLevel(double newSignificanceLevel)` Set the value of SignificanceLevel.
`void` | `setSortColumn(int newSortColumn)` Set the column to sort on, -1 means the default sorting.

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

Constructor Detail

### PairedTTester

    public PairedTTester()

Method Detail

### setResultMatrix

    public void setResultMatrix(ResultMatrix matrix)

  Sets the matrix to use to produce the output.

  Specified by:
    `setResultMatrix` in interface `Tester`
  Parameters:
    `matrix` - the instance to use to produce the output
  See Also:
    `ResultMatrix`

### getResultMatrix

    public ResultMatrix getResultMatrix()

  Gets the instance that produces the output.

  Specified by:
    `getResultMatrix` in interface `Tester`
  Returns:
    the instance to produce the output

### setShowStdDevs

    public void setShowStdDevs(boolean s)

  Set whether standard deviations are displayed or not.

  Specified by:
    `setShowStdDevs` in interface `Tester`
  Parameters:
    `s` - true if standard deviations are to be displayed

### getShowStdDevs

    public boolean getShowStdDevs()

  Returns true if standard deviations have been requested.

  Specified by:
    `getShowStdDevs` in interface `Tester`
  Returns:
    true if standard deviations are to be displayed.

### getNumDatasets

    public int getNumDatasets()

  Gets the number of datasets in the resultsets

  Specified by:
    `getNumDatasets` in interface `Tester`
  Returns:
    the number of datasets in the resultsets

### getNumResultsets

    public int getNumResultsets()

  Gets the number of resultsets in the data.

  Specified by:
    `getNumResultsets` in interface `Tester`
  Returns:
    the number of resultsets in the data

### getResultsetName

    public java.lang.String getResultsetName(int index)

  Gets a string descriptive of the specified resultset.

  Specified by:
    `getResultsetName` in interface `Tester`
  Parameters:
    `index` - the index of the resultset
  Returns:
    a descriptive string for the resultset

### displayResultset

    public boolean displayResultset(int index)

  Checks whether the resultset with the given index shall be displayed.

  Specified by:
    `displayResultset` in interface `Tester`
  Parameters:
    `index` - the index of the resultset to check whether it shall be displayed
  Returns:
    whether the specified resultset is displayed

### calculateStatistics

    public PairedStats calculateStatistics(Instance datasetSpecifier,
                                           int resultset1Index,
                                           int resultset2Index,
                                           int comparisonColumn)
                                    throws java.lang.Exception

  Computes a paired t-test comparison for a specified dataset between two resultsets.

  Specified by:
    `calculateStatistics` in interface `Tester`
  Parameters:
    `datasetSpecifier` - the dataset specifier
    `resultset1Index` - the index of the first resultset
    `resultset2Index` - the index of the second resultset
    `comparisonColumn` - the column containing values to compare
  Returns:
    the results of the paired comparison
  Throws:
    `java.lang.Exception` - if an error occurs

### resultsetKey

    public java.lang.String resultsetKey()

  Creates a key that maps resultset numbers to their descriptions.

  Specified by:
    `resultsetKey` in interface `Tester`
  Returns:
    a value of type 'String'

### header

    public java.lang.String header(int comparisonColumn)

  Creates a "header" string describing the current resultsets.

  Specified by:
    `header` in interface `Tester`
  Parameters:
    `comparisonColumn` - a value of type 'int'
  Returns:
    a value of type 'String'

### multiResultsetWins

    public int[][] multiResultsetWins(int comparisonColumn,
                                      int[][] nonSigWin)
                               throws java.lang.Exception

  Carries out a comparison between all resultsets, counting the number of datsets where one resultset outperforms the other.

  Specified by:
    `multiResultsetWins` in interface `Tester`
  Parameters:
    `comparisonColumn` - the index of the comparison column
    `nonSigWin` - for storing the non-significant wins
  Returns:
    a 2d array where element [i][j] is the number of times resultset j performed significantly better than resultset i.
  Throws:
    `java.lang.Exception` - if an error occurs

### multiResultsetSummary

    public java.lang.String multiResultsetSummary(int comparisonColumn)
                                           throws java.lang.Exception

  Carries out a comparison between all resultsets, counting the number of datsets where one resultset outperforms the other. The results are summarized in a table.

