com.lobsterman.JavaGrinders

Class NumberVariable

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList<E>

java.util.Vector<java.lang.Object>

com.lobsterman.JavaGrinders.Variable

com.lobsterman.JavaGrinders.NumberVariable

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<java.lang.Object>, java.util.Collection<java.lang.Object>, java.util.List<java.lang.Object>, java.util.RandomAccess

Direct Known Subclasses:

IntegerVariable

public class NumberVariable
extends Variable
implements java.lang.Cloneable

handles things that a general variable containing numbers should do or know about. Based on a more generic Variable it supports ways to select rows using a variety of criteria, and reports descriptive (parametric) statistics. All numbers are stored and handled as Doubles.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
NumberDescriptives	itsNDescriptives
java.lang.Object[]	validDataSorted

Fields inherited from class com.lobsterman.JavaGrinders.Variable

autoExtracted, hasDefaultColors, isSorted, itsDescriptives, itsFormula, itsLineColor, itsLocationColor, kEuclidian, kGower, kJaccard, kManhattan, kSquEuclidian, plotMarker, rand

Fields inherited from class java.util.Vector

capacityIncrement, elementCount, elementData

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor and Description
NumberVariable(java.lang.String varName, VariableOrganizer theOwner) Standard constructor for the root number Variable class using a VariableOrganizer
NumberVariable(java.lang.String varName, VariableOrganizer anOrganizer, double[] theData) Standard constructor for the NumberVariable class using a double array of data

