Code cleanup; fixed 3 minor bugs in the settings

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

@@ -4,7 +4,6 @@ import lombok.RequiredArgsConstructor;
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Random;
 import java.util.concurrent.ThreadLocalRandom;
 
 @RequiredArgsConstructor

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

@@ -74,13 +74,11 @@ public class DataLoader {
 
         }
 
-        final Forest forest = Forest.<O, FO>builder()
+        return Forest.<O, FO>builder()
                 .trees(treeList)
                 .treeResponseCombiner(treeResponseCombiner)
                 .build();
 
-        return forest;
-
     }
 
     @FunctionalInterface

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

@@ -22,7 +22,6 @@ import java.util.stream.Collectors;
 
 public class Main {
 
-
     public static void main(String[] args) throws IOException, ClassNotFoundException {
         if(args.length < 2){
             System.out.println("Must provide two arguments - the path to the settings.yaml file and instructions to either train or analyze.");
@@ -160,7 +159,7 @@ public class Main {
         yVarSettings.set("type", new TextNode("Double"));
         yVarSettings.set("name", new TextNode("y"));
 
-        final Settings settings =  Settings.builder()
+        return Settings.builder()
                 .covariates(Utils.easyList(
                         new NumericCovariateSettings("x1"),
                         new BooleanCovariateSettings("x2"),
@@ -181,9 +180,6 @@ public class Main {
                 .saveProgress(true)
                 .saveTreeLocation("trees/")
                 .build();
-
-
-        return settings;
     }
 
 }

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

@@ -133,7 +133,7 @@ public class Settings {
                     if(node.hasNonNull("times")){
                         final List<Double> timeList = new ArrayList<>();
                         node.get("times").elements().forEachRemaining(event -> timeList.add(event.asDouble()));
-                        times = eventList.stream().mapToDouble(db -> db).toArray();
+                        times = timeList.stream().mapToDouble(db -> db).toArray();
                     }
 
                     return new CompetingRiskResponseCombiner(events, times);
@@ -152,7 +152,7 @@ public class Settings {
                     if(node.hasNonNull("times")){
                         final List<Double> timeList = new ArrayList<>();
                         node.get("times").elements().forEachRemaining(event -> timeList.add(event.asDouble()));
-                        times = eventList.stream().mapToDouble(db -> db).toArray();
+                        times = timeList.stream().mapToDouble(db -> db).toArray();
                     }
 
                     return new CompetingRiskFunctionCombiner(events, times);
@@ -171,7 +171,7 @@ public class Settings {
                     if(node.hasNonNull("times")){
                         final List<Double> timeList = new ArrayList<>();
                         node.get("times").elements().forEachRemaining(event -> timeList.add(event.asDouble()));
-                        times = eventList.stream().mapToDouble(db -> db).toArray();
+                        times = timeList.stream().mapToDouble(db -> db).toArray();
                     }
 
                     final CompetingRiskResponseCombiner responseCombiner = new CompetingRiskResponseCombiner(events, times);
@@ -217,9 +217,7 @@ public class Settings {
         final ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
         //mapper.enableDefaultTyping();
 
-        final Settings settings = mapper.readValue(file, Settings.class);
+        return mapper.readValue(file, Settings.class);
-
-        return settings;
 
     }
 

src/main/java/ca/joeltherrien/randomforest/covariates/CovariateSettings.java

@@ -14,7 +14,6 @@ import lombok.NoArgsConstructor;
 @Getter
 @JsonTypeInfo(
         use = JsonTypeInfo.Id.NAME,
-        include = JsonTypeInfo.As.PROPERTY,
         property = "type")
 @JsonSubTypes({
         @JsonSubTypes.Type(value = BooleanCovariateSettings.class, name = "boolean"),

src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskFunctions.java

@@ -7,7 +7,6 @@ import lombok.Getter;
 
 import java.io.Serializable;
 import java.util.List;
-import java.util.Map;
 
 @Builder
 public class CompetingRiskFunctions implements Serializable {

src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskResponseWithCensorTime.java

@@ -3,6 +3,7 @@ package ca.joeltherrien.randomforest.responses.competingrisk;
 import ca.joeltherrien.randomforest.DataLoader;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import lombok.Data;
+import lombok.EqualsAndHashCode;
 import lombok.RequiredArgsConstructor;
 import org.apache.commons.csv.CSVRecord;
 
@@ -10,6 +11,7 @@ import org.apache.commons.csv.CSVRecord;
  * See Ishwaran paper on splitting rule modelled after Gray's test. This requires that we know the censor times.
  *
  */
+@EqualsAndHashCode(callSuper = true)
 @Data
 public final class CompetingRiskResponseWithCensorTime extends CompetingRiskResponse {
     private final double c;

