Package org.biojava.nbio.survival.cox

Class CoxInfo

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

  • Field Details

  • Constructor Details

    • CoxInfo

      public CoxInfo()

  • Method Details

    • getSurvivalInfoList

      public ArrayList<SurvivalInfo> getSurvivalInfoList()
      Returns:

    • setVariance

      public void setVariance(double[][] var) throws Exception
      Parameters:
      var -
      Throws:
      Exception

    • getVariance

      public double[][] getVariance()
      Returns:

    • setNaiveVariance

      public void setNaiveVariance(double[][] var) throws Exception
      Parameters:
      var -
      Throws:
      Exception

    • getNaiveVariance

      public double[][] getNaiveVariance()
      Returns:

    • setSurvivalInfoList

      public void setSurvivalInfoList(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(String name)
      Parameters:
      name -
      Returns:

    • setCoefficient

      public void setCoefficient(String name, CoxCoefficient coefficient)
      Parameters:
      name -
      coefficient -

    • getCoefficientText

      public String getCoefficientText(boolean header, String beginLine, String beginCell, String endCell, String endLine)
      Parameters:
      header -
      beginLine -
      beginCell -
      endCell -
      endLine -
      Returns:

    • fmt

      public static String fmt(Double d, int precision, int pad)
      Parameters:
      d -
      precision -
      pad -
      Returns:

    • dump

      public void dump()

    • fmtpr

      public String fmtpr(String d, int pad)
      Parameters:
      d -
      pad -
      Returns:

    • fmtpl

      public String fmtpl(String d, int pad)
      Pad left a string with spaces
      Parameters:
      d -
      pad -
      Returns:

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • toString

      public String toString(String beginLine, String del, 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 Double getRscore()
      Returns:
      the rscore

    • setRscore

      public void setRscore(Double rscore)
      Parameters:
      rscore - the rscore to set

    • getRscoreLogrankTestpvalue

      public Double getRscoreLogrankTestpvalue()
      Returns:
      the rscoreLogrankTestpvalue

    • setRscoreLogrankTestpvalue

      public void setRscoreLogrankTestpvalue(Double rscoreLogrankTestpvalue)
      Parameters:
      rscoreLogrankTestpvalue - the rscoreLogrankTestpvalue to set

    • getScoreLogrankTest

      public Double getScoreLogrankTest()
      Returns:
      the scoreLogrankTest

    • setScoreLogrankTest

      public void setScoreLogrankTest(Double scoreLogrankTest)
      Parameters:
      scoreLogrankTest - the scoreLogrankTest to set

    • getScoreLogrankTestpvalue

      public Double getScoreLogrankTestpvalue()
      Returns:
      the scoreLogrankTestpvalue

    • setScoreLogrankTestpvalue

      public void setScoreLogrankTestpvalue(Double scoreLogrankTestpvalue)
      Parameters:
      scoreLogrankTestpvalue - the scoreLogrankTestpvalue to set

    • getMetaDataFilter

      public LinkedHashMap<String,String> getMetaDataFilter()
      Returns:
      the metaDataFilter

    • setMetaDataFilter

      public void setMetaDataFilter(LinkedHashMap<String,String> metaDataFilter)
      Parameters:
      metaDataFilter - the metaDataFilter to set

    • getCoefficientsList

      public LinkedHashMap<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