Method Summary

Modifier and Type	Method and Description
NumberVariable	absolute() set the value to its absolute value
NumberVariable	add(double theScalar) adds the constant to each value of the variable
com.lobsterman.JavaGrinders.spatial.AngleVariable	asAngleVariable() return the variable as an AngleVariable with data representing angular degrees
void	asHistogram() Creates a presenter and plots the data as a frequency histogram
void	asHistogram(Grid theXGrid) Creates a presenter and plots the data as a frequency histogram
void	asNormalQuantilePlot() Creates a presenter and plots the data
com.lobsterman.JavaGrinders.spatial.TimeVariable	asTimeVariable() return the variable as an TimeVariable with data representing milliseconds
void	asXYPlot(NumberVariable theYs) Creates a presenter and plots the data as a scatter plot with another numeric variable
void	asXYPlot(NumberVariable theYs, boolean xDir, boolean yDir) Creates a presenter and plots the data as a scatterplot with another numeric variable
void	asXYPlot(NumberVariable theYs, boolean xDir, boolean yDir, boolean connected) Creates a presenter and plots the data as a scatter plot with another numeric variable
void	asXYPlot(NumberVariable theYs, com.lobsterman.JavaGrinders.spatial.GridSpace3D theGridSpace) Creates a presenter and plots the data as a scatterplot with another numeric variable
void	asXYPlot(NumberVariable theYs, com.lobsterman.JavaGrinders.spatial.GridSpace3D theGridSpace, boolean connected) Creates a presenter and plots the data as a scatterplot with another numeric variable
void	checkInOrder() examine whether this variables is locked
void	checkInOrder(boolean ascending) examine whether this variables is locked
NumberDescriptives	copyNumberDescriptives() returns descriptive Statistic for the variable using the currently selected set of rows
NumberVariable	distance(double theScalar) the absolute value after subtracting the constant from each value of the variable
NumberVariable	divide(double theScalar) divides each value of the variable by the constant
void	doCorrelationAnalysis(NumberVariable theOtherYVariable) fills the regression statistics for the variable with control over th intercept
java.util.ArrayList<java.lang.Integer>	doPruneClosePeaks(java.util.ArrayList<java.lang.Integer> inArrayL, NumberVariable theTimes, double exclusionWindow) removes the smaller peak if two are too close
NumberVariable	doRegressionAnalysis(NumberVariable theXVariable) fills the regression statistics for the variable with control over the intercept
NumberVariable	doRegressionAnalysis(NumberVariable theXVariable, int polyDegree) fills the regression statistics for the variable with control over the intercept
void	fillCompleteTerms(VariableOrganizer aXOrganizer, com.lobsterman.JavaGrinders.parametric.ANOVAResults theResults) fills the n-way interaction terms for the ANOVA
void	fillCP(NumberVariable theXVariable, com.lobsterman.JavaGrinders.parametric.SquaresCrossproductResults theSSCP) returns the sums of squares and crossproducts for the variable
void	fillDescriptives(java.lang.Double hypMean) fills the descriptive circular statistics for the angle variable with a comparison to an external mean
void	fillSS(com.lobsterman.JavaGrinders.parametric.SquaresCrossproductResults theSSCP) fills the sums of squares and crossproducts for the variable
void	fillWithFormula(java.lang.String aFormula) fills the variable with individual datavalues created through a formula
void	fillWithGaussRandom(double theMean, double theSD) fills the variable with random values from a Gaussian Distribution
void	fillWithParser(DataFileParser aParser, int varNum, boolean firstRowAsLabels) fills the variable with individual datavalues read from a textfile using a DataFileParser object
void	fillWithRandomFromDistribution(NumberVariable theDistribution) fills the variable with random values from a Gaussian Distribution
void	fillWithRowNum() fills the variable with individual datavalues created through a formula
void	fillWithUniformRandom() fills the variable with random values from a uniform distribution between 0 and 1
com.lobsterman.JavaGrinders.parametric.ANOVAResults	getANOVAResults(Variable theXVariable) fills the ANOVA statistics for the variable
com.lobsterman.JavaGrinders.parametric.ANOVAResults	getANOVAResults(VariableOrganizer aXOrganizer) fills the ANOVA statistics for a full factorial model
com.lobsterman.JavaGrinders.parametric.CorrelationResults	getAutoCorrelationResults() obtains the Autocorrelation statistics for the variable
VariableOrganizer	getBinMeans(NumberVariable YVar) returns a frequency distribution for a given set of bins
NumberVariable	getCentered() returns a variable containing each values relative to its mean
com.lobsterman.JavaGrinders.parametric.CorrelationResults	getCorrelationResults(NumberVariable theOtherYVariable) fills the regression statistics for the variable with control over th intercept
java.lang.Double	getDoubleValue(int row) returns the value stored at a given row of the Vector as a double
NumberVariable	getFirstDerivative(NumberVariable timeVar, int slopeWid) returns a variable containing each values relative to its mean
ContingencyTable	getFrequencies(Grid theGrid) returns a frequency distribution for a given set of bins
Descriptives[]	getGroupDescriptives(Variable theXVariable) returns the descriptives for the groups identified by X
com.lobsterman.JavaGrinders.parametric.ANOVAResults	getManWhitneyUResults(Variable theXVar, double hypAngle) returns the results from an analysis of differences in mean angle distance from a hypothetical direction
double	getMaxValue() returns the maximum value stored in the Vector as a double
double	getMeanValue() returns the average for values stored in the Vector as a double
double	getMinValue() returns the minimum value stored in the Vector as a double
NumberVariable	getMovingAverageSmoothing(int wid) returns a variable containing each values relative to its mean
com.lobsterman.JavaGrinders.parametric.MultRegressionResults	getMultLinRegressionResults(VariableOrganizer theXVariableOrganizer) fills the regression statistics for the variable with control over the intercept
NumberDescriptives	getNumberDescriptives() fills the descriptive statistics for the variable and returns the results
java.util.ArrayList<com.lobsterman.JavaGrinders.instruments.PeakData>	getPeakData(java.util.ArrayList<java.lang.Integer> peakLocs, NumberVariable theTimes) removes the smaller peak if two are too close
NumberVariable	getPeakIntervals(java.util.ArrayList<java.lang.Integer> peakLocs) removes the smaller peak if two are too close
java.util.ArrayList<java.lang.Integer>	getPeakLocations(NumberVariable timeVar, int smoothWidth, float amplitudeThresh, float slopeThresh) from Tom O'Haver's toh@umd.edu great tutorial at
java.util.ArrayList<java.lang.Integer>	getPeaksPalshikar(int windowSize, float stringency) A standard peak detector in time series by Jean-Yves Tinevez jeanyves.tinevez@gmail.com May 10, 2011 The goal of this class is to identify peaks in a 1D time series (float[]).
VariableOrganizer	getPeakTriggeredTraces(NumberVariable timeVar, java.util.ArrayList<java.lang.Integer> peakLocations, long timeWindow) from Tom O'Haver's toh@umd.edu great tutorial at
NumberVariable	getPeakValues(java.util.ArrayList<java.lang.Integer> peakLocs) removes the smaller peak if two are too close
double	getRange() returns the minimum value stored in the Vector as a double
NumberVariable	getRanks() return the ranks for the values in this array of the currently selected subset
NumberVariable	getRegressionResiduals(NumberVariable theXVariable) fills the regression statistics for the variable with control over the intercept
NumberVariable	getRegressionResiduals(NumberVariable theXVariable, int polyDegree) fills the regression statistics for the variable with control over the intercept
NumberVariable	getRegressionResiduals(NumberVariable theXVariable, int polyDegree, boolean centered) fills the regression statistics for the variable with control over th intercept
com.lobsterman.JavaGrinders.parametric.RegressionResults	getRegressionResults(NumberVariable theXVariable) fills the regression statistics for the variable with control over the intercept
com.lobsterman.JavaGrinders.parametric.RegressionResults	getRegressionResults(NumberVariable theXVariable, int polyDegree) fills the regression statistics for the variable with control over the intercept
com.lobsterman.JavaGrinders.parametric.RegressionResults	getRegressionResults(NumberVariable theXVariable, int polyDegree, boolean centered) fills the regression statistics for the variable with control over the intercept
double	getSDValue() returns the average for values stored in the Vector as a double
NumberVariable	getSignedRank(double CenterVal) returns the signed ranks of distances to the specified value
double	getSignedRankW(double CenterVal, boolean plus) fills the one-tailed sum of signed ranks
double	getSignedRankWProbability(double W) returns the one-tailed robability of obtaining this Signed Rank W or greater
double	getSquEuclidian(NumberVariable aVar) returns the Euclidian proximity measure to another variable
double	getSumValue() returns the average for values stored in the Vector as a double
com.lobsterman.JavaGrinders.parametric.tTestResults	gettTestResults(double mean) obtains the t-Test results for the variable
double	gettValue(double hypMean) returns the average for values stored in the Vector as a double
double	getVarianceValue() returns the average for values stored in the Vector as a double
NumberVariable	getzQuantiles() returns a variable containing each values relative to its mean
NumberVariable	getzTransform() returns a variable containing each values relative to its mean
void	invalidDescriptives() descriptive stats need to be updated
void	listCorrelationResults(NumberVariable theOtherYVariable) fills the regression statistics for the variable with control over th intercept
void	listGroupDescriptives(Variable theXVariable) lists the descriptives for the groups identified by X
void	listMultLinRegressionResults(VariableOrganizer theXVariableOrganizer) fills the regression statistics for the variable with control over the intercept
void	listPeaks(java.util.ArrayList<java.lang.Integer> peakLocations) from Tom O'Haver's toh@umd.edu great tutorial at
void	listRegressionResults(NumberVariable theXVariable) fills the regression statistics for the variable with control over the intercept
void	listRegressionResults(NumberVariable theXVariable, int polyDegree) fills the regression statistics for the variable with control over the intercept
void	listRegressionResults(NumberVariable theXVariable, int polyDegree, boolean centered) fills the regression statistics for the variable with control over the intercept
void	makeNewDescriptives() create a new set of descriptives for the variable the object
NumberVariable	multiply(double theScalar) multiplies the constant with each value of the variable
NumberVariable	multiply(NumberVariable theVar) multiplies the variable with the corresponding value of the other variable
NumberVariable	power(double pow) calculates the power of each entry and returns it as a new variable
NumberVariable	rank(boolean selectedOnly) rank the values in this array
void	selectAbove(double cutoffValue, boolean fromPrevSelected) select all rows with a value greater than the one provided
void	selectAboveEqual(double cutoffValue, boolean fromPrevSelected) select all rows with a value greater or equal than the one provided
void	selectBelow(double cutoffValue, boolean fromPrevSelected) select all rows with a value less than the one provided
void	selectBelowEqual(double cutoffValue, boolean fromPrevSelected) select all rows with a value less or equal than the one provided
void	selectEqual(double aValue, boolean fromPrevSelected) select all rows with a value greater or equal than the one provided
void	selectRange(double lowValue, double highValue, boolean fromPrevSelected) select all rows with a value between the lower and upper limits provided.
void	setContinuousType() sets the variable to type CONTINUOUS
NumberVariable	sign() returns the sign for each value of the variable
NumberVariable	subtract(double theScalar) subtracts the constant from each value of the variable

