Class CoxInfo


  • public class CoxInfo
    extends java.lang.Object
    Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R
    Author:
    Scooter Willis
    • Constructor Detail

      • CoxInfo

        public CoxInfo()
    • Method Detail

      • getSurvivalInfoList

        public java.util.ArrayList<SurvivalInfo> getSurvivalInfoList()
        Returns:
      • setVariance

        public void setVariance​(double[][] var)
                         throws java.lang.Exception
        Parameters:
        var -
        Throws:
        java.lang.Exception
      • getVariance

        public double[][] getVariance()
        Returns:
      • setNaiveVariance

        public void setNaiveVariance​(double[][] var)
                              throws java.lang.Exception
        Parameters:
        var -
        Throws:
        java.lang.Exception
      • getNaiveVariance

        public double[][] getNaiveVariance()
        Returns:
      • setSurvivalInfoList

        public void setSurvivalInfoList​(java.util.ArrayList<SurvivalInfo> data)
        Parameters:
        data -
      • getWeighted

        public double[] getWeighted()
        Returns:
      • getVariableResiduals

        public double[][] getVariableResiduals()
        Returns:
      • setVariableResiduals

        public void setVariableResiduals​(double[][] rr)
        Parameters:
        rr -
      • getNumberCoefficients

        public int getNumberCoefficients()
        Returns:
      • getCoefficient

        public CoxCoefficient getCoefficient​(java.lang.String name)
        Parameters:
        name -
        Returns:
      • setCoefficient

        public void setCoefficient​(java.lang.String name,
                                   CoxCoefficient coefficient)
        Parameters:
        name -
        coefficient -
      • getCoefficientText

        public java.lang.String getCoefficientText​(boolean header,
                                                   java.lang.String beginLine,
                                                   java.lang.String beginCell,
                                                   java.lang.String endCell,
                                                   java.lang.String endLine)
        Parameters:
        header -
        beginLine -
        beginCell -
        endCell -
        endLine -
        Returns:
      • fmt

        public static java.lang.String fmt​(java.lang.Double d,
                                           int precision,
                                           int pad)
        Parameters:
        d -
        precision -
        pad -
        Returns:
      • dump

        public void dump()
      • fmtpr

        public java.lang.String fmtpr​(java.lang.String d,
                                      int pad)
        Parameters:
        d -
        pad -
        Returns:
      • fmtpl

        public java.lang.String fmtpl​(java.lang.String d,
                                      int pad)
        Pad left a string with spaces
        Parameters:
        d -
        pad -
        Returns:
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • toString

        public java.lang.String toString​(java.lang.String beginLine,
                                         java.lang.String del,
                                         java.lang.String endLine)
        Parameters:
        beginLine -
        del -
        endLine -
        Returns:
      • getChiSquare

        public double getChiSquare()
        Returns:
        the scoreLogrankTest
      • getDegreeFreedom

        public double getDegreeFreedom()
        Returns:
        the degreeFreedom
      • getOverallModelFitPvalue

        public double getOverallModelFitPvalue()
        Returns:
        the scoreLogrankTestpvalue
      • getRscore

        public java.lang.Double getRscore()
        Returns:
        the rscore
      • setRscore

        public void setRscore​(java.lang.Double rscore)
        Parameters:
        rscore - the rscore to set
      • getRscoreLogrankTestpvalue

        public java.lang.Double getRscoreLogrankTestpvalue()
        Returns:
        the rscoreLogrankTestpvalue
      • setRscoreLogrankTestpvalue

        public void setRscoreLogrankTestpvalue​(java.lang.Double rscoreLogrankTestpvalue)
        Parameters:
        rscoreLogrankTestpvalue - the rscoreLogrankTestpvalue to set
      • getScoreLogrankTest

        public java.lang.Double getScoreLogrankTest()
        Returns:
        the scoreLogrankTest
      • setScoreLogrankTest

        public void setScoreLogrankTest​(java.lang.Double scoreLogrankTest)
        Parameters:
        scoreLogrankTest - the scoreLogrankTest to set
      • getScoreLogrankTestpvalue

        public java.lang.Double getScoreLogrankTestpvalue()
        Returns:
        the scoreLogrankTestpvalue
      • setScoreLogrankTestpvalue

        public void setScoreLogrankTestpvalue​(java.lang.Double scoreLogrankTestpvalue)
        Parameters:
        scoreLogrankTestpvalue - the scoreLogrankTestpvalue to set
      • getMetaDataFilter

        public java.util.LinkedHashMap<java.lang.String,​java.lang.String> getMetaDataFilter()
        Returns:
        the metaDataFilter
      • setMetaDataFilter

        public void setMetaDataFilter​(java.util.LinkedHashMap<java.lang.String,​java.lang.String> metaDataFilter)
        Parameters:
        metaDataFilter - the metaDataFilter to set
      • getCoefficientsList

        public java.util.LinkedHashMap<java.lang.String,​CoxCoefficient> getCoefficientsList()
        Returns:
        the coefficientsList
      • getWaldTestInfo

        public WaldTestInfo getWaldTestInfo()
        Returns:
        the waldTestInfo
      • getImat

        public double[][] getImat()
        Returns:
        the imat
      • getNaive_imat

        public double[][] getNaive_imat()
        Returns:
        the naive_imat
      • setDegreeFreedom

        public void setDegreeFreedom​(double degreeFreedom)
        Parameters:
        degreeFreedom - the degreeFreedom to set
      • setWaldTestInfo

        public void setWaldTestInfo​(WaldTestInfo waldTestInfo)
        Parameters:
        waldTestInfo - the waldTestInfo to set