flanagan.physchem

Class ImmunoAssay

java.lang.Object

flanagan.analysis.Regression

flanagan.physchem.ImmunoAssay

public class ImmunoAssay
extends Regression

Constructor Summary

Constructors

Constructor and Description
ImmunoAssay()
ImmunoAssay(double[] analytes, double[] responses)
ImmunoAssay(double[] analytes, double[] responses, double[] yWeights)
ImmunoAssay(double[] analytes, double[] responses, double[] xWeights, double[] yWeights)
ImmunoAssay(double[] analytes, double[] responses, double[] xWeights, double[] yWeights, java.lang.String title)
ImmunoAssay(double[] analytes, double[] responses, double[] yWeights, java.lang.String title)
ImmunoAssay(double[] analytes, double[] responses, java.lang.String title)
ImmunoAssay(java.lang.String title)

Method Summary

Modifier and Type	Method and Description
void	amershamFit()
void	amershamFit(double[] estimates)
int	bestPolynomialFit()
void	commonPrint(FileOutput fout)
void	compare()
void	compare(double significance)
void	compare(double significance, java.lang.String filename)
void	compare(int model1index, int model2index)
void	compare(int model1index, int model2index, double significance)
void	compare(int model1index, int degree1, double bottom1, double top1, int nTerms1, int model2index, int degree2, double bottom2, double top2, int nTerms2, double significance, java.lang.String filename)
void	compare(int model1index, int degree1, int model2index, int degree2)
void	compare(int model1index, int degree1, int model2index, int degree2, double significance)
void	compare(int model1index, int degree1, int model2index, int degree2, java.lang.String filename)
void	compare(int model1index, int model2index, java.lang.String filename)
void	compare(java.lang.String filename)
static java.util.ArrayList<java.lang.Object>	comparisonTest(int[] modelXindices, double sumOfSquares1, int nParameters1, int nData1, double sumOfSquares2, int nParameters2, int nData2, double significance)
static double	convertSurfaceToVolumeConcn(double surfaceConcn, double area, double volume)
void	cubicInterpolation()
void	cubicSpline()
void	deleteFile(java.lang.String fileName)
void	ec50Fit()
void	ec50Fit(double bottom, double top)
static double	effectiveRadius(double diffusionCoefficient, double viscosity, double temperature)
void	enterAnalyteConcns(double[] concn)
void	enterAnalyteConcnsAsLog10(double[] logconcn)
void	enterAnalyteConcnsAsLogE(double[] logconcn)
void	enterMultiplicativeWeights(double[] yWeights)
void	enterMultiplicativeWeightsAsLog10(double[] yWeights)
void	enterMultiplicativeWeightsAsLogE(double[] yWeights)
void	enterResponses(double[] responses)
void	enterResponsesAsLog10(double[] responses)
void	enterResponsesAsLogE(double[] responses)
void	enterTitle(java.lang.String title)
void	enterWeights(double[] yWeights)
void	enterWeightsAslog10(double[] yWeights)
void	enterWeightsAslogE(double[] yWeights)
static double	equivalentVolumeConcn(double effectiveRadius, double area, double volume)
static double	equivalentVolumeConcn(double molWt, double area, double volume, double specVol)
void	fiveParameterLogisticFit()
void	fiveParameterLogisticFit(double bottom, double top)
void	fourParameterLogisticFit()
void	fourParameterLogisticFit(double bottom, double top)
double[]	getAnalyteConcns()
double[]	getFittedStandardCurveConcns()
double[]	getFittedStandardCurveResponses()
double[]	getModelParameterErrors()
double[]	getModelParameterValues()
static double	getMolWeightIgA1()
static double	getMolWeightIgA2()
static double	getMolWeightIgD()
static double	getMolWeightIgE()
static double	getMolWeightIgG1()
static double	getMolWeightIgG2()
static double	getMolWeightIgG3()
static double	getMolWeightIgG4()
static double	getMolWeightIgM()
int	getNumberOfTurningPoints()
double[]	getResponses()
double	getSampleConcn(double response)
double	getSampleConcnError()
double	getSumOfSquares()
java.lang.String	getTitle()
double[]	getTurningPointConcns()
double[]	getTurningPointResponses()
double	getUnWeightedSumOfSquares()
double	getWeightedSumOfSquares()
double[]	getWorkingConcentrationRange()
double[]	getWorkingResponseRange()
static boolean	isMonotonic(double[] x)
void	linearInterpolation()
static double	molecularRadius(double molWt)
static double	molecularRadius(double molWt, double specVol)
void	nonIntegerPolynomialFit()
void	nonIntegerPolynomialFit(int polyNterms)
void	polynomialFit(int n)
void	print()
void	print(java.lang.String filename)
void	readFromFile()
void	readFromFile(java.lang.String filename)
void	rectangularHyperbolaFit()
void	resetNfittedCurve(int nInterp)
void	resetPlotOption(int opt)
void	selectEquation()
void	setData()
void	setNintyFiveLevel()
void	setNintyNineLevel()
void	setWeightsAsResponses()
void	setWeightsAsSqrtResponses()
void	shiftedRectangularHyperbolaFit()
void	sigmoidThresholdFit()
void	sipsSigmoidFit()
static double	surfaceMolarConcn(double effectiveRadius)
static double	surfaceMolarConcn(double molWt, double specVol)
static double	surfaceNumberConcn(double effectiveRadius)
static double	surfaceNumberConcn(double molWt, double specVol)

