ContingencyTable

java.lang.Object
- com.lobsterman.JavaGrinders.ContingencyTable

All Implemented Interfaces:

java.lang.Cloneable

Direct Known Subclasses:

DataTable, DominanceTable, InteractionTable
```
public class ContingencyTable
extends java.lang.Object
implements java.lang.Cloneable
```
contains a crosstabulation frequency table and performs a variety of statistics on it, including G-test, Chi-square, mantel, Kendall's Tau, etc.

Field Summary

Fields
Modifier and Type Field and Description

boolean diagonal

int iterated

double itsTotalSum

int MatrixCols

int MatrixRows

int NUM_MAXITERATOR

int PRECISIONMULT

Fields
Modifier and Type	Field and Description
`boolean`	`diagonal`
`int`	`iterated`
`double`	`itsTotalSum`
`int`	`MatrixCols`
`int`	`MatrixRows`
`int`	`NUM_MAXITERATOR`
`int`	`PRECISIONMULT`

Constructor Summary

Constructors
Constructor and Description
`ContingencyTable(double[][] theArray)` standard constructor for the ContingencyTable class
`ContingencyTable(double[][] theArray, boolean diagonal)` standard constructor for the ContingencyTable class
`ContingencyTable(int MatrixCols, int MatrixRows)` standard constructor for the ContingencyTable class
`ContingencyTable(int MatrixCols, int MatrixRows, boolean diagonal)` standard constructor for the ContingencyTable class
`ContingencyTable(int MatrixCols, int MatrixRows, boolean diagonal, java.lang.String theName)` standard constructor for the ContingencyTable class
`ContingencyTable(int MatrixCols, int MatrixRows, java.lang.String theName)` standard constructor for the ContingencyTable class
`ContingencyTable(com.lobsterman.JavaGrinders.Jama.Matrix aMatrix, boolean diagonal)` constructor for the ContingencyTable class with a JAMA Matrix provided

