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org.biojava.nbio.survival.cox.CoxInfo Maven / Gradle / Ivy
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.survival.cox;
import org.biojava.nbio.survival.cox.stats.ChiSq;
import org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure;
import org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.LinkedHashMap;
//import org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator;
/**
* Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R
* @author Scooter Willis
*/
public class CoxInfo {
private WaldTestInfo waldTestInfo = null;
String message = "";
Integer maxIterations = null;
Double eps = null;
Double toler = null;
CoxMethod method;
private double[][] imat = null; //:the variance matrix at beta=final
private double[][] naive_imat = null; //the original variance matrix used in residuals
double[] u = new double[0]; //:score vector
int iterations = 0; //:actual number of iterations used
int flag = 0; // success flag 1000 did not converge 1 to nvar: rank of the solution
double logTest = 0;
double logTestpval = 0;
double loglikInit = 0; //loglik at beta=initial values, at beta=final
double loglikFinal = 0;
Double scoreLogrankTest;
private Double rscore = null; //robust score
private Double rscoreLogrankTestpvalue = null;
private double degreeFreedom;
private Double scoreLogrankTestpvalue;
int numSamples = 0;
int numEvents = 0;
private LinkedHashMap metaDataFilter = null;
private LinkedHashMap coefficientsList = new LinkedHashMap<>();
LinkedHashMap baselineSurvivorFunction = new LinkedHashMap<>();
ArrayList survivalInfoList = new ArrayList<>();
/**
*
*/
public KaplanMeierFigure kmf = null;
/**
*
*/
public ExpressionFigure ef = null;
/**
*
* @return
*/
public ArrayList getSurvivalInfoList() {
return survivalInfoList;
}
/**
*
* @param var
* @throws Exception
*/
public void setVariance(double[][] var) throws Exception {
// if (Math.abs(var[0][1] - var[1][0]) > .0000000000001) { //in the CoxCC correction looks like a precision error keeps these from being equal 10-19
// throw new Exception("Expecting diagonal to be equal");
// }
imat = new double[var.length][var[0].length];
for (int i = 0; i < var.length; i++) {
for (int j = 0; j < var[0].length; j++) {
imat[i][j] = var[i][j];
}
}
calcSummaryValues();
}
/**
*
* @return
*/
public double[][] getVariance() {
double[][] var = new double[imat.length][imat[0].length];
for (int i = 0; i < var.length; i++) {
for (int j = 0; j < var[0].length; j++) {
var[i][j] = imat[i][j];
}
}
return var;
}
/**
*
* @param var
* @throws Exception
*/
public void setNaiveVariance(double[][] var) throws Exception {
// if (var[0][1] != var[1][0]) {
// throw new Exception("Expecting diagonal to be equal");
// }
naive_imat = new double[var.length][var[0].length];
for (int i = 0; i < var.length; i++) {
for (int j = 0; j < var[0].length; j++) {
naive_imat[i][j] = var[i][j];
}
}
calcSummaryValues();
}
/**
*
* @return
*/
public double[][] getNaiveVariance() {
double[][] var = new double[imat.length][imat[0].length];
for (int i = 0; i < var.length; i++) {
for (int j = 0; j < var[0].length; j++) {
var[i][j] = naive_imat[i][j];
}
}
return var;
}
/**
*
* @param data
*/
public void setSurvivalInfoList(ArrayList data) {
survivalInfoList = data;
numSamples = data.size();
for (SurvivalInfo si : data) {
if (si.getStatus() == 1) {
numEvents++;
}
}
}
/**
*
* @return
*/
public double[] getWeighted() {
double[] weighted = new double[survivalInfoList.size()];
int p = 0;
for (SurvivalInfo si : this.survivalInfoList) {
weighted[p] = si.getWeight();
p++;
}
return weighted;
}
/**
*
* @return
*/
public double[][] getVariableResiduals() {
ArrayList variables = new ArrayList<>(coefficientsList.keySet());
