Refactored competing risk combiners and differentiators into their own

packages.

src/main/java/ca/joeltherrien/randomforest/Main.java

@@ -5,6 +5,7 @@ import ca.joeltherrien.randomforest.covariates.Covariate;
 import ca.joeltherrien.randomforest.covariates.FactorCovariateSettings;
 import ca.joeltherrien.randomforest.covariates.NumericCovariateSettings;
 import ca.joeltherrien.randomforest.responses.competingrisk.*;
+import ca.joeltherrien.randomforest.responses.competingrisk.combiner.CompetingRiskFunctionCombiner;
 import ca.joeltherrien.randomforest.tree.Forest;
 import ca.joeltherrien.randomforest.tree.ForestTrainer;
 import ca.joeltherrien.randomforest.utils.MathFunction;
@@ -12,15 +13,9 @@ import ca.joeltherrien.randomforest.utils.Utils;
 import com.fasterxml.jackson.databind.node.JsonNodeFactory;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import com.fasterxml.jackson.databind.node.TextNode;
-import org.apache.commons.csv.CSVFormat;
-import org.apache.commons.csv.CSVParser;
-import org.apache.commons.csv.CSVRecord;
 
 import java.io.*;
-import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 import java.util.stream.Collectors;
 
 public class Main {

src/main/java/ca/joeltherrien/randomforest/Settings.java

@@ -2,6 +2,12 @@ package ca.joeltherrien.randomforest;
 
 import ca.joeltherrien.randomforest.covariates.CovariateSettings;
 import ca.joeltherrien.randomforest.responses.competingrisk.*;
+import ca.joeltherrien.randomforest.responses.competingrisk.combiner.CompetingRiskFunctionCombiner;
+import ca.joeltherrien.randomforest.responses.competingrisk.combiner.CompetingRiskResponseCombiner;
+import ca.joeltherrien.randomforest.responses.competingrisk.differentiator.GrayLogRankMultipleGroupDifferentiator;
+import ca.joeltherrien.randomforest.responses.competingrisk.differentiator.GrayLogRankSingleGroupDifferentiator;
+import ca.joeltherrien.randomforest.responses.competingrisk.differentiator.LogRankMultipleGroupDifferentiator;
+import ca.joeltherrien.randomforest.responses.competingrisk.differentiator.LogRankSingleGroupDifferentiator;
 import ca.joeltherrien.randomforest.responses.regression.MeanGroupDifferentiator;
 import ca.joeltherrien.randomforest.responses.regression.MeanResponseCombiner;
 import ca.joeltherrien.randomforest.responses.regression.WeightedVarianceGroupDifferentiator;

src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskFunctionCombiner.java

@@ -1,5 +1,6 @@
-package ca.joeltherrien.randomforest.responses.competingrisk;
+package ca.joeltherrien.randomforest.responses.competingrisk.combiner;
 
+import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskFunctions;
 import ca.joeltherrien.randomforest.tree.ResponseCombiner;
 import ca.joeltherrien.randomforest.utils.MathFunction;
 import ca.joeltherrien.randomforest.utils.Point;

src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskResponseCombiner.java

@@ -1,5 +1,7 @@
-package ca.joeltherrien.randomforest.responses.competingrisk;
+package ca.joeltherrien.randomforest.responses.competingrisk.combiner;
 
+import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskFunctions;
+import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskResponse;
 import ca.joeltherrien.randomforest.tree.ResponseCombiner;
 import ca.joeltherrien.randomforest.utils.MathFunction;
 import ca.joeltherrien.randomforest.utils.Point;

src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/differentiator/CompetingRiskGroupDifferentiator.java

@@ -1,5 +1,6 @@
-package ca.joeltherrien.randomforest.responses.competingrisk;
+package ca.joeltherrien.randomforest.responses.competingrisk.differentiator;
 
+import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskResponse;
 import ca.joeltherrien.randomforest.tree.GroupDifferentiator;
 import lombok.AllArgsConstructor;
 import lombok.Data;

src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/differentiator/GrayLogRankMultipleGroupDifferentiator.java

@@ -1,5 +1,6 @@
-package ca.joeltherrien.randomforest.responses.competingrisk;
+package ca.joeltherrien.randomforest.responses.competingrisk.differentiator;
 
+import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskResponseWithCensorTime;
 import lombok.RequiredArgsConstructor;
 
 import java.util.List;

src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/differentiator/GrayLogRankSingleGroupDifferentiator.java

@@ -1,5 +1,6 @@
-package ca.joeltherrien.randomforest.responses.competingrisk;
+package ca.joeltherrien.randomforest.responses.competingrisk.differentiator;
 
+import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskResponseWithCensorTime;
 import lombok.RequiredArgsConstructor;
 
 import java.util.List;

src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/differentiator/LogRankMultipleGroupDifferentiator.java

@@ -1,5 +1,6 @@
-package ca.joeltherrien.randomforest.responses.competingrisk;
+package ca.joeltherrien.randomforest.responses.competingrisk.differentiator;
 
+import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskResponse;
 import lombok.RequiredArgsConstructor;
 
 import java.util.List;

src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/differentiator/LogRankSingleGroupDifferentiator.java

@@ -1,5 +1,6 @@
-package ca.joeltherrien.randomforest.responses.competingrisk;
+package ca.joeltherrien.randomforest.responses.competingrisk.differentiator;
 
+import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskResponse;
 import lombok.RequiredArgsConstructor;
 
 import java.util.List;

src/test/java/ca/joeltherrien/randomforest/TestSavingLoading.java

@@ -3,7 +3,7 @@ package ca.joeltherrien.randomforest;
 import ca.joeltherrien.randomforest.covariates.BooleanCovariateSettings;
 import ca.joeltherrien.randomforest.covariates.Covariate;
 import ca.joeltherrien.randomforest.covariates.NumericCovariateSettings;
-import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskFunctionCombiner;
+import ca.joeltherrien.randomforest.responses.competingrisk.combiner.CompetingRiskFunctionCombiner;
 import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskFunctions;
 import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskResponse;
 import ca.joeltherrien.randomforest.tree.Forest;

src/test/java/ca/joeltherrien/randomforest/competingrisk/TestCompetingRiskResponseCombiner.java

@@ -2,12 +2,11 @@ package ca.joeltherrien.randomforest.competingrisk;
 
 import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskFunctions;
 import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskResponse;
-import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskResponseCombiner;
+import ca.joeltherrien.randomforest.responses.competingrisk.combiner.CompetingRiskResponseCombiner;
 import ca.joeltherrien.randomforest.utils.MathFunction;
 import org.junit.jupiter.api.Test;
 
 import static ca.joeltherrien.randomforest.TestUtils.closeEnough;
-import static org.junit.jupiter.api.Assertions.*;
 
 import java.util.ArrayList;
 import java.util.List;

src/test/java/ca/joeltherrien/randomforest/competingrisk/TestLogRankSingleGroupDifferentiator.java

@@ -1,6 +1,7 @@
 package ca.joeltherrien.randomforest.competingrisk;
 
 import ca.joeltherrien.randomforest.responses.competingrisk.*;
+import ca.joeltherrien.randomforest.responses.competingrisk.differentiator.LogRankSingleGroupDifferentiator;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;