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double[][]`	`as2DdoubleArray()` returns the private array of data values for the ContingencyTable
`java.lang.String[][]`	`as2DStringArray()` returns the private array of data values for the ContingencyTable
`com.lobsterman.JavaGrinders.Jama.Matrix`	`asJAMAMatrix()` returns the private array of data values for the ContingencyTable
`ContTableResults`	`calcContingencyResults(ContingencyTable expectMatrix)` calculates the test of independence and returns ChiSquare and GValue
`GoodnessOfFitResults`	`calcGoodnessOfFitResults()` calculates the test of independence and returns ChiSquare and GValue
`boolean`	`checkDiagonal()` does the matrix shave a diagonal?
`boolean`	`checkForColumnPs()` checks whether column probabiities have been set
`boolean`	`checkForZeros()` checks whether any column probabiities are zero
`boolean`	`checkMatchingMatrixDimensions(ContingencyTable BTable)` examine whether this matrix has the same dimensions as the one provided?
`void`	`checkMatrix()` examines the matrix for invalid entries
`boolean`	`checkMinimumN(int n)` checks whether column probabiities have been set
`boolean`	`checkSquare()` is matrix square?
`void`	`clearColumnPs()` clears the external probabilities
`void`	`clearPs()` clears the external probabilities
`void`	`clearSums()` zero the sums for rows, columns, and total of the ContingencyTable
`void`	`clearTable()` zero the sums for all individual cells of the ContingencyTable
`void`	`clearTablePs()` clears the external probabilities
`java.lang.Object`	`clone()` clone the object
`java.lang.String`	`colToString(int col)` returns the formatted object as a string
`double`	`DoWilliamsCorr()` calculates the William's correction
`int`	`fillPerms()` fills the array with all possible (or desired) permutations
`void`	`fillSums()` calculate sums for rows, columns and total of the ContingencyTable
`DataTable`	`fold(double[] cells, int rows, int cols, boolean diag)` folds an array of doubles into a DataTable and returns the object
`com.lobsterman.JavaGrinders.Applets.Cell`	`getCell(int xLoc, int yLoc)` returns the double from one element of this matrix
`double`	`getCellValue(int xLoc, int yLoc)` returns the double from one element of this matrix
`java.lang.String`	`getColLabel(int column)` returns a particular column label for the ContingencyTable
`java.lang.String[]`	`getColLabels()` returns column labels for the ContingencyTable
`double`	`getColSum(int col)` returns the sum for a particular row of the table
`double[]`	`getColSums()` returns the row sums of the table
`double[]`	`getColumnPs()` returns the dimensions of the Table
`ContTableResults`	`getContingencyTableResults()` returns the results for a test of independence with expected frequencies calculated from observed
`ContTableResults`	`getContingencyTableResults(ContingencyTable expectMatrix)` returns the results for a test of independence with the provided expected values
`int`	`getdf()` returns the degrees of freedom for the ContingencyTable
`ContingencyTable`	`getDifferenceTable(ContingencyTable bTable)` returns a matrix of dominance relationships between actor and receiver
`double[][]`	`getDominanceMatrix()` returns a matrix of dominance relationships between actor and receiver
`ContingencyTable`	`getExpectedMatrix()` returns a matrix of expected values for a test of independence
`ContingencyTable`	`getExpectedMatrix(boolean aDiagonal)` returns a matrix of expected values for a test of independence
`DataTable`	`getExpMatrixDia()` returns a matrix of expected values for a test of independence
`DataTable`	`getExpMatrixFromProbabilities()` returns a matrix of expected values for a test of independence
`ContingencyTable`	`getExpMatrixNoDia()` returns a matrix of expected values for a test of independence if the diagonal is structurally zero
`DataTable`	`getFTukeyDeviates()` returns Freeman-Tukey deviates for a cell wise examination of the table
`GoodnessOfFitResults`	`getGoodnessOfFitResults()` coordinates a replicated goodness of fit test
`double`	`getMantelP(ContingencyTable BTable, double actualMantelNumber)` performs Mantel's test with number of permutations limited by MaxPermutations
`double`	`getMantelZ(ContingencyTable BTable)` calculate Mantel's Z statistic for a matrix and a second matrix passed in
`int`	`getMatrixSize()` returns the dimensions of the Table
`com.lobsterman.JavaGrinders.Applets.Cell`	`getMaxValueCell()` returns a matrix of dominance relationships between actor and receiver
`com.lobsterman.JavaGrinders.Applets.Cell`	`getMinValueCell()` returns a matrix of dominance relationships between actor and receiver
`java.lang.String`	`getName()` returns the dimensions of the Table
`int`	`getNCells()` returns the total number of cells for the ContingencyTable
`int`	`getNCellsAboveEqualValue(double compVal)` returns the number of cells above or equal to a given value
`int`	`getNCellsAboveValue(double compVal)` returns the number of cells above a given value
`int`	`getNCellsBelowEqualValue(double compVal)` returns the number of cells below or equal to a given value
`int`	`getNCellsBelowValue(double compVal)` returns the number of cells below a given value
`int`	`getNCols()` returns the number of columns of the Table
`int`	`getNDiagonals()` returns the total number of cells for the ContingencyTable
`double[][]`	`getNoZeroCellMatrix()` returns the values from the matrix with a constant of 0.25 added to each cell
`int`	`getNRows()` returns the number of rows of the Table
`ContingencyTable`	`getPermutedTable(int[] permOrder)` gets a variant of the interactionTable with rows and columns switched with a given permutation
`ContingencyTable`	`getPropMatrixDia()` returns a matrix of expected values for proportional fitting with diagonal present
`ContingencyTable`	`getPropMatrixNoDia()` returns a matrix of expected values for proportional fitting with diagonal absent (see Bishop et al., 1975; following Freeman, 1992)
`java.lang.String`	`getRowLabel(int row)` returns a particular row label for the ContingencyTable
`java.lang.String[]`	`getRowLabels()` returns row labels for the ContingencyTable
`double`	`getRowSum(int row)` returns the sum for a particular row of the table
`double[]`	`getRowSums()` returns the row sums of the table
`double[][]`	`getTablePs()` returns the dimensions of the Table
`double`	`getTauKr()` organize a TauKr test for a correlation between actor and receiver matrix
`double`	`getTauKrP(double actualKrNumber)` performs the Kr test with number of permutations limited by MaxPermutations
`double[][]`	`getTotalsMatrix()` returns a matrix in which cells from actor and receiver section of the ContingencyTable have been summed into a total cell value
`double`	`getTotalSum()` returns the sum for a particular row of the table
`int`	`getZeroCells()` returns the number of empty cells for the ContingencyTable
`int`	`howManyPossiblePermutations()` calculates the number of possible permutations
`void`	`incrementCellValue(int xLoc, int yLoc)` increments a single cell for this matrix by one
`ContingencyTable`	`invertTable()` inverts the table with rows to colums and colums to rows
`boolean`	`isMatchingMatrix(ContingencyTable BTable)` is this matrix the same as the one provided?
`boolean`	`isSquare()` is matrix square?
`void`	`listContingencyTableResults()` does the test and returns its results
`void`	`listExpectedTable()` lists a matrix of expected values
`void`	`listFTukeyDeviates()` lists Freeman-Tukey deviates for a cell wise examination of the table
`void`	`listGoodnessOfFitResults()` reports the results for a replicated goodness of fit test with external hypothesis probabilities
`void`	`listMantelZResults(ContingencyTable BTable)` lists Mantel's Z for the table
`void`	`listTable()` lists the table
`void`	`listTable(boolean doSums)` lists the table
`void`	`listTauKrResults()` lists the Tau Kr for the table
`java.lang.String`	`noSumsToString()` returns the formatted table without sums as a string
`java.lang.String`	`rowToString(int row)` returns the formated object as a string
`void`	`set2DArray(double[][] inMatrix)` sets a 2D array of doubles for the ContingencyTable
`void`	`setCellValue(int xLoc, int yLoc, double inValue)` sets a single element for this matrix with a double
`void`	`setColLabel(int column, java.lang.String aString)` returns a particular column label for the ContingencyTable
`void`	`setColLabels(java.lang.String[] Labels)` sets new row and column labels for the ContingencyTable
`void`	`setColLabels(java.util.TreeMap<?,?> Labels)` sets new row and column labels for the ContingencyTable
`void`	`setColumnPs(double[] thePs)` sets the expected probabilities for different columns
`void`	`setDefaultRowColLabels()` sets default labels for row and column labels for the ContingencyTable
`void`	`setDiagonal(boolean diagonal)` sets the diagonal of the ContingencyTable and resets all cell values
`void`	`setMatrixDimensions(int MatrixCols, int MatrixRows, boolean diagonal)` sets new matrix dimensions for the ContingencyTable
`void`	`setMatrixSize(int MatrixSize)` sets the dimensions of the DominanceTable
`void`	`setName(java.lang.String theName)` sets the name for the ContingencyTable
`void`	`setNDiagonals()` returns the total number of cells for the ContingencyTable
`void`	`setRowColLabels(java.lang.String[] Labels)` sets new row and column labels for the ContingencyTable
`void`	`setRowColLabels(java.util.TreeMap<?,?> Labels)` sets new row and column labels for the ContingencyTable
`void`	`setRowLabel(int row, java.lang.String aString)` returns a particular column label for the ContingencyTable
`void`	`setRowLabels(java.lang.String[] Labels)` sets new row and column labels for the ContingencyTable
`void`	`setRowLabels(java.util.TreeMap<?,?> Labels)` sets new row and column labels for the ContingencyTable
`void`	`setTablePs(double[][] theTPs)` sets the expected probabilities for different columns
`double`	`TauKr(ContingencyTable BTable)` calculate Kendal's tau statistic for a matrix and a second matrix passed in
`void`	`toFile(java.io.BufferedWriter bw)` writes a ContingencyTable into the writer for a file
`java.lang.String`	`toString(boolean doSums)` returns the formatted object as a string
`ContingencyTable`	`transpose()` transposes the table between X and Y dimensions
`double[]`	`unfold(boolean includeDiagonal, boolean upperTriangleOnly)` unfold the table into an array of doubles

