Add alternative way where functions are computed only at final step.

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

@@ -6,8 +6,10 @@ 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.responses.competingrisk.combiner.alternative.CompetingRiskListCombiner;
 import ca.joeltherrien.randomforest.tree.Forest;
 import ca.joeltherrien.randomforest.tree.ForestTrainer;
+import ca.joeltherrien.randomforest.tree.ResponseCombiner;
 import ca.joeltherrien.randomforest.utils.MathFunction;
 import ca.joeltherrien.randomforest.utils.Utils;
 import com.fasterxml.jackson.databind.node.JsonNodeFactory;
@@ -54,16 +56,29 @@ public class Main {
 
             if(args.length < 3){
                 System.out.println("Specify error sample size");
+                return;
             }
 
             final String yVarType = settings.getYVarSettings().get("type").asText();
 
             if(!yVarType.equalsIgnoreCase("CompetingRiskResponse") && !yVarType.equalsIgnoreCase("CompetingRiskResponseWithCensorTime")){
                 System.out.println("Analyze currently only works on competing risk data");
+                return;
             }
 
-            final CompetingRiskFunctionCombiner responseCombiner = (CompetingRiskFunctionCombiner) settings.getTreeCombiner();
-            final int[] events = responseCombiner.getEvents();
+            final ResponseCombiner<?, CompetingRiskFunctions> responseCombiner = settings.getTreeCombiner();
+            final int[] events;
+
+            if(responseCombiner instanceof CompetingRiskFunctionCombiner){
+                events = ((CompetingRiskFunctionCombiner) responseCombiner).getEvents();
+            }
+            else if(responseCombiner instanceof CompetingRiskListCombiner){
+                events = ((CompetingRiskListCombiner) responseCombiner).getOriginalCombiner().getEvents();
+            }
+            else{
+                System.out.println("Unsupported tree combiner");
+                return;
+            }
 
             final List<Row<CompetingRiskResponse>> dataset = DataLoader.loadData(covariates, settings.getResponseLoader(), settings.getDataFileLocation());
 
@@ -72,7 +87,7 @@ public class Main {
             Utils.reduceListToSize(dataset, n);
 
             final File folder = new File(settings.getSaveTreeLocation());
-            final Forest<CompetingRiskFunctions, CompetingRiskFunctions> forest = DataLoader.loadForest(folder, responseCombiner);
+            final Forest<?, CompetingRiskFunctions> forest = DataLoader.loadForest(folder, responseCombiner);
 
             System.out.println("Finished loading trees + dataset; creating calculator and evaluating OOB predictions");
 

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

@@ -4,6 +4,8 @@ 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.combiner.alternative.CompetingRiskListCombiner;
+import ca.joeltherrien.randomforest.responses.competingrisk.combiner.alternative.CompetingRiskResponseCombinerToList;
 import ca.joeltherrien.randomforest.responses.competingrisk.differentiator.GrayLogRankMultipleGroupDifferentiator;
 import ca.joeltherrien.randomforest.responses.competingrisk.differentiator.GrayLogRankSingleGroupDifferentiator;
 import ca.joeltherrien.randomforest.responses.competingrisk.differentiator.LogRankMultipleGroupDifferentiator;
@@ -158,6 +160,30 @@ public class Settings {
                 }
         );
 
+        registerResponseCombinerConstructor("CompetingRiskListCombiner",
+                (node) -> {
+                    final List<Integer> eventList = new ArrayList<>();
+                    node.get("events").elements().forEachRemaining(event -> eventList.add(event.asInt()));
+                    final int[] events = eventList.stream().mapToInt(i -> i).toArray();
+
+                    double[] times = null;
+                    // note that times may be null
+                    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();
+                    }
+
+                    final CompetingRiskResponseCombiner responseCombiner = new CompetingRiskResponseCombiner(events, times);
+                    return new CompetingRiskListCombiner(responseCombiner);
+
+                }
+        );
+
+        registerResponseCombinerConstructor("CompetingRiskResponseCombinerToList",
+                (node) -> new CompetingRiskResponseCombinerToList()
+        );
+
 
     }
 

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

@@ -19,7 +19,7 @@ public class CompetingRiskErrorRateCalculator {
     private final List<Row<CompetingRiskResponse>> dataset;
     private final List<CompetingRiskFunctions> riskFunctions;
 