  Specified by:
    `multiResultsetSummary` in interface `Tester`
  Parameters:
    `comparisonColumn` - the index of the comparison column
  Returns:
    the results in a string
  Throws:
    `java.lang.Exception` - if an error occurs

### multiResultsetRanking

    public java.lang.String multiResultsetRanking(int comparisonColumn)
                                           throws java.lang.Exception

  returns a ranking of the resultsets

  Specified by:
    `multiResultsetRanking` in interface `Tester`
  Parameters:
    `comparisonColumn` - the column to compare with
  Returns:
    the ranking
  Throws:
    `java.lang.Exception` - if something goes wrong

### multiResultsetFull

    public java.lang.String multiResultsetFull(int baseResultset,
                                               int comparisonColumn)
                                        throws java.lang.Exception

  Creates a comparison table where a base resultset is compared to the other resultsets. Results are presented for every dataset.

  Specified by:
    `multiResultsetFull` in interface `Tester`
  Parameters:
    `baseResultset` - the index of the base resultset
    `comparisonColumn` - the index of the column to compare over
  Returns:
    the comparison table string
  Throws:
    `java.lang.Exception` - if an error occurs

### listOptions

    public java.util.Enumeration listOptions()

  Lists options understood by this object.

  Specified by:
    `listOptions` in interface `OptionHandler`
  Returns:
    an enumeration of Options.

### setOptions

    public void setOptions(java.lang.String[] options)
                    throws java.lang.Exception

  Parses a given list of options.

  Valid options are:

       -D <index,index2-index4,...>
        Specify list of columns that specify a unique
        dataset.
        First and last are valid indexes. (default none)

       -R <index>
        Set the index of the column containing the run number

       -F <index>
        Set the index of the column containing the fold number

       -G <index1,index2-index4,...>
        Specify list of columns that specify a unique
        'result generator' (eg: classifier name and options).
        First and last are valid indexes. (default none)

       -S <significance level>
        Set the significance level for comparisons (default 0.05)

       -V
        Show standard deviations

       -L
        Produce table comparisons in Latex table format

       -csv
        Produce table comparisons in CSV table format

       -html
        Produce table comparisons in HTML table format

       -significance
        Produce table comparisons with only the significance values

       -gnuplot
        Produce table comparisons output suitable for GNUPlot

  Specified by:
    `setOptions` in interface `OptionHandler`
  Parameters:
    `options` - an array containing options to set.
  Throws:
    `java.lang.Exception` - if invalid options are given

### getOptions

    public java.lang.String[] getOptions()

  Gets current settings of the PairedTTester.

  Specified by:
    `getOptions` in interface `OptionHandler`
  Returns:
    an array of strings containing current options.

### getResultsetKeyColumns

    public Range getResultsetKeyColumns()

  Get the value of ResultsetKeyColumns.

  Specified by:
    `getResultsetKeyColumns` in interface `Tester`
  Returns:
    Value of ResultsetKeyColumns.

### setResultsetKeyColumns

    public void setResultsetKeyColumns(Range newResultsetKeyColumns)

  Set the value of ResultsetKeyColumns.

  Specified by:
    `setResultsetKeyColumns` in interface `Tester`
  Parameters:
    `newResultsetKeyColumns` - Value to assign to ResultsetKeyColumns.

### getDisplayedResultsets

    public int[] getDisplayedResultsets()

  Gets the indices of the the datasets that are displayed (if `null` then all are displayed). The base is always displayed.

  Specified by:
    `getDisplayedResultsets` in interface `Tester`
  Returns:
    the indices of the datasets to display

### setDisplayedResultsets

    public void setDisplayedResultsets(int[] cols)

  Sets the indicies of the datasets to display (`null` means all). The base is always displayed.