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

- Field Detail
  - NUM_MAXITERATOR
```
public final int NUM_MAXITERATOR
```
    See Also:
    
    Constant Field Values
  - PRECISIONMULT
```
public int PRECISIONMULT
```
  - MatrixRows
```
public int MatrixRows
```
  - MatrixCols
```
public int MatrixCols
```
  - itsTotalSum
```
public double itsTotalSum
```
  - diagonal
```
public boolean diagonal
```
  - iterated
```
public int iterated
```
- Constructor Detail
  - ContingencyTable
```
public ContingencyTable(int MatrixCols,
                        int MatrixRows,
                        boolean diagonal,
                        java.lang.String theName)
```
    standard constructor for the ContingencyTable class
    
    Parameters:
    
    MatrixCols - number of columns in the table
    
    MatrixRows - number of rows in the table
    
    diagonal - does the table have a diagonal?
    
    theName - the name of the table
  - ContingencyTable
```
public ContingencyTable(int MatrixCols,
                        int MatrixRows,
                        boolean diagonal)
```
    standard constructor for the ContingencyTable class
    
    Parameters:
    
    MatrixCols - number of columns in the table
    
    MatrixRows - number of rows in the table
    
    diagonal - does the table have a diagonal?
  - ContingencyTable
```
public ContingencyTable(int MatrixCols,
                        int MatrixRows,
                        java.lang.String theName)
```
    standard constructor for the ContingencyTable class
    