double[][] rr = new double[survivalInfoList.size()][variables.size()];
int p = 0;
for (SurvivalInfo si : this.survivalInfoList) {
int i = 0;
for (String v : variables) {
rr[p][i] = si.getResidualVariable(v);
i++;
}
p++;
}
return rr;
}
/**
*
* @param rr
*/
public void setVariableResiduals(double[][] rr) {
ArrayList variables = new ArrayList<>(coefficientsList.keySet());
int p = 0;
for (SurvivalInfo si : this.survivalInfoList) {
int i = 0;
for (String v : variables) {
si.setResidualVariable(v, rr[p][i]);
i++;
}
p++;
}
}
/**
*
* @return
*/
public int getNumberCoefficients() {
return coefficientsList.size();
}
/**
*
* @param name
* @return
*/
public CoxCoefficient getCoefficient(String name) {
return coefficientsList.get(name);
}
/**
*
* @param name
* @param coefficient
*/
public void setCoefficient(String name, CoxCoefficient coefficient) {
coefficientsList.put(name, coefficient);
}
/**
*
* @param header
* @param beginLine
* @param beginCell
* @param endCell
* @param endLine
* @return
*/
public String getCoefficientText(boolean header, String beginLine, String beginCell, String endCell, String endLine) {
String o = "";
if (header) {
String robust = "";
if (naive_imat != null) {
robust = beginCell + "robust se" + endCell;
}
o = o + beginLine + beginCell + fmtpl("", 9) + endCell + beginCell + fmtpl("coef", 9) + endCell + beginCell + fmtpl("se(coef)", 9) + endCell + robust + beginCell + fmtpl("z", 9) + endCell + beginCell + fmtpl("p-value", 9) + endCell + beginCell + fmtpl("HR", 9) + endCell + beginCell + fmtpl("lower .95", 9) + endCell + beginCell + fmtpl("upper .95", 9) + endCell + endLine;
}//Coefficients,Coe,StdErr,HR,p-value,HR Lo 95%,HR Hi 95%
for (CoxCoefficient coe : coefficientsList.values()) {
String robust = "";
String stderror = "";
if (naive_imat != null) {
stderror = beginCell + fmt(coe.getRobustStdError(), 5, 9) + endCell;
robust = beginCell + fmt(coe.getStdError(), 5, 9) + endCell;
} else {
stderror = beginCell + fmt(coe.getStdError(), 5, 9) + endCell;
}
o = o + beginLine + beginCell + fmtpr(coe.getName(), 9) + endCell + beginCell + fmt(coe.getCoeff(), 5, 9) + stderror + robust + endCell + beginCell + fmt(coe.getZ(), 5, 9) + endCell + beginCell + fmt(coe.getPvalue(), 6, 9) + endCell + beginCell + fmt(coe.getHazardRatio(), 3, 9) + endCell + beginCell + fmt(coe.getHazardRatioLoCI(), 3, 9) + endCell + beginCell + fmt(coe.getHazardRatioHiCI(), 3, 9) + endCell + endLine;
}
return o;
}
/**
*
* @param d
* @param precision
* @param pad
* @return
*/
public static String fmt(Double d, int precision, int pad) {
if(d == null)
return "";
if(Double.isNaN(d))
return "";
String value = "";
DecimalFormat dfe = new DecimalFormat("0.00E0");
String dpad = "0.";
double p = 1.0;
for (int i = 0; i < (precision); i++) {
dpad = dpad + "0";
p = p / 10.0;
}
DecimalFormat df = new DecimalFormat(dpad);
if (Math.abs(d) >= p) {
value = df.format(d);
} else {
value = dfe.format(d);
}
int length = value.length();
int extra = pad - length;
if (extra > 0) {
for (int i = 0; i < extra; i++) {
value = " " + value;
}
}
return value;
}
/**
*
*/
private void calcSummaryValues() {
//beta
ArrayList variables = new ArrayList<>(coefficientsList.keySet());
for (int i = 0; i < variables.size(); i++) {
String variable = variables.get(i);
CoxCoefficient coe = coefficientsList.get(variable);
coe.setStdError(Math.sqrt(imat[i][i])); //values can be updated to reflect new error
if (naive_imat != null) {
coe.setRobustStdError(Math.sqrt(naive_imat[i][i]));
}
coe.setZ(coe.getCoeff() / coe.getStdError());
coe.setPvalue(ChiSq.norm(Math.abs(coe.getCoeff() / coe.getStdError())));
//z <- qnorm((1 + conf.int)/2, 0, 1)
double z = 1.959964;
coe.setHazardRatioLoCI(Math.exp(coe.getCoeff() - z * coe.getStdError()));