Methods inherited from class flanagan.analysis.Regression

addConstraint, addConstraint, addConstraint, addLegends, bestPolynomial, bestPolynomial, bestPolynomialPlot, bestPolynomialPlot, bestPolynomialPlot, bestPolynomialPlot, beta, betaMinMax, betaMinMaxPlot, betaPlot, calculateCumulativeValues, checkYallSmall, checkZeroNeg, constant, constantPlot, constantPlot, ec50, ec50constrained, ec50constrainedPlot, ec50Plot, enterData, enterData, enterData, enterData, enterData, enterData, enterData, enterData, enterData, enterData, enterData, enterData, enterData, enterData, erlang, erlangPlot, exponential, exponentialMultiple, exponentialMultiple, exponentialMultiplePlot, exponentialMultiplePlot, exponentialOnePar, exponentialOneParPlot, exponentialPlot, exponentialSimple, exponentialSimplePlot, exponentialStandard, exponentialStandardPlot, fitOneOrSeveralDistributions, fiveParameterLogistic, fiveParameterLogistic, fiveParameterLogisticPlot, fiveParameterLogisticPlot, fourParameterLogistic, fourParameterLogisticConstrained, fourParameterLogisticConstrainedPlot, fourParameterLogisticPlot, frechet, frechetPlot, frechetStandard, frechetStandardPlot, frechetTwoPar, frechetTwoParPlot, gamma, gammaPlot, gammaStandard, gammaStandardPlot, gaussian, gaussian, gaussianPlot, gaussianPlot, getAdjustedCoefficientOfDetermination, getBestEstimates, getBestEstimatesErrors, getbestestimatesStandardDeviations, getBestEstimatesStandardDeviations, getCFmaxIter, getCFtolerance, getChiSquare, getCoeff, getCoeffDeterminationFratio, getCoeffDeterminationFratioProb, getCoefficientOfDetermination, getCoeffSd, getCoeffVar, getCorrCoeffMatrix, getCovMatrix, getDegFree, getDelta, getFirstDerivatives, getFtestSignificance, getGrad, getInitialEstimates, getInitialSteps, getInversionCheck, getKayValue, getMinTest, getNdata, getNiter, getNlrStatus, getNmax, getNMcontract, getNMextend, getNmin, getNMreflect, getNparameters, getNrestarts, getNrestartsMax, getPosVarCheck, getPseudoErrors, getPseudoSd, getPvalues, getReducedChiSquare, getRegressionSumOfWeightedSquares, getResiduals, getSampleR, getScale, getScaledInitialEstimates, getScaledInitialSteps, getSimplexSd, getSumOfUnweightedResidualSquares, getSumOfWeightedResidualSquares, getTolerance, getTotalSumOfWeightedSquares, getTrueFreq, getTvalues, getVarianceOfObserations, getWeightedResiduals, getWeights, getXdata, getXYcorrCoeff, getYcalc, getYdata, getYscale, getYscaleOption, getYYcorrCoeff, gumbelMax, gumbelMaxOnePar, gumbelMaxOneParPlot, gumbelMaxPlot, gumbelMaxStandard, gumbelMaxStandardPlot, gumbelMin, gumbelMinOnePar, gumbelMinOneParPlot, gumbelMinPlot, gumbelMinStandard, gumbelMinStandardPlot, histogramBins, histogramBins, histogramBins, ignoreDofFcheck, infinityCheck, linear, linear, linearDual, linearGeneral, linearGeneralDual, linearGeneralMono, linearGeneralPlot, linearGeneralPlot, linearGeneralPlotDual, linearGeneralPlotDual, linearGeneralPlotMono, linearGeneralPlotMono, linearMono, linearMono, linearPlot, linearPlot, linearPlot, linearPlot, linearPlotDual, linearPlotDual, linearPlotDual, linearPlotDual, linearPlotMono, linearPlotMono, linearPlotMono, linearPlotMono, logistic, logisticPlot, logNormal, logNormalPlot, logNormalThreePar, logNormalThreeParPlot, logNormalTwoPar, logNormalTwoParPlot, lorentzian, lorentzianPlot, multipleGaussiansPlot, nonIntegerPolynomial, nonIntegerPolynomial, nonIntegerPolynomialPlot, nonIntegerPolynomialPlot, nonIntegerPolynomialPlot, nonIntegerPolynomialPlot, normal, normal, normalPlot, normalPlot, oneMinusExponential, oneMinusExponentialPlot, pareto, paretoOnePar, paretoOneParPlot, paretoPlot, paretoShifted, paretoShiftedPlot, paretoThreePar, paretoThreeParPlot, paretoTwoPar, paretoTwoParPlot, plotXY, plotXYfixed, plotXYnonlinear, plotYY, plotYY, poisson, poissonPlot, polynomial, polynomial, polynomialBest, polynomialBest, polynomialPlot, polynomialPlot, polynomialPlot, polynomialPlot, print, print, rayleigh, rayleighPlot, rectangularHyperbola, rectangularHyperbolaPlot, reinstateStats, removeConstraints, resetCFmaxIter, resetCFtolerance, reverseYsign, setCloseChoice, setConstraintTolerance, setDelta, setDenominatorToN, setDenominatorToNminusOne, setErrorsAsScaled, setErrorsAsSD, setFtestSignificance, setMinTest, setNmax, setNMcontract, setNMextend, setNmin, setNMreflect, setNrestartsMax, setScale, setScale, setTitle, setTolerance, setTrueFreq, setXlegend, setYlegend, setYscale, setYscaleFactor, setYscaleOption, shiftedRectangularHyperbola, shiftedRectangularHyperbolaPlot, sigmoidHillSips, sigmoidHillSipsPlot, sigmoidThreshold, sigmoidThresholdPlot, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex, simplex2, simplex2, simplex2, simplex2, simplex2, simplex2, simplex2, simplex2, simplex2, simplex2, simplex2, simplex2, simplex2, simplex2, simplex2, simplex2, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, simplexPlot2, stepFunction, stepFunctionPlot, supressErrorMessages, supressPrint, supressStats, supressYYplot, testOfAdditionalTerms_ArrayList, testOfAdditionalTerms_ArrayList, testOfAdditionalTerms, testOfAdditionalTerms, testOfAdditionalTermsFprobability, testOfAdditionalTermsFprobability, testOfAdditionalTermsFprobabilty, testOfAdditionalTermsFratio, testOfAdditionalTermsFratio, weibull, weibullPlot, weibullStandard, weibullStandardPlot, weibullTwoPar, weibullTwoParPlot

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ImmunoAssay

public ImmunoAssay()

ImmunoAssay

public ImmunoAssay(java.lang.String title)

ImmunoAssay

public ImmunoAssay(double[] analytes,
                   double[] responses)

