From a7f591c2d31ba469d07acb941dae1543874f950b Mon Sep 17 00:00:00 2001
From: Joel Therrien <joel@joeltherrien.ca>
Date: Mon, 18 Feb 2019 14:57:26 -0800
Subject: [PATCH] Add integration capabilities to RightContinuousStepFunction;
 use it for calculating mortality

---
 .../competingrisk/CompetingRiskFunctions.java | 29 +--------
 ...ContinuousStepFunctionIntegrationTest.java | 63 +++++++++++++++++++
 2 files changed, 64 insertions(+), 28 deletions(-)
 create mode 100644 src/test/java/ca/joeltherrien/randomforest/utils/RightContinuousStepFunctionIntegrationTest.java

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 aaaea11..7dcddfb 100644
--- a/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskFunctions.java
+++ b/src/main/java/ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskFunctions.java
@@ -42,33 +42,6 @@ public class CompetingRiskFunctions implements Serializable {
 
     public double calculateEventSpecificMortality(final int event, final double tau){
         final RightContinuousStepFunction cif = getCumulativeIncidenceFunction(event);
-
-        double summation = 0.0;
-
-        Double previousTime = null;
-        Double previousY = null;
-
-        final double[] cifTimes = cif.getX();
-        for(int i=0; i<cifTimes.length; i++){
-            final double time = cifTimes[i];
-
-            if(time > tau){
-                break;
-            }
-
-            if(previousTime != null){
-                summation += previousY * (time - previousTime);
-            }
-            previousTime = time;
-            previousY = cif.evaluateByIndex(i);
-        }
-
-        // this is to ensure that we integrate over the proper range
-        if(previousTime != null){
-            summation += cif.evaluate(tau) * (tau - previousTime);
-        }
-
-        return summation;
-
+        return cif.integrate(0, tau);
     }
 }
diff --git a/src/test/java/ca/joeltherrien/randomforest/utils/RightContinuousStepFunctionIntegrationTest.java b/src/test/java/ca/joeltherrien/randomforest/utils/RightContinuousStepFunctionIntegrationTest.java
new file mode 100644
index 0000000..04de18b
--- /dev/null
+++ b/src/test/java/ca/joeltherrien/randomforest/utils/RightContinuousStepFunctionIntegrationTest.java
@@ -0,0 +1,63 @@
+package ca.joeltherrien.randomforest.utils;
+
+import ca.joeltherrien.randomforest.TestUtils;
+import org.junit.jupiter.api.Test;
+
+public class RightContinuousStepFunctionIntegrationTest {
+
+    private RightContinuousStepFunction createTestFunction(){
+
+        final double defaultY = 1;
+        final double[] x = new double[]{1.0, 2.0, 3.0, 4.0, 5.0};
+        final double[] y = new double[]{2.0, 3.0, -0.5, -1.0, 3.0};
+
+        return new RightContinuousStepFunction(x, y, defaultY);
+    }
+
+    @Test
+    public void testIntegration(){
+        final RightContinuousStepFunction function = createTestFunction();
+
+        // Test whether it can handle both from and to being before all the x-values
+        TestUtils.closeEnough(0.9,
+                function.integrate(0, 0.9)
+                , 0.00000001);
+
+        // Test whether it can handle both from and to being after all the x-values
+        TestUtils.closeEnough(3.0,
+                function.integrate(6, 7)
+                , 0.00000001);
+
+        TestUtils.closeEnough(6.0,
+                function.integrate(0, 3)
+                , 0.00000001);
+
+        TestUtils.closeEnough(4.5,
+                function.integrate(0, 2.5)
+                , 0.00000001);
+
+        TestUtils.closeEnough(7.5,
+                function.integrate(0, 6)
+                , 0.00000001);
+
+        TestUtils.closeEnough(-0.5,
+                function.integrate(3, 4)
+                , 0.00000001);
+
+        TestUtils.closeEnough(-0.5*0.8,
+                function.integrate(3.1, 3.9)
+                , 0.00000001);
+
+        TestUtils.closeEnough(1.5,
+                function.integrate(3, 6)
+                , 0.00000001);
+
+        TestUtils.closeEnough(3.0,
+                function.integrate(2.5, 6)
+                , 0.00000001);
+
+
+    }
+
+
+}