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

@@ -7,9 +7,7 @@ import ca.joeltherrien.randomforest.utils.Point;
 import lombok.RequiredArgsConstructor;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 @RequiredArgsConstructor
 public class CompetingRiskFunctionCombiner implements ResponseCombiner<CompetingRiskFunctions, CompetingRiskFunctions> {

src/main/java/ca/joeltherrien/randomforest/tree/Forest.java

@@ -2,7 +2,6 @@ package ca.joeltherrien.randomforest.tree;
 
 import ca.joeltherrien.randomforest.CovariateRow;
 import lombok.Builder;
-import lombok.RequiredArgsConstructor;
 
 import java.util.Collection;
 import java.util.Collections;

src/main/java/ca/joeltherrien/randomforest/tree/ForestTrainer.java

@@ -184,7 +184,7 @@ public class ForestTrainer<Y, TO, FO> {
         private final int treeIndex;
         private final List<Tree<TO>> treeList;
 
-        public TreeInMemoryWorker(final List<Row<Y>> data, final int treeIndex, final List<Tree<TO>> treeList) {
+        TreeInMemoryWorker(final List<Row<Y>> data, final int treeIndex, final List<Tree<TO>> treeList) {
             this.bootstrapper = new Bootstrapper<>(data);
             this.treeIndex = treeIndex;
             this.treeList = treeList;

src/main/java/ca/joeltherrien/randomforest/tree/TreeTrainer.java

@@ -43,9 +43,7 @@ public class TreeTrainer<Y, O> {
     public Tree<O> growTree(List<Row<Y>> data){
 
         final Node<O> rootNode = growNode(data, 0);
-        final Tree<O> tree = new Tree<>(rootNode, data.stream().mapToInt(Row::getId).toArray());
+        return new Tree<>(rootNode, data.stream().mapToInt(Row::getId).toArray());
-
-        return tree;
 
     }
 
@@ -95,8 +93,8 @@ public class TreeTrainer<Y, O> {
         final List<Covariate> splitCovariates = new ArrayList<>(covariates);
         Collections.shuffle(splitCovariates, ThreadLocalRandom.current());
 
-        for(int treeIndex = splitCovariates.size()-1; treeIndex >= mtry; treeIndex--){
+        if (splitCovariates.size() > mtry) {
-            splitCovariates.remove(treeIndex);
+            splitCovariates.subList(mtry, splitCovariates.size()).clear();
         }
 
         return splitCovariates;

src/main/java/ca/joeltherrien/randomforest/utils/Utils.java

@@ -74,9 +74,7 @@ public class Utils {
     public static <T> List<T> easyList(T... array){
         final List<T> list = new ArrayList<>(array.length);
 
-        for(final T item : array){
+        Collections.addAll(list, array);
-            list.add(item);
-        }
 
         return list;
 

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

@@ -16,7 +16,6 @@ import static org.junit.jupiter.api.Assertions.*;
 import java.io.File;
 import java.io.IOException;
 import java.util.List;
-import java.util.Map;
 import java.util.stream.Collectors;
 
 public class TestSavingLoading {

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

@@ -19,7 +19,6 @@ import static org.junit.jupiter.api.Assertions.*;
 
 import java.io.IOException;
 import java.util.List;
-import java.util.Map;
 import java.util.stream.Collectors;
 
 public class TestCompetingRisk {

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

@@ -26,9 +26,7 @@ public class TestCompetingRiskResponseCombiner {
 
         final CompetingRiskResponseCombiner combiner = new CompetingRiskResponseCombiner(new int[]{1,2}, null);
 
-        final CompetingRiskFunctions functions = combiner.combine(data);
+        return combiner.combine(data);
-
-        return functions;
     }
 
     @Test

src/test/java/ca/joeltherrien/randomforest/csv/TestLoadingCSV.java

@@ -18,6 +18,7 @@ import java.util.List;
 import java.util.stream.Collectors;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class TestLoadingCSV {
 
@@ -51,9 +52,7 @@ public class TestLoadingCSV {
 
         final DataLoader.ResponseLoader loader = settings.getResponseLoader();
 
-        final List<Row<Double>> data = DataLoader.loadData(covariates, loader, settings.getDataFileLocation());
+        return DataLoader.loadData(covariates, loader, settings.getDataFileLocation());
-
-        return data;
     }
 
     @Test
@@ -94,9 +93,9 @@ public class TestLoadingCSV {
 
         row = data.get(3);
         assertEquals(-3.0, (double)row.getResponse());
-        assertEquals(true, row.getCovariateValue("x1").isNA());
+        assertTrue(row.getCovariateValue("x1").isNA());
-        assertEquals(true, row.getCovariateValue("x2").isNA());
+        assertTrue(row.getCovariateValue("x2").isNA());
-        assertEquals(true, row.getCovariateValue("x3").isNA());
+        assertTrue(row.getCovariateValue("x3").isNA());
     }
 
 }

src/test/java/ca/joeltherrien/randomforest/settings/TestPersistence.java

@@ -12,7 +12,6 @@ import org.junit.jupiter.api.Test;
 
 import java.io.File;
 import java.io.IOException;
-import java.util.List;
 
 public class TestPersistence {