Methods inherited from class com.lobsterman.JavaGrinders.Variable

addValue, addValue, addValue, addValue, append, asJAMAMatrix, asVariableOrganizer, checkAllUseRows, checkLocked, checkMatchingRows, checkMinUseRows, checkNumberIDs, checkSameIDs, checkSameNRows, checkSameNSelectRows, checkSameSelectRows, checkSameSelectRows, checkSameUseRows, checkSameUseRows, checkValidRowRange, clone, cloneSelectedRowsOnly, cloneVariableFrom, combineSelectedWithSavedSelectedRows, copyDescriptives, copySelectStateFrom, customColorFromData, customColorSelectedRows, customColorSelectedRows, deleteAllRows, deleteDuplicateRows, deleteMissingRows, deleteNonSelectedRows, deleteRow, deleteRowNoCheck, deleteSelectedRows, deselectAllRows, fill, fill, fill, fill, fill, fill, fillDescriptives, fillMoreDescriptives, fillWithParser, fillWithVariable, findFirstSelectRow, findFirstUseRow, findLastSelectRow, findLastUseRow, findNextNonMissingRow, findNextSelectRow, findNextUseRow, findNextValue, findPreviousSelectRow, findPreviousUseRow, getabasedintValue, getAbasedintValue, getArray, getbooleanValue, getcharValue, getCombinedIDs, getCrossTabulation, getCrossTabulation, getCustomColorRow, getDescriptives, getdoubleArray, getdoubleValue, getfloatValue, getFrequencies, getHighliteColor, getHighlitedRow, getIDMap, getIDs, getIDString, getIDStrings, getInteractions, getintValue, getJaccard, getLineColor, getLocationColor, getlongValue, getManhattan, getMissingRow, getName, getNIDs, getNMissingRows, getNotes, getNRows, getNSelectRows, getNUseRows, getOrganizer, getProximity, getProximity, getRandomValue, getRowNumbers, getRowOrder, getRowOrderRow, getSelectRow, getStringArray, getStringValue, getTransitions, getUseRow, getValue, getVariableDesignRole, getVariableDesignRoleString, getVariableFormat, getVariableType, highliteSelectedRows, highliteSelectedRows, invertSelectedRows, isAngleType, isContinuousType, isDateTimeFormat, isLocationType, isLocked, isNominalType, isNumberFormat, isOrdinalType, isStringFormat, isValidRowRange, isXVariable, isYVariable, listDescriptives, listDescriptives, listGroupDescriptivesNoDia, listRow, listRowOrder, listRows, listRows, listRows, listRows, listSelectedRows, listSelectState, listSelectState, listUseRows, makeTableSubSet, matchedIDs, replaceSelectedRows, restoreSelectedRows, restrictToMatchingUseRows, restrictToMatchingUseRows, restrictToValidRowsOnly, reverseRows, saveRowsToFile, saveRowsToFile, saveSelectedRows, selectAllRows, selectDuplicateRows, selectEveryNthRow, selectRows, selectUseRows, selectValue, setAnglesType, setCustomColorRow, setFormula, setHighliteColor, setHighlitedRow, setLineColor, setLocationColor, setLocationsType, setLock, setMissingRow, setName, setNominalType, setNotes, setNRows, setOrdinalType, setOrganizer, setRowOrder, setRowOrderRow, setSelectRow, setSelectRows, setSelectRowsToMissing, setValue, setValue, setValue, setValue, setValue, setValue, setVariableDesignRole, setVariableFormat, setVariableType, sort, sort, sort2, updateRowOrder