coe.setHazardRatioHiCI(Math.exp(coe.getCoeff() + z * coe.getStdError()));
}
logTest = -2 * (loglikInit - loglikFinal);
logTestpval = ChiSq.chiSq(logTest, (int) degreeFreedom);
scoreLogrankTestpvalue = ChiSq.chiSq(scoreLogrankTest, (int) degreeFreedom);
if (rscore != null) {
rscoreLogrankTestpvalue = ChiSq.chiSq(rscore, (int) degreeFreedom);
}
}
/**
*
*/
public void dump() {
//need an ordered list for comparing to R dumps
// ArrayList orderedSurvivalInfoList = new ArrayList(survivalInfoList);
// SurvivalInfoComparator sicSort = new SurvivalInfoComparator();
// Collections.sort(orderedSurvivalInfoList,sicSort);
System.out.println();
System.out.println("$coef");
for (CoxCoefficient coe : coefficientsList.values()) {
System.out.print(coe.getCoeff() + " ");
}
System.out.println();
System.out.println("$means");
for (CoxCoefficient coe : coefficientsList.values()) {
System.out.print(coe.getMean() + " ");
}
System.out.println();
System.out.println("$u");
for (double d : u) {
System.out.print(d + " ");
}
System.out.println();
System.out.println("$imat");
for (int i = 0; i < imat.length; i++) {
for (int j = 0; j < imat[0].length; j++) {
System.out.print(imat[i][j] + " ");
}
System.out.println();
}
if (this.naive_imat != null) {
System.out.println("$naive_imat");
for (int i = 0; i < naive_imat.length; i++) {
for (int j = 0; j < naive_imat[0].length; j++) {
System.out.print(naive_imat[i][j] + " ");
}
System.out.println();
}
}
System.out.println();
System.out.println("$loglik");
System.out.println(loglikInit + " " + loglikFinal);
System.out.println();
System.out.println("$sctest");
System.out.println(this.scoreLogrankTest);
System.out.println("$iter");
System.out.println(this.iterations);
System.out.println("$flag");
System.out.println(flag);
System.out.println();
// if (false) {
// System.out.println("ID LP Score Residuals");
// for (SurvivalInfo si : orderedSurvivalInfoList) {
// System.out.println(si.getOrder() + " " + si.getLinearPredictor() + " " + si.getScore() + " " + si.getResidual());
//
// }
// System.out.println();
// ArrayList variables = new ArrayList(coefficientsList.keySet());
// System.out.print("Sample");
// for (String v : variables) {
// System.out.print(" " + v);
// }
// System.out.println("rr");
// for (SurvivalInfo si : orderedSurvivalInfoList) {
// System.out.print(si.getOrder());
// for (String v : variables) {
// System.out.print(" " + si.getResidualVariable(v));
// }
// System.out.println();
// }
// }
}
/**
*
* @param d
* @param pad
* @return
*/
public String fmtpr(String d, int pad) {
int length = d.length();
int extra = pad - length;
if (extra < 0) {
extra = 0;
}
String v = d;
for (int i = 0; i < extra; i++) {
v = v + " ";
}
return v;
}
/**
* Pad left a string with spaces
*
* @param d
* @param pad
* @return
*/
public String fmtpl(String d, int pad) {
int length = d.length();
int extra = pad - length;
if (extra < 0) {
extra = 0;
}
String v = d;
for (int i = 0; i < extra; i++) {
v = " " + v;
}
return v;
}
@Override
public String toString() {
return toString("", " ", "\r\n");
}
/**
*
* @param beginLine
* @param del
* @param endLine
* @return
*/
public String toString(String beginLine, String del, String endLine) {
String o = beginLine + fmtpl("", 9) + fmtpl("Avg", 9) + fmtpl("SD", 9) + endLine;
for (CoxCoefficient coe : coefficientsList.values()) {
o = o + beginLine + fmtpr(coe.getName(), 9) + fmt(coe.getMean(), 4, 9) + fmt(coe.getStandardDeviation(), 4, 9) + endLine;
}
o = o + beginLine + endLine;
o = o + beginLine + "n= " + this.numSamples + ", number of events=" + this.numEvents + endLine;
o = o + getCoefficientText(true, beginLine, del, "", endLine);
o = o + beginLine + endLine;