    Parameters:
    
    MatrixCols - number of columns in the table
    
    MatrixRows - number of rows in the table
    
    theName - the name of the table
  - ContingencyTable
```
public ContingencyTable(int MatrixCols,
                        int MatrixRows)
```
    standard constructor for the ContingencyTable class
    
    Parameters:
    
    MatrixCols - number of columns in the table
    
    MatrixRows - number of rows in the table
  - ContingencyTable
```
public ContingencyTable(double[][] theArray)
```
    standard constructor for the ContingencyTable class
    
    Parameters:
    
    theArray - the 2D array to install into the Table
  - ContingencyTable
```
public ContingencyTable(double[][] theArray,
                        boolean diagonal)
```
    standard constructor for the ContingencyTable class
    
    Parameters:
    
    theArray - the array to install into the Table
    
    diagonal - does the table have a diagonal?
  - ContingencyTable
```
public ContingencyTable(com.lobsterman.JavaGrinders.Jama.Matrix aMatrix,
                        boolean diagonal)
```
    constructor for the ContingencyTable class with a JAMA Matrix provided
    
    Parameters:
    
    aMatrix - a JAMA matrix
    
    diagonal - does the table have a diagonal?
- Method Detail
  - getName
```
public java.lang.String getName()
```
    returns the dimensions of the Table
    
    Returns:
    
    the name of the table
  - setName
```
public void setName(java.lang.String theName)
```
    sets the name for the ContingencyTable
    
    Parameters:
    
    theName - the name of the table
  - setCellValue
```
public void setCellValue(int xLoc,
                         int yLoc,
                         double inValue)
```
    sets a single element for this matrix with a double
    
    Parameters:
    
    xLoc - x Capture in grid
    
    yLoc - y Capture in grid
    
    inValue - double value to set
  - incrementCellValue
```
public void incrementCellValue(int xLoc,
                               int yLoc)
```
    increments a single cell for this matrix by one
    
    Parameters:
    
    xLoc - x Capture in grid
    
    yLoc - y Capture in grid
  - getCellValue
```
public double getCellValue(int xLoc,
                           int yLoc)
```
    returns the double from one element of this matrix
    
    Parameters:
    
    xLoc - x Capture in grid
    
    yLoc - y Capture in grid
    
    Returns:
    
    the cell value
  - getCell
```
public com.lobsterman.JavaGrinders.Applets.Cell getCell(int xLoc,
                                                        int yLoc)
```
    returns the double from one element of this matrix
    
    Parameters:
    
    xLoc - x Capture in grid
    
    yLoc - y Capture in grid
    
    Returns:
    
    the cell
  - setTablePs
```
public void setTablePs(double[][] theTPs)
                throws java.lang.Exception
```
    sets the expected probabilities for different columns
    
    Parameters:
    
    theTPs - the array of probabilities
    
    Throws:
    
    java.lang.Exception - ...
  - setColumnPs
```
public void setColumnPs(double[] thePs)
                 throws java.lang.Exception
```
    sets the expected probabilities for different columns
    
    Parameters:
    
    thePs - the array of probabilities
    
    Throws:
    
    java.lang.Exception - ...
  - clearColumnPs
```
public void clearColumnPs()
```
    clears the external probabilities
  - clearTablePs
```
public void clearTablePs()
```
    clears the external probabilities
  - clearPs
```
public void clearPs()
```
    clears the external probabilities
  - getTablePs
```
public double[][] getTablePs()
```
    returns the dimensions of the Table
    
    Returns:
    
    the cell probabilities
  - getColumnPs
```
public double[] getColumnPs()
```
    returns the dimensions of the Table
    
    Returns:
    
    the column probabilities
  - setMatrixDimensions
```
public void setMatrixDimensions(int MatrixCols,
                                int MatrixRows,
                                boolean diagonal)
                         throws java.lang.Exception
```
    sets new matrix dimensions for the ContingencyTable
    
    Parameters:
    
    MatrixCols - number of columns in the table
    
    MatrixRows - number of rows in the table
    
    diagonal - does the table have a diagonal?
    