Methods inherited from class java.util.Vector

add, add, addAll, addAll, addElement, capacity, clear, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, firstElement, forEach, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, iterator, lastElement, lastIndexOf, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeIf, removeRange, replaceAll, retainAll, set, setElementAt, setSize, size, sort, spliterator, subList, toArray, toArray, toString, trimToSize

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Collection

parallelStream, stream

Field Detail

validDataSorted

public java.lang.Object[] validDataSorted

itsNDescriptives

public NumberDescriptives itsNDescriptives

Constructor Detail

NumberVariable

public NumberVariable(java.lang.String varName,
                      VariableOrganizer theOwner)
               throws java.lang.Exception

Standard constructor for the root number Variable class using a VariableOrganizer

Parameters:

varName - assigns a name (String) to the variable

theOwner - an instance of VariableOrganizer class coordinates a set of variables with respect to number of data points available and the rows that are currently selected

Throws:

java.lang.Exception

NumberVariable

public NumberVariable(java.lang.String varName,
                      VariableOrganizer anOrganizer,
                      double[] theData)
               throws java.lang.Exception

Standard constructor for the NumberVariable class using a double array of data

Parameters:

varName - assigns a name (String) to the variable

anOrganizer - an instance of VariableOrganizer class coordinates a set of variables with respect to number of data points available and the rows that are currently selected

theData - a double array of data

Throws:

java.lang.Exception

Method Detail

setContinuousType

public void setContinuousType()
                       throws java.lang.Exception

sets the variable to type CONTINUOUS

Throws:

java.lang.Exception

fillWithParser

public void fillWithParser(DataFileParser aParser,
                           int varNum,
                           boolean firstRowAsLabels)
                    throws java.lang.Exception

fills the variable with individual datavalues read from a textfile using a DataFileParser object

Overrides:

fillWithParser in class Variable

Parameters:

aParser - the DataFileParser that was used to read data values from a text file

varNum - marks the number of the column to be filled into the variable

firstRowAsLabels - whether the first row contains a variable label

Throws:

java.lang.Exception - if ...

fillWithUniformRandom

public void fillWithUniformRandom()
                           throws java.lang.Exception

fills the variable with random values from a uniform distribution between 0 and 1

Throws:

java.lang.Exception

fillWithGaussRandom

public void fillWithGaussRandom(double theMean,
                                double theSD)
                         throws java.lang.Exception

fills the variable with random values from a Gaussian Distribution

Parameters:

theMean - the mean for the gaussian distribution

theSD - the standard devaiation for the gaussian distribution

Throws:

java.lang.Exception

fillWithRandomFromDistribution

public void fillWithRandomFromDistribution(NumberVariable theDistribution)
                                    throws java.lang.Exception

fills the variable with random values from a Gaussian Distribution

Parameters:

theDistribution - a distribution from which to sample random numbers

Throws:

java.lang.Exception

fillWithFormula

public void fillWithFormula(java.lang.String aFormula)
                     throws java.lang.Exception

fills the variable with individual datavalues created through a formula

Parameters:

aFormula - the formula to use for filling the variable with values

Throws:

java.lang.Exception

fillWithRowNum

public void fillWithRowNum()
                    throws java.lang.Exception

fills the variable with individual datavalues created through a formula

Throws:

java.lang.Exception

asTimeVariable

public com.lobsterman.JavaGrinders.spatial.TimeVariable asTimeVariable()
                                                                throws java.lang.Exception

return the variable as an TimeVariable with data representing milliseconds

Throws:

java.lang.Exception

asAngleVariable

public com.lobsterman.JavaGrinders.spatial.AngleVariable asAngleVariable()
                                                                  throws java.lang.Exception

return the variable as an AngleVariable with data representing angular degrees

Throws:

java.lang.Exception

selectEqual

public void selectEqual(double aValue,
                        boolean fromPrevSelected)
                 throws java.lang.Exception

select all rows with a value greater or equal than the one provided

Parameters:

aValue - lists the comparison value

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectAboveEqual

public void selectAboveEqual(double cutoffValue,
                             boolean fromPrevSelected)
                      throws java.lang.Exception

select all rows with a value greater or equal than the one provided

Parameters:

cutoffValue - lists the comparison value

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectAbove

public void selectAbove(double cutoffValue,
                        boolean fromPrevSelected)
                 throws java.lang.Exception

select all rows with a value greater than the one provided

Parameters:

cutoffValue - lists the comparison value

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectBelowEqual

public void selectBelowEqual(double cutoffValue,
                             boolean fromPrevSelected)
                      throws java.lang.Exception

select all rows with a value less or equal than the one provided

Parameters:

cutoffValue - lists the comparison value

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectBelow

public void selectBelow(double cutoffValue,
                        boolean fromPrevSelected)
                 throws java.lang.Exception

select all rows with a value less than the one provided

Parameters:

cutoffValue - lists the comparison value

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectRange

public void selectRange(double lowValue,
                        double highValue,
                        boolean fromPrevSelected)
                 throws java.lang.Exception

select all rows with a value between the lower and upper limits provided. This includes values equal to the lower limit and excludes the upper limit