if (baselineSurvivorFunction.size() > 0) {
o = o + beginLine + "Baseline Survivor Function (at predictor means)" + endLine;
for (Double time : baselineSurvivorFunction.keySet()) {
Double mean = baselineSurvivorFunction.get(time);
o = o + beginLine + fmt(time, 4, 10) + fmt(mean, 4, 10) + endLine;
}
}
o = o + beginLine + endLine;
o = o + beginLine + "Overall Model Fit" + endLine;
o = o + beginLine + "Iterations=" + iterations + endLine;
o = o + beginLine + "Likelihood ratio test = " + fmt(this.logTest, 2, 0) + " df=" + this.degreeFreedom + " p-value=" + fmt(this.logTestpval, 7, 0) + endLine;
o = o + beginLine + "Wald test = " + fmt(waldTestInfo.getTest(), 2, 0) + " df=" + waldTestInfo.getDf() + " p-value=" + fmt(waldTestInfo.getPvalue(), 7, 0) + endLine;
o = o + beginLine + "Score (logrank) test = " + fmt(scoreLogrankTest, 2, 0) + " df=" + ((int) (this.degreeFreedom)) + " p-value=" + fmt(this.scoreLogrankTestpvalue, 7, 0);
if (this.rscore != null) {
o = o + ", Robust = " + fmt(rscore, 2, 0) + " p-value=" + fmt(rscoreLogrankTestpvalue, 7, 0);
}
o = o + endLine;
// o = o + "Rank of solution flag=" + flag + "\r\n";
// o = o + "Log lik Initial=" + loglikInit + "\r\n";
// o = o + "Log lik Final=" + loglikFinal + "\r\n";
o = o + beginLine + "Method=" + method.name() + endLine;
return o;
}
/**
* @return the scoreLogrankTest
*/
public double getChiSquare() {
return scoreLogrankTest;
}
/**
* @return the degreeFreedom
*/
public double getDegreeFreedom() {
return degreeFreedom;
}
/**
* @return the scoreLogrankTestpvalue
*/
public double getOverallModelFitPvalue() {
return scoreLogrankTestpvalue;
}
/**
* @return the rscore
*/
public Double getRscore() {
return rscore;
}
/**
* @param rscore the rscore to set
*/
public void setRscore(Double rscore) {
this.rscore = rscore;
if (rscore != null) {
rscoreLogrankTestpvalue = ChiSq.chiSq(rscore, (int) degreeFreedom);
}
}
/**
* @return the rscoreLogrankTestpvalue
*/
public Double getRscoreLogrankTestpvalue() {
return rscoreLogrankTestpvalue;
}
/**
* @param rscoreLogrankTestpvalue the rscoreLogrankTestpvalue to set
*/
public void setRscoreLogrankTestpvalue(Double rscoreLogrankTestpvalue) {
this.rscoreLogrankTestpvalue = rscoreLogrankTestpvalue;
}
/**
* @return the scoreLogrankTest
*/
public Double getScoreLogrankTest() {
return scoreLogrankTest;
}
/**
* @param scoreLogrankTest the scoreLogrankTest to set
*/
public void setScoreLogrankTest(Double scoreLogrankTest) {
this.scoreLogrankTest = scoreLogrankTest;
}
/**
* @return the scoreLogrankTestpvalue
*/
public Double getScoreLogrankTestpvalue() {
return scoreLogrankTestpvalue;
}
/**
* @param scoreLogrankTestpvalue the scoreLogrankTestpvalue to set
*/
public void setScoreLogrankTestpvalue(Double scoreLogrankTestpvalue) {
this.scoreLogrankTestpvalue = scoreLogrankTestpvalue;
}
/**
* @return the metaDataFilter
*/
public LinkedHashMap getMetaDataFilter() {
return metaDataFilter;
}
/**
* @param metaDataFilter the metaDataFilter to set
*/
public void setMetaDataFilter(LinkedHashMap metaDataFilter) {
this.metaDataFilter = metaDataFilter;
}
/**
* @return the coefficientsList
*/
public LinkedHashMap getCoefficientsList() {
return coefficientsList;
}
/**
* @return the waldTestInfo
*/
public WaldTestInfo getWaldTestInfo() {
return waldTestInfo;
}
/**
* @return the imat
*/
public double[][] getImat() {
return imat;
}
/**
* @return the naive_imat
*/
public double[][] getNaive_imat() {
return naive_imat;
}
/**
* @param degreeFreedom the degreeFreedom to set
*/
public void setDegreeFreedom(double degreeFreedom) {
this.degreeFreedom = degreeFreedom;
}
/**
* @param waldTestInfo the waldTestInfo to set
*/
public void setWaldTestInfo(WaldTestInfo waldTestInfo) {
this.waldTestInfo = waldTestInfo;
}
}