    Throws:
    
    java.lang.Exception - ...
  - getMatrixSize
```
public int getMatrixSize()
```
    returns the dimensions of the Table
    
    Returns:
    
    the size of the matrix
  - setMatrixSize
```
public void setMatrixSize(int MatrixSize)
```
    sets the dimensions of the DominanceTable
    
    Parameters:
    
    MatrixSize - number of rows and columns in the table
  - getNRows
```
public int getNRows()
```
    returns the number of rows of the Table
    
    Returns:
    
    the number of rows
  - getNCols
```
public int getNCols()
```
    returns the number of columns of the Table
    
    Returns:
    
    the number of columns
  - setDiagonal
```
public void setDiagonal(boolean diagonal)
```
    sets the diagonal of the ContingencyTable and resets all cell values
    
    Parameters:
    
    diagonal - does the table contain a diagonal?
  - setDefaultRowColLabels
```
public void setDefaultRowColLabels()
```
    sets default labels for row and column labels for the ContingencyTable
  - setRowColLabels
```
public void setRowColLabels(java.util.TreeMap<?,?> Labels)
```
    sets new row and column labels for the ContingencyTable
    
    Parameters:
    
    Labels - the distinct IDs for columns and rows
  - setRowColLabels
```
public void setRowColLabels(java.lang.String[] Labels)
```
    sets new row and column labels for the ContingencyTable
    
    Parameters:
    
    Labels - the distinct IDs for columns and rows
  - setRowLabels
```
public void setRowLabels(java.util.TreeMap<?,?> Labels)
```
    sets new row and column labels for the ContingencyTable
    
    Parameters:
    
    Labels - the distinct IDs for rows
  - setRowLabels
```
public void setRowLabels(java.lang.String[] Labels)
```
    sets new row and column labels for the ContingencyTable
    
    Parameters:
    
    Labels - the distinct IDs for rows
  - setColLabels
```
public void setColLabels(java.util.TreeMap<?,?> Labels)
```
    sets new row and column labels for the ContingencyTable
    
    Parameters:
    
    Labels - the distinct IDs for columns
  - setColLabels
```
public void setColLabels(java.lang.String[] Labels)
```
    sets new row and column labels for the ContingencyTable
    
    Parameters:
    
    Labels - the distinct IDs for rows
  - getRowLabels
```
public java.lang.String[] getRowLabels()
```
    returns row labels for the ContingencyTable
  - getColLabels
```
public java.lang.String[] getColLabels()
```
    returns column labels for the ContingencyTable
  - setColLabel
```
public void setColLabel(int column,
                        java.lang.String aString)
```
    returns a particular column label for the ContingencyTable
    
    Parameters:
    
    column - the column of the table
    
    aString - the string to set
  - getColLabel
```
public java.lang.String getColLabel(int column)
```
    returns a particular column label for the ContingencyTable
    
    Parameters:
    
    column - the column of the table
  - setRowLabel
```
public void setRowLabel(int row,
                        java.lang.String aString)
```
    returns a particular column label for the ContingencyTable
    
    Parameters:
    
    row - the row of the table
    
    aString - the string to set
  - getRowLabel
```
public java.lang.String getRowLabel(int row)
```
    returns a particular row label for the ContingencyTable
    
    Parameters:
    
    row - the row of the table
  - set2DArray
```
public void set2DArray(double[][] inMatrix)
                throws java.lang.Exception
```
    sets a 2D array of doubles for the ContingencyTable
    
    Parameters:
    
    inMatrix - 2D array of doubles to fill the table
    
    Throws:
    
    java.lang.Exception
  - as2DdoubleArray
```
public double[][] as2DdoubleArray()
```
    returns the private array of data values for the ContingencyTable
  - as2DStringArray
```
public java.lang.String[][] as2DStringArray()
```
    returns the private array of data values for the ContingencyTable
  - asJAMAMatrix
```
public com.lobsterman.JavaGrinders.Jama.Matrix asJAMAMatrix()
```
    returns the private array of data values for the ContingencyTable
  - clearSums
```
public void clearSums()
```
    zero the sums for rows, columns, and total of the ContingencyTable
  - clearTable
```
public void clearTable()
```
    zero the sums for all individual cells of the ContingencyTable
  - fillSums
```
public void fillSums()
```
    calculate sums for rows, columns and total of the ContingencyTable
  - getRowSums
```
public double[] getRowSums()
```
    returns the row sums of the table
  - getRowSum
```
public double getRowSum(int row)
                 throws java.lang.Exception
```
    returns the sum for a particular row of the table
    
    Throws:
    
    java.lang.Exception
  - getColSums
```
public double[] getColSums()
```
    returns the row sums of the table
  - getColSum
```
public double getColSum(int col)
                 throws java.lang.Exception
```
    returns the sum for a particular row of the table
    
    Throws:
    
    java.lang.Exception
  - getTotalSum
```
public double getTotalSum()
                   throws java.lang.Exception
```
    returns the sum for a particular row of the table
    