-    public CompetingRiskErrorRateCalculator(final List<Row<CompetingRiskResponse>> dataset, final Forest<CompetingRiskFunctions, CompetingRiskFunctions> forest){
+    public CompetingRiskErrorRateCalculator(final List<Row<CompetingRiskResponse>> dataset, final Forest<?, CompetingRiskFunctions> forest){
         this.dataset = dataset;
         this.riskFunctions = dataset.stream()
                 .map(forest::evaluateOOB)

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

@@ -6,8 +6,10 @@ import lombok.Data;
 import lombok.RequiredArgsConstructor;
 import org.apache.commons.csv.CSVRecord;
 
+import java.io.Serializable;
+
 @Data
-public class CompetingRiskResponse {
+public class CompetingRiskResponse implements Serializable {
 
     private final int delta;
     private final double u;

src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/alternative/CompetingRiskListCombiner.java

@@ -0,0 +1,26 @@
+package ca.joeltherrien.randomforest.responses.competingrisk.combiner.alternative;
+
+import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskFunctions;
+import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskResponse;
+import ca.joeltherrien.randomforest.responses.competingrisk.combiner.CompetingRiskResponseCombiner;
+import ca.joeltherrien.randomforest.tree.ResponseCombiner;
+import lombok.Getter;
+import lombok.RequiredArgsConstructor;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+@RequiredArgsConstructor
+public class CompetingRiskListCombiner implements ResponseCombiner<CompetingRiskResponse[], CompetingRiskFunctions> {
+
+    @Getter
+    private final CompetingRiskResponseCombiner originalCombiner;
+
+    @Override
+    public CompetingRiskFunctions combine(List<CompetingRiskResponse[]> responses) {
+        final List<CompetingRiskResponse> completeList = responses.stream().flatMap(Arrays::stream).collect(Collectors.toList());
+
+        return originalCombiner.combine(completeList);
+    }
+}

src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/alternative/CompetingRiskResponseCombinerToList.java

@@ -0,0 +1,29 @@
+package ca.joeltherrien.randomforest.responses.competingrisk.combiner.alternative;
+
+import ca.joeltherrien.randomforest.responses.competingrisk.CompetingRiskResponse;
+import ca.joeltherrien.randomforest.tree.ResponseCombiner;
+
+import java.util.List;
+
+/**
+ * This class takes all of the observations in a terminal node and 'combines' them into just a list of the observations.
+ *
+ * This is used in the alternative approach to only compute the functions at the final stage when combining trees.
+ *
+ */
+public class CompetingRiskResponseCombinerToList implements ResponseCombiner<CompetingRiskResponse, CompetingRiskResponse[]> {
+
+    @Override
+    public CompetingRiskResponse[] combine(List<CompetingRiskResponse> responses) {
+        final CompetingRiskResponse[] array = new CompetingRiskResponse[responses.size()];
+
+        for(int i=0; i<array.length; i++){
+            array[i] = responses.get(i);
+        }
+
+        return array;
+    }
+
+
+
+}

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

@@ -27,7 +27,7 @@ public class Forest<O, FO> { // O = output of trees, FO = forest output. In prac
     public FO evaluateOOB(CovariateRow row){
 
         return treeResponseCombiner.combine(
-          trees.stream()
+          trees.parallelStream()
           .filter(tree -> !tree.idInBootstrapSample(row.getId()))
           .map(node -> node.evaluate(row))
           .collect(Collectors.toList())

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

@@ -10,7 +10,13 @@ public class Tree<Y> implements Node<Y> {
 
     private final Node<Y> rootNode;
     private final int[] bootstrapRowIds;
-    private boolean bootStrapRowIdsSorted = false;
+
+
+    public Tree(Node<Y> rootNode, int[] bootstrapRowIds) {
+        this.rootNode = rootNode;
+        this.bootstrapRowIds = bootstrapRowIds;
+        Arrays.sort(bootstrapRowIds);
+    }
 
     @Override
     public Y evaluate(CovariateRow row) {
@@ -21,21 +27,8 @@ public class Tree<Y> implements Node<Y> {
         return bootstrapRowIds.clone();
     }
 
-    /**
-     * Sort bootstrapRowIds. This is not done automatically for efficiency purposes, as in many cases we may not be interested in using bootstrapRowIds();
-     *
-     */
-    public void sortBootstrapRowIds(){
-        if(!bootStrapRowIdsSorted){
-            Arrays.sort(bootstrapRowIds);
-            bootStrapRowIdsSorted = true;
-        }
-
-    }
 
     public boolean idInBootstrapSample(int id){
-        this.sortBootstrapRowIds();
-
         return Arrays.binarySearch(this.bootstrapRowIds, id) >= 0;
     }