ImmunoAssay

public ImmunoAssay(double[] analytes,
                   double[] responses,
                   double[] yWeights)

ImmunoAssay

public ImmunoAssay(double[] analytes,
                   double[] responses,
                   double[] xWeights,
                   double[] yWeights)

ImmunoAssay

public ImmunoAssay(double[] analytes,
                   double[] responses,
                   double[] yWeights,
                   java.lang.String title)

ImmunoAssay

public ImmunoAssay(double[] analytes,
                   double[] responses,
                   java.lang.String title)

ImmunoAssay

public ImmunoAssay(double[] analytes,
                   double[] responses,
                   double[] xWeights,
                   double[] yWeights,
                   java.lang.String title)

Method Detail

enterAnalyteConcns

public void enterAnalyteConcns(double[] concn)

enterAnalyteConcnsAsLog10

public void enterAnalyteConcnsAsLog10(double[] logconcn)

enterAnalyteConcnsAsLogE

public void enterAnalyteConcnsAsLogE(double[] logconcn)

enterResponses

public void enterResponses(double[] responses)

enterResponsesAsLog10

public void enterResponsesAsLog10(double[] responses)

enterResponsesAsLogE

public void enterResponsesAsLogE(double[] responses)

enterWeights

public void enterWeights(double[] yWeights)

enterWeightsAslog10

public void enterWeightsAslog10(double[] yWeights)

enterWeightsAslogE

public void enterWeightsAslogE(double[] yWeights)

enterMultiplicativeWeights

public void enterMultiplicativeWeights(double[] yWeights)

enterMultiplicativeWeightsAsLog10

public void enterMultiplicativeWeightsAsLog10(double[] yWeights)

enterMultiplicativeWeightsAsLogE

public void enterMultiplicativeWeightsAsLogE(double[] yWeights)

setWeightsAsResponses

public void setWeightsAsResponses()

setWeightsAsSqrtResponses

public void setWeightsAsSqrtResponses()

enterTitle

public void enterTitle(java.lang.String title)

readFromFile

public void readFromFile()

readFromFile

public void readFromFile(java.lang.String filename)

getAnalyteConcns

public double[] getAnalyteConcns()

getResponses

public double[] getResponses()

getTitle

public java.lang.String getTitle()

cubicSpline

public void cubicSpline()

cubicInterpolation

public void cubicInterpolation()

linearInterpolation

public void linearInterpolation()

polynomialFit

public void polynomialFit(int n)

bestPolynomialFit

public int bestPolynomialFit()

nonIntegerPolynomialFit

public void nonIntegerPolynomialFit(int polyNterms)

nonIntegerPolynomialFit

public void nonIntegerPolynomialFit()

sigmoidThresholdFit

public void sigmoidThresholdFit()

sipsSigmoidFit

public void sipsSigmoidFit()

fourParameterLogisticFit

public void fourParameterLogisticFit()

ec50Fit

public void ec50Fit()

fourParameterLogisticFit

public void fourParameterLogisticFit(double bottom,
                                     double top)

ec50Fit

public void ec50Fit(double bottom,
                    double top)

fiveParameterLogisticFit

public void fiveParameterLogisticFit()

fiveParameterLogisticFit

public void fiveParameterLogisticFit(double bottom,
                                     double top)

shiftedRectangularHyperbolaFit

public void shiftedRectangularHyperbolaFit()

rectangularHyperbolaFit

public void rectangularHyperbolaFit()

amershamFit

public void amershamFit()

amershamFit

public void amershamFit(double[] estimates)

selectEquation

public void selectEquation()

setData

public void setData()

setNintyNineLevel

public void setNintyNineLevel()

setNintyFiveLevel

public void setNintyFiveLevel()

resetPlotOption

public void resetPlotOption(int opt)

getSampleConcn

public double getSampleConcn(double response)

getSampleConcnError

public double getSampleConcnError()

resetNfittedCurve

public void resetNfittedCurve(int nInterp)

getFittedStandardCurveConcns

public double[] getFittedStandardCurveConcns()

getFittedStandardCurveResponses

public double[] getFittedStandardCurveResponses()

getWorkingConcentrationRange

public double[] getWorkingConcentrationRange()

getWorkingResponseRange

public double[] getWorkingResponseRange()

getModelParameterValues

public double[] getModelParameterValues()

getModelParameterErrors

public double[] getModelParameterErrors()

getNumberOfTurningPoints

public int getNumberOfTurningPoints()

getSumOfSquares

public double getSumOfSquares()