    Throws:
    
    java.lang.Exception
  - transpose
```
public ContingencyTable transpose()
                           throws java.lang.Exception
```
    transposes the table between X and Y dimensions
    
    Throws:
    
    java.lang.Exception
  - clone
```
public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException
```
    clone the object
    
    Overrides:
    
    clone in class java.lang.Object
    
    Throws:
    
    java.lang.CloneNotSupportedException
  - getTotalsMatrix
```
public double[][] getTotalsMatrix()
```
    returns a matrix in which cells from actor and receiver section of the ContingencyTable have been summed into a total cell value
  - getNoZeroCellMatrix
```
public double[][] getNoZeroCellMatrix()
```
    returns the values from the matrix with a constant of 0.25 added to each cell
  - getDifferenceTable
```
public ContingencyTable getDifferenceTable(ContingencyTable bTable)
```
    returns a matrix of dominance relationships between actor and receiver
  - getMinValueCell
```
public com.lobsterman.JavaGrinders.Applets.Cell getMinValueCell()
```
    returns a matrix of dominance relationships between actor and receiver
  - getMaxValueCell
```
public com.lobsterman.JavaGrinders.Applets.Cell getMaxValueCell()
```
    returns a matrix of dominance relationships between actor and receiver
  - getDominanceMatrix
```
public double[][] getDominanceMatrix()
```
    returns a matrix of dominance relationships between actor and receiver
  - getExpMatrixDia
```
public DataTable getExpMatrixDia()
                          throws java.lang.Exception
```
    returns a matrix of expected values for a test of independence
    
    Throws:
    
    java.lang.Exception
  - getExpMatrixFromProbabilities
```
public DataTable getExpMatrixFromProbabilities()
                                        throws java.lang.Exception
```
    returns a matrix of expected values for a test of independence
    
    Throws:
    
    java.lang.Exception
  - listExpectedTable
```
public void listExpectedTable()
```
    lists a matrix of expected values
  - getExpectedMatrix
```
public ContingencyTable getExpectedMatrix()
```
    returns a matrix of expected values for a test of independence
  - getExpectedMatrix
```
public ContingencyTable getExpectedMatrix(boolean aDiagonal)
```
    returns a matrix of expected values for a test of independence
  - getExpMatrixNoDia
```
public ContingencyTable getExpMatrixNoDia()
                                   throws java.lang.Exception
```
    returns a matrix of expected values for a test of independence if the diagonal is structurally zero
    
    Throws:
    
    java.lang.Exception
  - getPropMatrixDia
```
public ContingencyTable getPropMatrixDia()
                                  throws java.lang.Exception
```
    returns a matrix of expected values for proportional fitting with diagonal present
    
    Throws:
    
    java.lang.Exception
  - getPropMatrixNoDia
```
public ContingencyTable getPropMatrixNoDia()
                                    throws java.lang.Exception
```
    returns a matrix of expected values for proportional fitting with diagonal absent (see Bishop et al., 1975; following Freeman, 1992)
    
    Throws:
    
    java.lang.Exception
  - listFTukeyDeviates
```
public void listFTukeyDeviates()
```
    lists Freeman-Tukey deviates for a cell wise examination of the table
  - getFTukeyDeviates
```
public DataTable getFTukeyDeviates()
                            throws java.lang.Exception
```
    returns Freeman-Tukey deviates for a cell wise examination of the table
    
    Throws:
    
    java.lang.Exception
  - getdf
```
public int getdf()
```
    returns the degrees of freedom for the ContingencyTable
  - getZeroCells
```
public int getZeroCells()
```
    returns the number of empty cells for the ContingencyTable
  - getNCells
```
public int getNCells()
```
    returns the total number of cells for the ContingencyTable
  - setNDiagonals
```
public void setNDiagonals()
                   throws java.lang.Exception
```
    returns the total number of cells for the ContingencyTable
    
    Throws:
    
    java.lang.Exception
  - getNDiagonals
```
public int getNDiagonals()
                  throws java.lang.Exception
```
    returns the total number of cells for the ContingencyTable
    
    Throws:
    
    java.lang.Exception
  - getNCellsAboveValue
```
public int getNCellsAboveValue(double compVal)
```
    returns the number of cells above a given value
  - getNCellsAboveEqualValue
```
public int getNCellsAboveEqualValue(double compVal)
```
    returns the number of cells above or equal to a given value
  - getNCellsBelowValue
```
public int getNCellsBelowValue(double compVal)
```
    returns the number of cells below a given value
  - getNCellsBelowEqualValue
```
public int getNCellsBelowEqualValue(double compVal)
```
    returns the number of cells below or equal to a given value
  - DoWilliamsCorr
```
public double DoWilliamsCorr()
```
    calculates the William's correction
  - calcContingencyResults
```
public ContTableResults calcContingencyResults(ContingencyTable expectMatrix)
                                        throws java.lang.Exception
```
    calculates the test of independence and returns ChiSquare and GValue
    