Parameters:

lowValue - the lower limit (included)

highValue - the upper limit (excluded)

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

getMaxValue

public double getMaxValue()
                   throws java.lang.Exception

returns the maximum value stored in the Vector as a double

Throws:

java.lang.Exception

getMinValue

public double getMinValue()
                   throws java.lang.Exception

returns the minimum value stored in the Vector as a double

Throws:

java.lang.Exception

getRange

public double getRange()
                throws java.lang.Exception

returns the minimum value stored in the Vector as a double

Throws:

java.lang.Exception

getMeanValue

public double getMeanValue()
                    throws java.lang.Exception

returns the average for values stored in the Vector as a double

Throws:

java.lang.Exception

getSumValue

public double getSumValue()
                   throws java.lang.Exception

returns the average for values stored in the Vector as a double

Throws:

java.lang.Exception

getVarianceValue

public double getVarianceValue()
                        throws java.lang.Exception

returns the average for values stored in the Vector as a double

Throws:

java.lang.Exception

getSDValue

public double getSDValue()
                  throws java.lang.Exception

returns the average for values stored in the Vector as a double

Throws:

java.lang.Exception

gettValue

public double gettValue(double hypMean)
                 throws java.lang.Exception

returns the average for values stored in the Vector as a double

Throws:

java.lang.Exception

getzTransform

public NumberVariable getzTransform()
                             throws java.lang.Exception

returns a variable containing each values relative to its mean

Throws:

java.lang.Exception

getzQuantiles

public NumberVariable getzQuantiles()
                             throws java.lang.Exception

returns a variable containing each values relative to its mean

Throws:

java.lang.Exception

getFrequencies

public ContingencyTable getFrequencies(Grid theGrid)
                                throws java.lang.Exception

returns a frequency distribution for a given set of bins

Parameters:

theGrid - the bins for the distribution

Throws:

java.lang.Exception

getBinMeans

public VariableOrganizer getBinMeans(NumberVariable YVar)
                              throws java.lang.Exception

returns a frequency distribution for a given set of bins

Parameters:

YVar - the NumberVariable to use

Throws:

java.lang.Exception

getCentered

public NumberVariable getCentered()
                           throws java.lang.Exception

returns a variable containing each values relative to its mean

Throws:

java.lang.Exception

getRanks

public NumberVariable getRanks()
                        throws java.lang.Exception

return the ranks for the values in this array of the currently selected subset

Throws:

java.lang.Exception

add

public NumberVariable add(double theScalar)
                   throws java.lang.Exception

adds the constant to each value of the variable

Parameters:

theScalar - the number to add

Throws:

java.lang.Exception

subtract

public NumberVariable subtract(double theScalar)
                        throws java.lang.Exception

subtracts the constant from each value of the variable

Parameters:

theScalar - the number to subtract

Throws:

java.lang.Exception

divide

public NumberVariable divide(double theScalar)
                      throws java.lang.Exception

divides each value of the variable by the constant

Parameters:

theScalar - the number to devide by

Throws:

java.lang.Exception

multiply

public NumberVariable multiply(double theScalar)
                        throws java.lang.Exception

multiplies the constant with each value of the variable

Parameters:

theScalar - the number to multiply

Throws:

java.lang.Exception

multiply

public NumberVariable multiply(NumberVariable theVar)
                        throws java.lang.Exception

multiplies the variable with the corresponding value of the other variable

Parameters:

theVar - the numbers to multiply

Throws:

java.lang.Exception

power

public NumberVariable power(double pow)
                     throws java.lang.Exception

calculates the power of each entry and returns it as a new variable

Parameters:

pow - calculate this power for each entry

Throws:

java.lang.Exception

distance

public NumberVariable distance(double theScalar)
                        throws java.lang.Exception

the absolute value after subtracting the constant from each value of the variable

Parameters:

theScalar - the number to subtract

Throws:

java.lang.Exception

sign

public NumberVariable sign()
                    throws java.lang.Exception

returns the sign for each value of the variable

Throws:

java.lang.Exception

absolute

public NumberVariable absolute()
                        throws java.lang.Exception

set the value to its absolute value

Throws:

java.lang.Exception

rank

public NumberVariable rank(boolean selectedOnly)
                    throws java.lang.Exception

rank the values in this array

Parameters:

selectedOnly - only use the selected values of the sample, the others will be set to missing

Throws:

java.lang.Exception

makeNewDescriptives

public void makeNewDescriptives()

create a new set of descriptives for the variable the object

Overrides:

makeNewDescriptives in class Variable

getNumberDescriptives

public NumberDescriptives getNumberDescriptives()
                                         throws java.lang.Exception

fills the descriptive statistics for the variable and returns the results

Throws:

java.lang.Exception

copyNumberDescriptives

public NumberDescriptives copyNumberDescriptives()
                                          throws java.lang.Exception

returns descriptive Statistic for the variable using the currently selected set of rows

Throws:

java.lang.Exception

invalidDescriptives

public void invalidDescriptives()

descriptive stats need to be updated

Overrides:

invalidDescriptives in class Variable

fillDescriptives

public void fillDescriptives(java.lang.Double hypMean)
                      throws java.lang.Exception

fills the descriptive circular statistics for the angle variable with a comparison to an external mean

