Add OTFI imputation when training forest.

No tests have been written yet so this is still WIP.

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

@@ -1,12 +1,9 @@
 package ca.joeltherrien.randomforest;
 
-import ca.joeltherrien.randomforest.exceptions.MissingValueException;
 import lombok.Getter;
 import lombok.RequiredArgsConstructor;
 
 import java.util.*;
-import java.util.concurrent.ThreadLocalRandom;
-import java.util.stream.Collectors;
 
 @RequiredArgsConstructor
 public class BooleanCovariate implements Covariate<Boolean>{
@@ -28,9 +25,9 @@ public class BooleanCovariate implements Covariate<Boolean>{
 
     public class BooleanValue implements Value<Boolean>{
 
-        private final boolean value;
+        private final Boolean value;
 
-        private BooleanValue(final boolean value){
+        private BooleanValue(final Boolean value){
             this.value = value;
         }
 
@@ -43,6 +40,11 @@ public class BooleanCovariate implements Covariate<Boolean>{
         public Boolean getValue() {
             return value;
         }
+
+        @Override
+        public boolean isNA() {
+            return value == null;
+        }
     }
 
     public class BooleanSplitRule implements SplitRule<Boolean>{
@@ -58,15 +60,12 @@ public class BooleanCovariate implements Covariate<Boolean>{
         }
 
         @Override
-        public boolean isLeftHand(CovariateRow row) {
+        public boolean isLeftHand(final Value<Boolean> value) {
-            final Value<?> x = row.getCovariateValue(getParent().getName());
+            if(value.isNA()) {
-            if(x == null) {
+                throw new IllegalArgumentException("Trying to determine split on missing value");
-                throw new MissingValueException(row, this);
             }
 
-            final boolean xBoolean = (Boolean) x.getValue();
+            return !value.getValue();
-
-            return !xBoolean;
         }
     }
 }

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

@@ -1,9 +1,8 @@
 package ca.joeltherrien.randomforest;
 
 import java.io.Serializable;
-import java.util.Collection;
+import java.util.*;
-import java.util.LinkedList;
+import java.util.concurrent.ThreadLocalRandom;
-import java.util.List;
 
 public interface Covariate<V> extends Serializable {
 
@@ -19,6 +18,8 @@ public interface Covariate<V> extends Serializable {
 
         V getValue();
 
+        boolean isNA();
+
     }
 
     interface SplitRule<V> extends Serializable{
@@ -37,9 +38,22 @@ public interface Covariate<V> extends Serializable {
             final List<Row<Y>> leftHand = new LinkedList<>();
             final List<Row<Y>> rightHand = new LinkedList<>();
 
-            for(final Row<Y> row : rows) {
+            final List<Boolean> nonMissingDecisions = new ArrayList<>();
+            final List<Row<Y>> missingValueRows = new ArrayList<>();
 
-                if(isLeftHand(row)){
+
+            for(final Row<Y> row : rows) {
+                final Value<V> value = (Value<V>) row.getCovariateValue(getParent().getName());
+
+                if(value.isNA()){
+                    missingValueRows.add(row);
+                    continue;
+                }
+
+                final boolean isLeftHand = isLeftHand(value);
+                nonMissingDecisions.add(isLeftHand);
+
+                if(isLeftHand){
                     leftHand.add(row);
                 }
                 else{
@@ -48,10 +62,31 @@ public interface Covariate<V> extends Serializable {
 
             }
 
+            if(nonMissingDecisions.size() == 0 && missingValueRows.size() > 0){
+                throw new IllegalArgumentException("Can't apply " + this + " when there are rows with missing data and no non-missing value rows");
+            }
+
+            final Random random = ThreadLocalRandom.current();
+            for(final Row<Y> missingValueRow : missingValueRows){
+                final boolean randomDecision = nonMissingDecisions.get(random.nextInt(nonMissingDecisions.size()));
+
+                if(randomDecision){
+                    leftHand.add(missingValueRow);
+                }
+                else{
+                    rightHand.add(missingValueRow);
+                }
+            }
+
             return new Split<>(leftHand, rightHand);
         }
 
-        boolean isLeftHand(CovariateRow row);
+        default boolean isLeftHand(CovariateRow row){
+            final Value<V> value = (Value<V>) row.getCovariateValue(getParent().getName());
+            return isLeftHand(value);
+        }
+
+        boolean isLeftHand(Value<V> value);
     }
 