    Parameters:
    
    expectMatrix - a ContingencyTable with the matrix of expected values
    
    Throws:
    
    java.lang.Exception
  - getContingencyTableResults
```
public ContTableResults getContingencyTableResults()
                                            throws java.lang.Exception
```
    returns the results for a test of independence with expected frequencies calculated from observed
    
    Throws:
    
    java.lang.Exception
  - getContingencyTableResults
```
public ContTableResults getContingencyTableResults(ContingencyTable expectMatrix)
                                            throws java.lang.Exception
```
    returns the results for a test of independence with the provided expected values
    
    Parameters:
    
    expectMatrix - a ContingencyTable with the matrix of exp0ected values
    
    Throws:
    
    java.lang.Exception
  - listContingencyTableResults
```
public void listContingencyTableResults()
```
    does the test and returns its results
  - calcGoodnessOfFitResults
```
public GoodnessOfFitResults calcGoodnessOfFitResults()
                                              throws java.lang.Exception
```
    calculates the test of independence and returns ChiSquare and GValue
    
    Throws:
    
    java.lang.Exception
  - getGoodnessOfFitResults
```
public GoodnessOfFitResults getGoodnessOfFitResults()
                                             throws java.lang.Exception
```
    coordinates a replicated goodness of fit test
    
    Throws:
    
    java.lang.Exception
  - listGoodnessOfFitResults
```
public void listGoodnessOfFitResults()
```
    reports the results for a replicated goodness of fit test with external hypothesis probabilities
  - invertTable
```
public ContingencyTable invertTable()
```
    inverts the table with rows to colums and colums to rows
  - getTauKr
```
public double getTauKr()
```
    organize a TauKr test for a correlation between actor and receiver matrix
  - TauKr
```
public double TauKr(ContingencyTable BTable)
```
    calculate Kendal's tau statistic for a matrix and a second matrix passed in
    
    Parameters:
    
    BTable - second ContingencyTable for the TauKr value
  - getMantelZ
```
public double getMantelZ(ContingencyTable BTable)
                  throws java.lang.Exception
```
    calculate Mantel's Z statistic for a matrix and a second matrix passed in
    
    Parameters:
    
    BTable - second ContingencyTable for the correlation
    
    Throws:
    
    java.lang.Exception
  - unfold
```
public double[] unfold(boolean includeDiagonal,
                       boolean upperTriangleOnly)
                throws java.lang.Exception
```
    unfold the table into an array of doubles
    
    Throws:
    
    java.lang.Exception
  - fold
```
public DataTable fold(double[] cells,
                      int rows,
                      int cols,
                      boolean diag)
               throws java.lang.Exception
```
    folds an array of doubles into a DataTable and returns the object
    
    Parameters:
    
    cells - the numbers to fill into the cells of the table
    
    rows - the number of rows for the table
    
    cols - the number of columns for the table
    
    diag - does the table have a diagonal?
    
    Throws:
    
    java.lang.Exception
  - howManyPossiblePermutations
```
public int howManyPossiblePermutations()
                                throws java.lang.Exception
```
    calculates the number of possible permutations
    
    Throws:
    
    java.lang.Exception
  - getPermutedTable
```
public ContingencyTable getPermutedTable(int[] permOrder)
                                  throws java.lang.Exception
```
    gets a variant of the interactionTable with rows and columns switched with a given permutation
    
    Parameters:
    
    permOrder - indicates a particular permutation
    
    Throws:
    
    java.lang.Exception
  - fillPerms
```
public int fillPerms()
              throws java.lang.Exception
```
    fills the array with all possible (or desired) permutations
    
    Throws:
    
    java.lang.Exception
  - getTauKrP
```
public double getTauKrP(double actualKrNumber)
```
    performs the Kr test with number of permutations limited by MaxPermutations
    
    Parameters:
    
    actualKrNumber - empirically derived TauKr
  - getMantelP
```
public double getMantelP(ContingencyTable BTable,
                         double actualMantelNumber)
```
    performs Mantel's test with number of permutations limited by MaxPermutations
    
    Parameters:
    
