ContingencyTable

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JavaGrinders
Class ContingencyTable

java.lang.Object
  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
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
`boolean`	`diagonal`
`int`	`iterated`
`double`	`itsTotalSum`
`int`	`MatrixCols`
`int`	`MatrixRows`
`int`	`NUM_MAXITERATOR`
`int`	`PRECISIONMULT`

Constructor Summary
`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, 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(Matrix aMatrix, boolean diagonal)` constructor for the ContingencyTable class with a JAMA Matrix provided

Method Summary
`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
`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`	`checkForColumnPs()` checks whether column probabiities have been set
`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`	`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
`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
`java.lang.String`	`getName()` returns the dimensions of the Table
`int`	`getNCells()` returns the total number of cells for the ContingencyTable
`int`	`getNCols()` returns the number of columns of the Table
`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`	`listContingencyResults()` 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
`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`	`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()` unfold the table into an array of doubles
`double[]`	`unfoldUpperTriangle()` unfold the upper triangle of 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

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(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

setName

public void setName(java.lang.String theName)

sets the name for the ContingencyTable

Parameters:: theName - the name of the table

checkForColumnPs

public boolean checkForColumnPs()
                         throws java.lang.Exception

checks whether column probabiities have been set

Throws:: java.lang.Exception

getColumnPs

public double[] getColumnPs()

returns the dimensions of the Table

getTablePs

public double[][] getTablePs()

returns the dimensions of the Table

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

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

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

getNCols

public int getNCols()

returns the number of columns of the Table

setDiagonal

public void setDiagonal(boolean diagonal)

sets the diagonal of the ContingencyTable

Parameters:: diagonal - does the table contain a diagonal?

setDefaultRowColLabels

public void setDefaultRowColLabels()

sets default labels for row and column labels for the ContingencyTable