Overrides:

getSumOfSquares in class Regression

getUnWeightedSumOfSquares

public double getUnWeightedSumOfSquares()

getWeightedSumOfSquares

public double getWeightedSumOfSquares()

getTurningPointConcns

public double[] getTurningPointConcns()

getTurningPointResponses

public double[] getTurningPointResponses()

print

public void print()

Overrides:

print in class Regression

print

public void print(java.lang.String filename)

Overrides:

print in class Regression

commonPrint

public void commonPrint(FileOutput fout)

compare

public void compare()

compare

public void compare(double significance)

compare

public void compare(java.lang.String filename)

compare

public void compare(double significance,
                    java.lang.String filename)

compare

public void compare(int model1index,
                    int model2index)

compare

public void compare(int model1index,
                    int model2index,
                    double significance)

compare

public void compare(int model1index,
                    int degree1,
                    int model2index,
                    int degree2,
                    double significance)

compare

public void compare(int model1index,
                    int model2index,
                    java.lang.String filename)

compare

public void compare(int model1index,
                    int degree1,
                    int model2index,
                    int degree2,
                    java.lang.String filename)

compare

public void compare(int model1index,
                    int degree1,
                    int model2index,
                    int degree2)

compare

public void compare(int model1index,
                    int degree1,
                    double bottom1,
                    double top1,
                    int nTerms1,
                    int model2index,
                    int degree2,
                    double bottom2,
                    double top2,
                    int nTerms2,
                    double significance,
                    java.lang.String filename)

comparisonTest

public static java.util.ArrayList<java.lang.Object> comparisonTest(int[] modelXindices,
                                                                   double sumOfSquares1,
                                                                   int nParameters1,
                                                                   int nData1,
                                                                   double sumOfSquares2,
                                                                   int nParameters2,
                                                                   int nData2,
                                                                   double significance)

deleteFile

public void deleteFile(java.lang.String fileName)

isMonotonic

public static boolean isMonotonic(double[] x)

surfaceNumberConcn

public static double surfaceNumberConcn(double molWt,
                                        double specVol)

surfaceNumberConcn

public static double surfaceNumberConcn(double effectiveRadius)

surfaceMolarConcn

public static double surfaceMolarConcn(double molWt,
                                       double specVol)

surfaceMolarConcn

public static double surfaceMolarConcn(double effectiveRadius)

equivalentVolumeConcn

public static double equivalentVolumeConcn(double molWt,
                                           double area,
                                           double volume,
                                           double specVol)

equivalentVolumeConcn

public static double equivalentVolumeConcn(double effectiveRadius,
                                           double area,
                                           double volume)

convertSurfaceToVolumeConcn

public static double convertSurfaceToVolumeConcn(double surfaceConcn,
                                                 double area,
                                                 double volume)

molecularRadius

public static double molecularRadius(double molWt,
                                     double specVol)

molecularRadius

public static double molecularRadius(double molWt)

effectiveRadius

public static double effectiveRadius(double diffusionCoefficient,
                                     double viscosity,
                                     double temperature)

getMolWeightIgG1

public static double getMolWeightIgG1()

getMolWeightIgG2

public static double getMolWeightIgG2()

getMolWeightIgG3

public static double getMolWeightIgG3()

getMolWeightIgG4

public static double getMolWeightIgG4()

getMolWeightIgM

public static double getMolWeightIgM()

getMolWeightIgA1

public static double getMolWeightIgA1()

getMolWeightIgA2

public static double getMolWeightIgA2()

getMolWeightIgD

public static double getMolWeightIgD()

getMolWeightIgE

public static double getMolWeightIgE()