 

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

@@ -9,6 +9,7 @@ public final class FactorCovariate implements Covariate<String>{
 
     private final String name;
     private final Map<String, FactorValue> factorLevels;
+    private final FactorValue naValue;
     private final int numberOfPossiblePairings;
 
 
@@ -28,6 +29,7 @@ public final class FactorCovariate implements Covariate<String>{
         }
         this.numberOfPossiblePairings = numberOfPossiblePairingsTemp-1;
 
+        this.naValue = new FactorValue(null);
     }
 
 
@@ -67,6 +69,10 @@ public final class FactorCovariate implements Covariate<String>{
 
     @Override
     public FactorValue createValue(String value) {
+        if(value == null){
+            return this.naValue;
+        }
+
         final FactorValue factorValue = factorLevels.get(value);
 
         if(factorValue == null){
@@ -94,6 +100,11 @@ public final class FactorCovariate implements Covariate<String>{
         public String getValue() {
             return value;
         }
+
+        @Override
+        public boolean isNA() {
+            return value == null;
+        }
     }
 
     @EqualsAndHashCode
@@ -111,12 +122,12 @@ public final class FactorCovariate implements Covariate<String>{
         }
 
         @Override
-        public boolean isLeftHand(CovariateRow row) {
+        public boolean isLeftHand(final Value<String> value) {
-            final FactorValue value = (FactorValue) row.getCovariateValue(getName()).getValue();
+            if(value.isNA()){
+                throw new IllegalArgumentException("Trying to determine split on missing value");
+            }
 
             return leftSideValues.contains(value);
-
-
         }
     }
 }

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

@@ -1,6 +1,5 @@
 package ca.joeltherrien.randomforest;
 
-import ca.joeltherrien.randomforest.exceptions.MissingValueException;
 import lombok.Getter;
 import lombok.RequiredArgsConstructor;
 
@@ -19,6 +18,9 @@ public class NumericCovariate implements Covariate<Double>{
 
         final Random random = ThreadLocalRandom.current();
 
+        // only work with non-NA values
+        data = data.stream().filter(value -> !value.isNA()).collect(Collectors.toList());
+
         // for this implementation we need to shuffle the data
         final List<Value<Double>> shuffledData;
         if(number > data.size()){
@@ -55,9 +57,9 @@ public class NumericCovariate implements Covariate<Double>{
 
     public class NumericValue implements Covariate.Value<Double>{
 
-        private final double value;
+        private final Double value; // may be null
 
-        private NumericValue(final double value){
+        private NumericValue(final Double value){
             this.value = value;
         }
 
@@ -70,6 +72,11 @@ public class NumericCovariate implements Covariate<Double>{
         public Double getValue() {
             return value;
         }
+
+        @Override
+        public boolean isNA() {
+            return value == null;
+        }
     }
 
     public class NumericSplitRule implements Covariate.SplitRule<Double>{
@@ -91,13 +98,12 @@ public class NumericCovariate implements Covariate<Double>{
         }
 
         @Override
-        public boolean isLeftHand(CovariateRow row) {
+        public boolean isLeftHand(final Value<Double> x) {
-            final Covariate.Value<?> x = row.getCovariateValue(getParent().getName());
+            if(x.isNA()) {
-            if(x == null) {
+                throw new IllegalArgumentException("Trying to determine split on missing value");
-                throw new MissingValueException(row, this);
             }
 
-            final double xNum = (Double) x.getValue();
+            final double xNum = x.getValue();
 
             return xNum <= threshold;
         }

src/main/java/ca/joeltherrien/randomforest/exceptions/MissingValueException.java

@@ -1,17 +0,0 @@
-package ca.joeltherrien.randomforest.exceptions;
-
-import ca.joeltherrien.randomforest.Covariate;
-import ca.joeltherrien.randomforest.CovariateRow;
-
-public class MissingValueException extends RuntimeException{
-
-	/**
-	 * 
-	 */
-	private static final long serialVersionUID = 6808060079431207726L;
-	
-	public MissingValueException(CovariateRow row, Covariate.SplitRule rule) {
-		super("Missing value at CovariateRow " + row + rule);
-	}
-
-}