Overrides:

fillDescriptives in class Variable

Parameters:

hypMean - the value of the a-priori hypothesis mean

Throws:

java.lang.Exception - if ...

getGroupDescriptives

public Descriptives[] getGroupDescriptives(Variable theXVariable)
                                    throws java.lang.Exception

returns the descriptives for the groups identified by X

Parameters:

theXVariable - the independent NumberVariable

Throws:

java.lang.Exception

listGroupDescriptives

public void listGroupDescriptives(Variable theXVariable)
                           throws java.lang.Exception

lists the descriptives for the groups identified by X

Overrides:

listGroupDescriptives in class Variable

Parameters:

theXVariable - the independent NumberVariable

Throws:

java.lang.Exception - if ...

getMovingAverageSmoothing

public NumberVariable getMovingAverageSmoothing(int wid)
                                         throws java.lang.Exception

returns a variable containing each values relative to its mean

Parameters:

wid - the number of rows to include on either side

Throws:

java.lang.Exception

getDoubleValue

public java.lang.Double getDoubleValue(int row)
                                throws java.lang.Exception

returns the value stored at a given row of the Vector as a double

Overrides:

getDoubleValue in class Variable

Parameters:

row - marks the row in the vector

Returns:

the returned Double

Throws:

java.lang.Exception - if ...

getFirstDerivative

public NumberVariable getFirstDerivative(NumberVariable timeVar,
                                         int slopeWid)
                                  throws java.lang.Exception

returns a variable containing each values relative to its mean

Parameters:

slopeWid - the slope between this many rows to either side

Throws:

java.lang.Exception

getPeaksPalshikar

public java.util.ArrayList<java.lang.Integer> getPeaksPalshikar(int windowSize,
                                                                float stringency)
                                                         throws java.lang.Exception

A standard peak detector in time series by Jean-Yves Tinevez jeanyves.tinevez@gmail.com May 10, 2011 The goal of this class is to identify peaks in a 1D time series (float[]). It simply implements G.K. Palshikar's Simple Algorithms for Peak Detection in Time-Series (Proc. 1st Int. Conf. Advanced Data Analysis, Business Analytics and Intelligence (ICADABAI2009), Ahmedabad, 6-7 June 2009), We retained the first "spikiness" function he proposed, based on computing the max signed distance to left and right neighbors. Return the peak locations as array index for the time series set at creation.

Parameters:

windowSize - the window size to look for peaks. a neighborhood of +/- windowSize will be inspected to search for peaks. Typical values start at 3.

stringency - threshold for peak values. Peak with values lower than mean + stringency * std will be rejected. Mean and std are calculated on the spikiness function. Typical values range from 1 to 3.

Returns:

an int array, with one element by retained peak, containing the index of the peak in the time series array.

Throws:

java.lang.Exception

getPeakLocations

public java.util.ArrayList<java.lang.Integer> getPeakLocations(NumberVariable timeVar,
                                                               int smoothWidth,
                                                               float amplitudeThresh,
                                                               float slopeThresh)
                                                        throws java.lang.Exception

from Tom O'Haver's toh@umd.edu great tutorial at

Parameters:

timeVar - the NumberVariable containing time references, set to null if measures at constant intervals

smoothWidth - the number of positions to include from either side in calculations of first derivative

amplitudeThresh - the threshold for minimum peak size

slopeThresh - the threshold for minimum negative peak slope

Returns:

an int array, with one element by retained peak, containing the index of the peak in the time series array.

Throws:

java.lang.Exception

listPeaks

public void listPeaks(java.util.ArrayList<java.lang.Integer> peakLocations)
               throws java.lang.Exception

from Tom O'Haver's toh@umd.edu great tutorial at

Parameters:

peakLocations - the locations of peaks in the record

Throws:

java.lang.Exception

getPeakTriggeredTraces

public VariableOrganizer getPeakTriggeredTraces(NumberVariable timeVar,
                                                java.util.ArrayList<java.lang.Integer> peakLocations,
                                                long timeWindow)
                                         throws java.lang.Exception

from Tom O'Haver's toh@umd.edu great tutorial at

Parameters:

timeVar - the NumberVariable containing time references, set to null if measures at constant intervals

peakLocations - the rows in which peaks were found

Returns:

a VariableOrganizer with measures relative to the peaks

Throws:

java.lang.Exception

doPruneClosePeaks

public java.util.ArrayList<java.lang.Integer> doPruneClosePeaks(java.util.ArrayList<java.lang.Integer> inArrayL,
                                                                NumberVariable theTimes,
                                                                double exclusionWindow)
                                                         throws java.lang.Exception

removes the smaller peak if two are too close

Parameters:

inArrayL - the array to prune

exclusionWindow - the size of the excluded overlap in capture positions

Throws:

java.lang.Exception

getPeakIntervals

public NumberVariable getPeakIntervals(java.util.ArrayList<java.lang.Integer> peakLocs)
                                throws java.lang.Exception

removes the smaller peak if two are too close

Parameters:

peakLocs - the locations of peaks in the record

Throws:

java.lang.Exception

getPeakValues

public NumberVariable getPeakValues(java.util.ArrayList<java.lang.Integer> peakLocs)
                             throws java.lang.Exception

removes the smaller peak if two are too close

Parameters:

peakLocs - the row numbers for the peaks

Throws:

java.lang.Exception

getPeakData

public java.util.ArrayList<com.lobsterman.JavaGrinders.instruments.PeakData> getPeakData(java.util.ArrayList<java.lang.Integer> peakLocs,
                                                                                         NumberVariable theTimes)
                                                                                  throws java.lang.Exception

removes the smaller peak if two are too close

Parameters:

peakLocs - the row numbers for the peaks

theTimes - the times

Throws:

java.lang.Exception

asHistogram

public void asHistogram()
                 throws java.lang.Exception

Creates a presenter and plots the data as a frequency histogram

Throws:

java.lang.Exception

asHistogram

public void asHistogram(Grid theXGrid)
                 throws java.lang.Exception