  Specified by:
    `setDisplayedResultsets` in interface `Tester`
  Parameters:
    `cols` - the indices of the datasets to display

### getSignificanceLevel

    public double getSignificanceLevel()

  Get the value of SignificanceLevel.

  Specified by:
    `getSignificanceLevel` in interface `Tester`
  Returns:
    Value of SignificanceLevel.

### setSignificanceLevel

    public void setSignificanceLevel(double newSignificanceLevel)

  Set the value of SignificanceLevel.

  Specified by:
    `setSignificanceLevel` in interface `Tester`
  Parameters:
    `newSignificanceLevel` - Value to assign to SignificanceLevel.

### getDatasetKeyColumns

    public Range getDatasetKeyColumns()

  Get the value of DatasetKeyColumns.

  Specified by:
    `getDatasetKeyColumns` in interface `Tester`
  Returns:
    Value of DatasetKeyColumns.

### setDatasetKeyColumns

    public void setDatasetKeyColumns(Range newDatasetKeyColumns)

  Set the value of DatasetKeyColumns.

  Specified by:
    `setDatasetKeyColumns` in interface `Tester`
  Parameters:
    `newDatasetKeyColumns` - Value to assign to DatasetKeyColumns.

### getRunColumn

    public int getRunColumn()

  Get the value of RunColumn.

  Specified by:
    `getRunColumn` in interface `Tester`
  Returns:
    Value of RunColumn.

### setRunColumn

    public void setRunColumn(int newRunColumn)

  Set the value of RunColumn.

  Specified by:
    `setRunColumn` in interface `Tester`
  Parameters:
    `newRunColumn` - Value to assign to RunColumn.

### getFoldColumn

    public int getFoldColumn()

  Get the value of FoldColumn.

  Specified by:
    `getFoldColumn` in interface `Tester`
  Returns:
    Value of FoldColumn.

### setFoldColumn

    public void setFoldColumn(int newFoldColumn)

  Set the value of FoldColumn.

  Specified by:
    `setFoldColumn` in interface `Tester`
  Parameters:
    `newFoldColumn` - Value to assign to FoldColumn.

### getSortColumnName

    public java.lang.String getSortColumnName()

  Returns the name of the column to sort on.

  Specified by:
    `getSortColumnName` in interface `Tester`
  Returns:
    the name of the column to sort on.

### getSortColumn

    public int getSortColumn()

  Returns the column to sort on, -1 means the default sorting.

  Specified by:
    `getSortColumn` in interface `Tester`
  Returns:
    the column to sort on.

### setSortColumn

    public void setSortColumn(int newSortColumn)

  Set the column to sort on, -1 means the default sorting.

  Specified by:
    `setSortColumn` in interface `Tester`
  Parameters:
    `newSortColumn` - the new sort column.

### getInstances

    public Instances getInstances()

  Get the value of Instances.

  Specified by:
    `getInstances` in interface `Tester`
  Returns:
    Value of Instances.

### setInstances

    public void setInstances(Instances newInstances)

  Set the value of Instances.

  Specified by:
    `setInstances` in interface `Tester`
  Parameters:
    `newInstances` - Value to assign to Instances.

### assign

    public void assign(Tester tester)

  retrieves all the settings from the given Tester

  Specified by:
    `assign` in interface `Tester`
  Parameters:
    `tester` - the Tester to get the settings from

### getToolTipText

    public java.lang.String getToolTipText()

  returns a string that is displayed as tooltip on the "perform test" button in the experimenter

  Specified by:
    `getToolTipText` in interface `Tester`
  Returns:
    the tool tip

### getDisplayName

    public java.lang.String getDisplayName()

  returns the name of the tester

  Specified by:
    `getDisplayName` in interface `Tester`
  Returns:
    the display name

### getRevision

    public java.lang.String getRevision()

  Returns the revision string.

  Specified by:
    `getRevision` in interface `RevisionHandler`
  Returns:
    the revision

### main

    public static void main(java.lang.String[] args)

  Test the class from the command line.

  Parameters:
    `args` - contains options for the instance ttests

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