Field Detail

• kmf

  public KaplanMeierFigure kmf

• ef

  public ExpressionFigure ef

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