Creates a presenter and plots the data as a frequency histogram

Parameters:

theXGrid - the grid for the x dimension

Throws:

java.lang.Exception

asNormalQuantilePlot

public void asNormalQuantilePlot()
                          throws java.lang.Exception

Creates a presenter and plots the data

Throws:

java.lang.Exception

asXYPlot

public void asXYPlot(NumberVariable theYs,
                     boolean xDir,
                     boolean yDir)
              throws java.lang.Exception

Creates a presenter and plots the data as a scatterplot with another numeric variable

Parameters:

theYs - the Y variable

xDir - the direction of the x-axis

yDir - the direction of the y-axis

Throws:

java.lang.Exception

asXYPlot

public void asXYPlot(NumberVariable theYs,
                     boolean xDir,
                     boolean yDir,
                     boolean connected)
              throws java.lang.Exception

Creates a presenter and plots the data as a scatter plot with another numeric variable

Parameters:

theYs - the Y variable

xDir - the direction of the x-axis

yDir - the direction of the y-axis

Throws:

java.lang.Exception

asXYPlot

public void asXYPlot(NumberVariable theYs)
              throws java.lang.Exception

Creates a presenter and plots the data as a scatter plot with another numeric variable

Parameters:

theYs - the Y variable

Throws:

java.lang.Exception

asXYPlot

public void asXYPlot(NumberVariable theYs,
                     com.lobsterman.JavaGrinders.spatial.GridSpace3D theGridSpace)
              throws java.lang.Exception

Creates a presenter and plots the data as a scatterplot with another numeric variable

Parameters:

theYs - the Y variable

Throws:

java.lang.Exception

asXYPlot

public void asXYPlot(NumberVariable theYs,
                     com.lobsterman.JavaGrinders.spatial.GridSpace3D theGridSpace,
                     boolean connected)
              throws java.lang.Exception

Creates a presenter and plots the data as a scatterplot with another numeric variable

Parameters:

theYs - the Y variable

Throws:

java.lang.Exception

getSquEuclidian

public double getSquEuclidian(NumberVariable aVar)
                       throws java.lang.Exception

returns the Euclidian proximity measure to another variable

Parameters:

aVar - a second variable

Throws:

java.lang.Exception

getSignedRank

public NumberVariable getSignedRank(double CenterVal)
                             throws java.lang.Exception

returns the signed ranks of distances to the specified value

Parameters:

CenterVal - the median/center of the sample

Throws:

java.lang.Exception

getSignedRankW

public double getSignedRankW(double CenterVal,
                             boolean plus)
                      throws java.lang.Exception

fills the one-tailed sum of signed ranks

Parameters:

CenterVal - the mean/median of the sample

plus - the positive tail of the distribution

Throws:

java.lang.Exception

getSignedRankWProbability

public double getSignedRankWProbability(double W)
                                 throws java.lang.Exception

returns the one-tailed robability of obtaining this Signed Rank W or greater

Parameters:

W - Wilcoxon's Signed Rank Statistic W

Throws:

java.lang.Exception

doCorrelationAnalysis

public void doCorrelationAnalysis(NumberVariable theOtherYVariable)
                           throws java.lang.Exception

fills the regression statistics for the variable with control over th intercept

Parameters:

theOtherYVariable - the independent NumberVariable

Throws:

java.lang.Exception

getCorrelationResults

public com.lobsterman.JavaGrinders.parametric.CorrelationResults getCorrelationResults(NumberVariable theOtherYVariable)
                                                                                throws java.lang.Exception

fills the regression statistics for the variable with control over th intercept

Parameters:

theOtherYVariable - the independent NumberVariable

Throws:

java.lang.Exception

listCorrelationResults

public void listCorrelationResults(NumberVariable theOtherYVariable)

fills the regression statistics for the variable with control over th intercept

Parameters:

theOtherYVariable - the independent NumberVariable

doRegressionAnalysis

public NumberVariable doRegressionAnalysis(NumberVariable theXVariable)
                                    throws java.lang.Exception

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariable - the independent NumberVariable

Throws:

java.lang.Exception

doRegressionAnalysis

public NumberVariable doRegressionAnalysis(NumberVariable theXVariable,
                                           int polyDegree)
                                    throws java.lang.Exception

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariable - the independent NumberVariable

polyDegree - the number of polynomial terms

Throws:

java.lang.Exception

listRegressionResults

public void listRegressionResults(NumberVariable theXVariable)

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariable - the independent NumberVariable

listRegressionResults

public void listRegressionResults(NumberVariable theXVariable,
                                  int polyDegree)

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariable - the independent NumberVariable

polyDegree - the number of polynomial terms

listRegressionResults

public void listRegressionResults(NumberVariable theXVariable,
                                  int polyDegree,
                                  boolean centered)

