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Small changes; more tests.

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This commit is contained in:
Joel Therrien 2019-02-18 14:57:13 -08:00
parent 9f513ab75b
commit e74ba23177
8 changed files with 519 additions and 3 deletions
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6
src/main/java/ca/joeltherrien/randomforest/covariates/Covariate.java
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@ -24,7 +24,7 @@ import java.io.Serializable;
import java.util.*;
import java.util.concurrent.ThreadLocalRandom;
public interface Covariate<V> extends Serializable {
public interface Covariate<V> extends Serializable, Comparable<Covariate> {
String getName();
@ -44,6 +44,10 @@ public interface Covariate<V> extends Serializable {
boolean hasNAs();
default int compareTo(Covariate other){
return getIndex() - other.getIndex();
}
interface Value<V> extends Serializable{
Covariate<V> getParent();

1
src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/differentiator/GrayLogRankMultipleGroupDifferentiator.java
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@ -45,6 +45,7 @@ public class GrayLogRankMultipleGroupDifferentiator extends CompetingRiskGroupDi
for(final int eventOfFocus : events){
final LogRankValue valueOfInterest = specificLogRankValue(eventOfFocus, competingRiskSets);
// we use varianceSqrt instead of variance because numerator is not the same as the individual score
numerator += valueOfInterest.getNumerator()*valueOfInterest.getVarianceSqrt();
denominatorSquared += valueOfInterest.getVariance();

1
src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/differentiator/LogRankMultipleGroupDifferentiator.java
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@ -45,6 +45,7 @@ public class LogRankMultipleGroupDifferentiator extends CompetingRiskGroupDiffer
for(final int eventOfFocus : events){
final LogRankValue valueOfInterest = specificLogRankValue(eventOfFocus, competingRiskSets);
// we use varianceSqrt instead of variance because numerator is not the same as the individual score
numerator += valueOfInterest.getNumerator()*valueOfInterest.getVarianceSqrt();
denominatorSquared += valueOfInterest.getVariance();

2
src/main/java/ca/joeltherrien/randomforest/tree/Forest.java
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@ -67,7 +67,7 @@ public class Forest<O, FO> { // O = output of trees, FO = forest output. In prac
}
public Map<Covariate, Integer> findSplitsByCovariate(){
final Map<Covariate, Integer> countMap = new HashMap<>();
final Map<Covariate, Integer> countMap = new TreeMap<>();
for(final Tree<O> tree : getTrees()){
final Node<O> rootNode = tree.getRootNode();

1
src/main/java/ca/joeltherrien/randomforest/tree/TreeTrainer.java
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@ -63,7 +63,6 @@ public class TreeTrainer<Y, O> {
}
public Tree<O> growTree(List<Row<Y>> data, Random random){
final Node<O> rootNode = growNode(data, 0, random);
return new Tree<>(rootNode, data.stream().mapToInt(Row::getId).toArray());

67
src/main/java/ca/joeltherrien/randomforest/utils/RightContinuousStepFunction.java
View file

@ -120,4 +120,71 @@ public final class RightContinuousStepFunction extends StepFunction {
return builder.toString();
}
public double integrate(final double from, final double to){
if(to == from){
return 0;
}
if(to < from){
return integrate(to, from);
}
double summation = 0.0;
final double[] xPoints = getX();
final int startingIndex;
if(from > xPoints[0]){
// find largest index of time such that it's less than or equal to from
final int firstLevelIndex = Utils.binarySearchLessThan(0, xPoints.length, xPoints, from);
final double currentHeight = evaluateByIndex(firstLevelIndex);
startingIndex = firstLevelIndex+1; // the looping part of the code will start at the next index
if(startingIndex == xPoints.length){ // turns out that 'from' is beyond the last point
return currentHeight * (to - from);
}
final double timeAtNextHeight = xPoints[startingIndex];
if(timeAtNextHeight >= to){
return currentHeight * (to - from);
}
summation += currentHeight * (timeAtNextHeight - from);
}
else if(from < xPoints[0]){
if(to <= xPoints[0]){
return defaultY*(to - from);
}
startingIndex = 0;
summation += defaultY * (xPoints[0] - from);
}
else{
startingIndex = 0;
}
int i;
for(i=startingIndex; i<xPoints.length; i++){
final double currentTime = xPoints[i];
final double currentHeight = evaluateByIndex(i);
if(i == xPoints.length-1 || xPoints[i+1] > to){
summation += currentHeight * (to - currentTime);
return summation;
}
final double nextTime = xPoints[i+1];
summation += currentHeight * (nextTime - currentTime);
}
// We should have returned at some point before now
throw new RuntimeException("Serious bug in integration code; this line should have never been run");
}
}

22
src/test/java/ca/joeltherrien/randomforest/competingrisk/TestLogRankMultipleGroupDifferentiator.java
View file

@ -91,6 +91,28 @@ public class TestLogRankMultipleGroupDifferentiator {
}
@Test
public void testSplitRuleV2() throws IOException {
final LogRankMultipleGroupDifferentiator groupDifferentiator = new LogRankMultipleGroupDifferentiator(new int[]{1,2});
final List<Row<CompetingRiskResponse>> data = loadData("src/test/resources/new_data_that_triggers_difference_composite.csv").getRows();
final List<Row<CompetingRiskResponse>> group1Bad = data.subList(0, 196);
final List<Row<CompetingRiskResponse>> group2Bad = data.subList(196, data.size());
final double scoreBad = groupDifferentiator.differentiate(turnIntoSplitIterator(group1Bad, group2Bad)).getScore();
final List<Row<CompetingRiskResponse>> group1Good = data.subList(0, 199);
final List<Row<CompetingRiskResponse>> group2Good= data.subList(199, data.size());
final double scoreGood = groupDifferentiator.differentiate(turnIntoSplitIterator(group1Good, group2Good)).getScore();
// expected results calculated manually using survival::survdiff in R; see issue #10 in Gitea
closeEnough(71.41135, scoreBad, 0.00001);
closeEnough(71.5354, scoreGood, 0.00001);
}
private void closeEnough(double expected, double actual, double margin){
assertTrue(Math.abs(expected - actual) < margin, "Expected " + expected + " but saw " + actual);
}

422
src/test/resources/new_data_that_triggers_difference_composite.csv Normal file
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@ -0,0 +1,422 @@
"T","J","x1","x2","x3","set","C","u","delta"
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6.26589199230665,1,-1.54140235787167,-2.30006437514968,0.233748690841754,"d1",25.4117258257213,6.26589199230665,1
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2.78052458150272,2,-0.551926772252824,-2.09000455633969,-0.177623152985041,"d1",30.9898108972197,2.78052458150272,2
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0.451999953016639,2,-0.812418624513425,-1.55229147176324,-0.349728885283845,"d1",20.7824087638621,0.451999953016639,2
0.66187332617119,2,-0.508034279805,-1.53046688766278,-0.125548243031678,"d1",1.05018629103254,0.66187332617119,2
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6.06766719635048,1,-1.55037485195067,-1.34567809527089,-0.760841361837919,"d1",1.09786237904911,1.09786237904911,0
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1 T J x1 x2 x3 set C u delta
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