    BTable - second ContingencyTable for the TauKr value
    
    actualMantelNumber - empirically derived Mantels' z
  - listTauKrResults
```
public void listTauKrResults()
```
    lists the Tau Kr for the table
  - listMantelZResults
```
public void listMantelZResults(ContingencyTable BTable)
```
    lists Mantel's Z for the table
    
    Parameters:
    
    BTable - second ContingencyTable for the TauKr value
  - rowToString
```
public java.lang.String rowToString(int row)
```
    returns the formated object as a string
    
    Parameters:
    
    row - the row
  - colToString
```
public java.lang.String colToString(int col)
```
    returns the formatted object as a string
    
    Parameters:
    
    col - the colum
  - toString
```
public java.lang.String toString(boolean doSums)
```
    returns the formatted object as a string
  - noSumsToString
```
public java.lang.String noSumsToString()
```
    returns the formatted table without sums as a string
  - listTable
```
public void listTable()
```
    lists the table
  - listTable
```
public void listTable(boolean doSums)
```
    lists the table
    
    Parameters:
    
    doSums - specifies whether to include sums
  - toFile
```
public void toFile(java.io.BufferedWriter bw)
            throws java.lang.Exception
```
    writes a ContingencyTable into the writer for a file
    
    Parameters:
    
    bw - the BufferedWriter to write into
    
    Throws:
    
    java.lang.Exception
  - checkForColumnPs
```
public boolean checkForColumnPs()
                         throws java.lang.Exception
```
    checks whether column probabiities have been set
    
    Throws:
    
    java.lang.Exception
  - checkMatrix
```
public void checkMatrix()
                 throws java.lang.Exception
```
    examines the matrix for invalid entries
    
    Throws:
    
    java.lang.Exception
  - checkDiagonal
```
public boolean checkDiagonal()
                      throws java.lang.Exception
```
    does the matrix shave a diagonal?
    
    Throws:
    
    java.lang.Exception
  - isSquare
```
public boolean isSquare()
                 throws java.lang.Exception
```
    is matrix square?
    
    Throws:
    
    java.lang.Exception
  - checkSquare
```
public boolean checkSquare()
                    throws java.lang.Exception
```
    is matrix square?
    
    Throws:
    
    java.lang.Exception
  - checkMatchingMatrixDimensions
```
public boolean checkMatchingMatrixDimensions(ContingencyTable BTable)
                                      throws java.lang.Exception
```
    examine whether this matrix has the same dimensions as the one provided?
    
    Parameters:
    
    BTable - a ContingencyTable to compare with
    
    Throws:
    
    java.lang.Exception
  - isMatchingMatrix
```
public boolean isMatchingMatrix(ContingencyTable BTable)
```
    is this matrix the same as the one provided?
    
    Parameters:
    
    BTable - a ContingencyTable to compare with
  - checkMinimumN
```
public boolean checkMinimumN(int n)
                      throws java.lang.Exception
```
    checks whether column probabiities have been set
    
    Parameters:
    
    n - the minimum sample size
    
    Throws:
    
    java.lang.Exception
  - checkForZeros
```
public boolean checkForZeros()
                      throws java.lang.Exception
```
    checks whether any column probabiities are zero
    
    Throws:
    
    java.lang.Exception

Class ContingencyTable

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

NUM_MAXITERATOR

PRECISIONMULT

MatrixRows

MatrixCols

itsTotalSum

diagonal

iterated

Constructor Detail

ContingencyTable

ContingencyTable

ContingencyTable

ContingencyTable

ContingencyTable

ContingencyTable

ContingencyTable

Method Detail

getName

setName

setCellValue

incrementCellValue

getCellValue

getCell

setTablePs

setColumnPs

clearColumnPs

clearTablePs

clearPs

getTablePs

getColumnPs

setMatrixDimensions

getMatrixSize

setMatrixSize

getNRows

getNCols

setDiagonal

setDefaultRowColLabels

setRowColLabels

setRowColLabels

setRowLabels

setRowLabels

setColLabels

setColLabels

getRowLabels

getColLabels

setColLabel

getColLabel

setRowLabel

getRowLabel

set2DArray

as2DdoubleArray

as2DStringArray

asJAMAMatrix

clearSums

clearTable

fillSums

getRowSums

getRowSum

getColSums

getColSum

getTotalSum

transpose

clone

getTotalsMatrix

getNoZeroCellMatrix

getDifferenceTable

getMinValueCell

getMaxValueCell

getDominanceMatrix

getExpMatrixDia

getExpMatrixFromProbabilities

listExpectedTable

getExpectedMatrix

getExpectedMatrix

getExpMatrixNoDia