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariable - the independent NumberVariable

polyDegree - the number of polynomial terms

centered - should the x variable be centered?

getRegressionResults

public com.lobsterman.JavaGrinders.parametric.RegressionResults getRegressionResults(NumberVariable theXVariable)
                                                                              throws java.lang.Exception

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariable - the independent NumberVariable

Throws:

java.lang.Exception

getRegressionResults

public com.lobsterman.JavaGrinders.parametric.RegressionResults getRegressionResults(NumberVariable theXVariable,
                                                                                     int polyDegree)
                                                                              throws java.lang.Exception

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariable - the independent NumberVariable

polyDegree - the number of polynomial terms

Throws:

java.lang.Exception

getRegressionResults

public com.lobsterman.JavaGrinders.parametric.RegressionResults getRegressionResults(NumberVariable theXVariable,
                                                                                     int polyDegree,
                                                                                     boolean centered)
                                                                              throws java.lang.Exception

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariable - the independent NumberVariable

polyDegree - the number of polynomial terms

centered - should the x variable be centered?

Throws:

java.lang.Exception

getRegressionResiduals

public NumberVariable getRegressionResiduals(NumberVariable theXVariable)
                                      throws java.lang.Exception

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariable - the independent NumberVariable

Throws:

java.lang.Exception

getRegressionResiduals

public NumberVariable getRegressionResiduals(NumberVariable theXVariable,
                                             int polyDegree)
                                      throws java.lang.Exception

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariable - the independent NumberVariable

polyDegree - the number of polynomial terms

Throws:

java.lang.Exception

getRegressionResiduals

public NumberVariable getRegressionResiduals(NumberVariable theXVariable,
                                             int polyDegree,
                                             boolean centered)
                                      throws java.lang.Exception

fills the regression statistics for the variable with control over th intercept

Parameters:

theXVariable - the independent NumberVariable

polyDegree - the number of polynomial terms

Throws:

java.lang.Exception

getMultLinRegressionResults

public com.lobsterman.JavaGrinders.parametric.MultRegressionResults getMultLinRegressionResults(VariableOrganizer theXVariableOrganizer)
                                                                                         throws java.lang.Exception

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariableOrganizer - the independent variables in a VariableOrganizer

Throws:

java.lang.Exception

listMultLinRegressionResults

public void listMultLinRegressionResults(VariableOrganizer theXVariableOrganizer)

fills the regression statistics for the variable with control over the intercept

Parameters:

theXVariableOrganizer - the independent variables in a VariableOrganizer

fillCompleteTerms

public void fillCompleteTerms(VariableOrganizer aXOrganizer,
                              com.lobsterman.JavaGrinders.parametric.ANOVAResults theResults)
                       throws java.lang.Exception

fills the n-way interaction terms for the ANOVA

Throws:

java.lang.Exception

getAutoCorrelationResults

public com.lobsterman.JavaGrinders.parametric.CorrelationResults getAutoCorrelationResults()
                                                                                    throws java.lang.Exception

obtains the Autocorrelation statistics for the variable

Throws:

java.lang.Exception

gettTestResults

public com.lobsterman.JavaGrinders.parametric.tTestResults gettTestResults(double mean)
                                                                    throws java.lang.Exception

obtains the t-Test results for the variable

Parameters:

mean - the mean to compare to

Throws:

java.lang.Exception

getANOVAResults

public com.lobsterman.JavaGrinders.parametric.ANOVAResults getANOVAResults(Variable theXVariable)
                                                                    throws java.lang.Exception

fills the ANOVA statistics for the variable

Parameters:

theXVariable - the independent Variable

Throws:

java.lang.Exception

getANOVAResults

public com.lobsterman.JavaGrinders.parametric.ANOVAResults getANOVAResults(VariableOrganizer aXOrganizer)
                                                                    throws java.lang.Exception

fills the ANOVA statistics for a full factorial model

Parameters:

aXOrganizer - the VariableOrganizer containing independent variables

Throws:

java.lang.Exception

fillSS

public void fillSS(com.lobsterman.JavaGrinders.parametric.SquaresCrossproductResults theSSCP)
            throws java.lang.Exception

fills the sums of squares and crossproducts for the variable

Parameters:

theSSCP - the ss/cp results to fill

Throws:

java.lang.Exception

fillCP

public void fillCP(NumberVariable theXVariable,
                   com.lobsterman.JavaGrinders.parametric.SquaresCrossproductResults theSSCP)
            throws java.lang.Exception

returns the sums of squares and crossproducts for the variable

Parameters:

theXVariable - the independent NumberVariable

Throws:

java.lang.Exception

getManWhitneyUResults

public com.lobsterman.JavaGrinders.parametric.ANOVAResults getManWhitneyUResults(Variable theXVar,
                                                                                 double hypAngle)
                                                                          throws java.lang.Exception

returns the results from an analysis of differences in mean angle distance from a hypothetical direction

Parameters:

theXVar - variable that contains information on group assignment

Throws:

java.lang.Exception

checkInOrder

public void checkInOrder()
                  throws java.lang.Exception

examine whether this variables is locked

Throws:

java.lang.Exception

checkInOrder

public void checkInOrder(boolean ascending)
                  throws java.lang.Exception

examine whether this variables is locked

Throws:

java.lang.Exception