From 949c8789e7cb45103aed6cabd9f90cbc3d17c60e Mon Sep 17 00:00:00 2001
From: Joel Therrien <joel@joeltherrien.ca>
Date: Mon, 27 Aug 2018 19:15:06 -0700
Subject: [PATCH] Switch HashMaps in CompetingRiskFunctions for ArrayLists

Provides a mild performance improvement.
---
 .../competingrisk/CompetingRiskFunctions.java       |  9 +++++----
 .../combiner/CompetingRiskFunctionCombiner.java     | 13 +++++++------
 .../combiner/CompetingRiskResponseCombiner.java     | 12 ++++++------
 3 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskFunctions.java b/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskFunctions.java
index 2e6baf9..4aa4470 100644
--- a/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskFunctions.java
+++ b/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskFunctions.java
@@ -6,23 +6,24 @@ import lombok.Builder;
 import lombok.Getter;
 
 import java.io.Serializable;
+import java.util.List;
 import java.util.Map;
 
 @Builder
 public class CompetingRiskFunctions implements Serializable {
 
-    private final Map<Integer, MathFunction> causeSpecificHazardFunctionMap;
-    private final Map<Integer, MathFunction> cumulativeIncidenceFunctionMap;
+    private final List<MathFunction> causeSpecificHazards;
+    private final List<MathFunction> cumulativeIncidenceCurves;
 
     @Getter
     private final MathFunction survivalCurve;
 
     public MathFunction getCauseSpecificHazardFunction(int cause){
-        return causeSpecificHazardFunctionMap.get(cause);
+        return causeSpecificHazards.get(cause-1);
     }
 
     public MathFunction getCumulativeIncidenceFunction(int cause) {
-        return cumulativeIncidenceFunctionMap.get(cause);
+        return cumulativeIncidenceCurves.get(cause-1);
     }
 
     public double calculateEventSpecificMortality(final int event, final double tau){
diff --git a/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskFunctionCombiner.java b/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskFunctionCombiner.java
index 8da1d91..ed5fff2 100644
--- a/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskFunctionCombiner.java
+++ b/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskFunctionCombiner.java
@@ -55,8 +55,9 @@ public class CompetingRiskFunctionCombiner implements ResponseCombiner<Competing
         }
 
         final MathFunction survivalFunction = new MathFunction(survivalPoints, new Point(0.0, 1.0));
-        final Map<Integer, MathFunction> causeSpecificCumulativeHazardFunctionMap = new HashMap<>();
-        final Map<Integer, MathFunction> cumulativeIncidenceFunctionMap = new HashMap<>();
+
+        final List<MathFunction> causeSpecificCumulativeHazardFunctionList = new ArrayList<>(events.length);
+        final List<MathFunction> cumulativeIncidenceFunctionList = new ArrayList<>(events.length);
 
         for(final int event : events){
 
@@ -78,14 +79,14 @@ public class CompetingRiskFunctionCombiner implements ResponseCombiner<Competing
 
             }
 
-            causeSpecificCumulativeHazardFunctionMap.put(event, new MathFunction(cumulativeHazardFunctionPoints));
-            cumulativeIncidenceFunctionMap.put(event, new MathFunction(cumulativeIncidenceFunctionPoints));
+            causeSpecificCumulativeHazardFunctionList.add(event-1, new MathFunction(cumulativeHazardFunctionPoints));
+            cumulativeIncidenceFunctionList.add(event-1, new MathFunction(cumulativeIncidenceFunctionPoints));
 
         }
 
         return CompetingRiskFunctions.builder()
-                .causeSpecificHazardFunctionMap(causeSpecificCumulativeHazardFunctionMap)
-                .cumulativeIncidenceFunctionMap(cumulativeIncidenceFunctionMap)
+                .causeSpecificHazards(causeSpecificCumulativeHazardFunctionList)
+                .cumulativeIncidenceCurves(cumulativeIncidenceFunctionList)
                 .survivalCurve(survivalFunction)
                 .build();
     }
diff --git a/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskResponseCombiner.java b/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskResponseCombiner.java
index 0f4a1ac..505bd16 100644
--- a/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskResponseCombiner.java
+++ b/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskResponseCombiner.java
@@ -33,8 +33,8 @@ public class CompetingRiskResponseCombiner implements ResponseCombiner<Competing
     @Override
     public CompetingRiskFunctions combine(List<CompetingRiskResponse> responses) {
 
-        final Map<Integer, MathFunction> causeSpecificCumulativeHazardFunctionMap = new HashMap<>();
-        final Map<Integer, MathFunction> cumulativeIncidenceFunctionMap = new HashMap<>();
+        final List<MathFunction> causeSpecificCumulativeHazardFunctionList = new ArrayList<>(events.length);
+        final List<MathFunction> cumulativeIncidenceFunctionList = new ArrayList<>(events.length);
 
         final double[] timesToUse;
         if(times != null){
@@ -103,16 +103,16 @@ public class CompetingRiskResponseCombiner implements ResponseCombiner<Competing
             }
 
             final MathFunction causeSpecificCumulativeHazardFunction = new MathFunction(hazardFunctionPoints);
-            causeSpecificCumulativeHazardFunctionMap.put(event, causeSpecificCumulativeHazardFunction);
+            causeSpecificCumulativeHazardFunctionList.add(event-1, causeSpecificCumulativeHazardFunction);
 
             final MathFunction cifFunction = new MathFunction(cifPoints);
-            cumulativeIncidenceFunctionMap.put(event, cifFunction);
+            cumulativeIncidenceFunctionList.add(event-1, cifFunction);
         }
 
 
         return CompetingRiskFunctions.builder()
-                .causeSpecificHazardFunctionMap(causeSpecificCumulativeHazardFunctionMap)
-                .cumulativeIncidenceFunctionMap(cumulativeIncidenceFunctionMap)
+                .causeSpecificHazards(causeSpecificCumulativeHazardFunctionList)
+                .cumulativeIncidenceCurves(cumulativeIncidenceFunctionList)
                 .survivalCurve(survivalCurve)
                 .build();
     }