org.biojava.nbio.survival.cox

Class CoxR

java.lang.Object

org.biojava.nbio.survival.cox.CoxR

public class CoxR
extends Object

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor and Description
CoxR()

Method Summary

Methods

Modifier and Type	Method and Description
static void	calculateWaldTestInfo(CoxInfo ci)
void	coxphfitSCleanup(CoxInfo ci, boolean useWeighted, boolean robust, ArrayList<String> cluster)
double	coxsafe(double x)
static void	main(String[] args)
CoxInfo	process(ArrayList<String> variables, ArrayList<SurvivalInfo> DataT, boolean useStrata, boolean useWeighted, boolean robust, boolean cluster)
CoxInfo	process(ArrayList<String> variables, ArrayList<SurvivalInfo> data, int maxiter, CoxMethod method, double eps, double toler, double[] beta, int doscale, boolean useStrata, boolean useWeighted, boolean robust, boolean cluster)

Methods inherited from class java.lang.Object

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

Constructor Detail

CoxR

public CoxR()

Method Detail

process

public CoxInfo process(ArrayList<String> variables,
              ArrayList<SurvivalInfo> DataT,
              boolean useStrata,
              boolean useWeighted,
              boolean robust,
              boolean cluster)
                throws Exception

Parameters:

variables -

DataT -

useStrata -

useWeighted -

robust -

cluster -

Returns:

Throws:

Exception

process

public CoxInfo process(ArrayList<String> variables,
              ArrayList<SurvivalInfo> data,
              int maxiter,
              CoxMethod method,
              double eps,
              double toler,
              double[] beta,
              int doscale,
              boolean useStrata,
              boolean useWeighted,
              boolean robust,
              boolean cluster)
                throws Exception

Parameters:

variables -

data -

maxiter -

method -

eps -

toler -

beta -

doscale -

useStrata -

useWeighted -

robust -

cluster -

Returns:

Throws:

Exception

coxphfitSCleanup

public void coxphfitSCleanup(CoxInfo ci,
                    boolean useWeighted,
                    boolean robust,
                    ArrayList<String> cluster)
                      throws Exception

Parameters:

ci -

useWeighted -

robust -

cluster -

Throws:

Exception

calculateWaldTestInfo

public static void calculateWaldTestInfo(CoxInfo ci)

main

public static void main(String[] args)

Parameters:

args - the command line arguments

coxsafe

public double coxsafe(double x)

Parameters:

x -

Returns: