One Pass Statistics

(cherry picked from commit 005fba9c76)

Signed-off-by: Christoph Ruegg <git@cdrnet.ch>

src/Numerics/Statistics/Correlation.cs

@@ -32,6 +32,7 @@ namespace MathNet.Numerics.Statistics
 {
     using System;
     using System.Collections.Generic;
+    using Properties;
 
     /// <summary>
     /// A class with correlation measures between two datasets.
@@ -49,12 +50,10 @@ namespace MathNet.Numerics.Statistics
             int n = 0;
             double r = 0.0;
 
-            // BUG: PERFORMANCE degraded due to tripple iteration over both IEnumerables
+            double meanA = 0;
-            
+            double meanB = 0;
-            double meanA = dataA.Mean();
+            double varA = 0;
-            double meanB = dataB.Mean();
+            double varB = 0;
-            double sdevA = dataA.StandardDeviation();
-            double sdevB = dataB.StandardDeviation();
 
             using (IEnumerator<double> ieA = dataA.GetEnumerator())
             using (IEnumerator<double> ieB = dataB.GetEnumerator())
@@ -65,9 +64,21 @@ namespace MathNet.Numerics.Statistics
                     {
                         throw new ArgumentOutOfRangeException("dataB", "Datasets dataA and dataB need to have the same length. dataB is shorter.");
                     }
+                    double Acurrent = ieA.Current;
+                    double Bcurrent = ieB.Current;
 
-                    n++;
+                    double deltaA = Acurrent - meanA;
-                    r += (ieA.Current - meanA) * (ieB.Current - meanB) / (sdevA * sdevB);
+                    double scaleDeltaA = deltaA / ++n;
+
+                    double deltaB = Bcurrent - meanB;
+                    double scaleDeltaB = deltaB / n;
+
+                    meanA += scaleDeltaA;
+                    meanB += scaleDeltaB;
+
+                    varA += scaleDeltaA * deltaA * (n - 1);
+                    varB += scaleDeltaB * deltaB * (n - 1);
+                    r += ((deltaA * deltaB * (n - 1)) / n);
                 }
                 if (ieB.MoveNext())
                 {
@@ -75,7 +86,7 @@ namespace MathNet.Numerics.Statistics
                 }
             }
 
-            return r / (n - 1);
+            return r / Math.Sqrt(varA * varB);
         }
     }
 }

src/Numerics/Statistics/DescriptiveStatistics.cs

@@ -45,7 +45,8 @@ namespace MathNet.Numerics.Statistics
         /// Initializes a new instance of the <see cref="DescriptiveStatistics"/> class.
         /// </summary>
         /// <param name="data">The sample data.</param>
-        public DescriptiveStatistics(IEnumerable<double> data) : this(data, false)
+        public DescriptiveStatistics(IEnumerable<double> data)
+            : this(data, false)
         {
         }
 
@@ -53,7 +54,8 @@ namespace MathNet.Numerics.Statistics
         /// Initializes a new instance of the <see cref="DescriptiveStatistics"/> class.
         /// </summary>
         /// <param name="data">The sample data.</param>
-        public DescriptiveStatistics(IEnumerable<double?> data) : this(data, false)
+        public DescriptiveStatistics(IEnumerable<double?> data)
+            : this(data, false)
         {
         }
 
@@ -71,6 +73,11 @@ namespace MathNet.Numerics.Statistics
         /// </remarks>
         public DescriptiveStatistics(IEnumerable<double> data, bool increasedAccuracy)
         {
+            if (data == null)
+            {
+                throw new ArgumentNullException("data");
+            }
+
             if (increasedAccuracy)
             {
                 ComputeHA(data);
@@ -97,6 +104,12 @@ namespace MathNet.Numerics.Statistics
         /// </remarks>
         public DescriptiveStatistics(IEnumerable<double?> data, bool increasedAccuracy)
         {
+            if (data == null)
+            {
+                throw new ArgumentNullException("data");
+            }
+
+
             if (increasedAccuracy)
             {
                 ComputeHA(data);
@@ -171,9 +184,8 @@ namespace MathNet.Numerics.Statistics
         /// <param name="data">A sequence of datapoints.</param>
         private void Compute(IEnumerable<double> data)
         {
-            Mean = data.Mean();
+            double mean = 0;
             double variance = 0;
-            double correction = 0;
             double skewness = 0;
             double kurtosis = 0;
             double minimum = Double.PositiveInfinity;
@@ -181,40 +193,26 @@ namespace MathNet.Numerics.Statistics
             int n = 0;
             foreach (var xi in data)
             {
-                double diff = xi - Mean;
+                double delta = xi - mean;
-                correction += diff;
+                double scaleDelta = delta / ++n;
-                double tmp = diff * diff;
+                double scaleDeltaSQR = scaleDelta * scaleDelta;
-                variance += tmp;
+                double tmpDelta = delta * (n - 1);
-                tmp *= diff;
+
-                skewness += tmp;
+                mean += scaleDelta;
-                tmp *= diff;
+
-                kurtosis += tmp;
+                kurtosis += tmpDelta * scaleDelta * scaleDeltaSQR * (n * n - 3 * n + 3)
+                    + 6 * scaleDeltaSQR * variance - 4 * scaleDelta * skewness;
+
+                skewness += tmpDelta * scaleDeltaSQR * (n - 2) - 3 * scaleDelta * variance;
+                variance += tmpDelta * scaleDelta;
+
                 if (minimum > xi) { minimum = xi; }
                 if (maximum < xi) { maximum = xi; }
-                n++;
             }
+            SetStatistics(mean, variance, skewness, kurtosis, minimum, maximum, n);
+        }
 
-            Count = n;
-            Minimum = minimum;
-            Maximum = maximum;
-            Variance = (variance - (correction * correction / n)) / (n - 1);
-            StandardDeviation = Math.Sqrt(Variance);
-            if (Variance != 0)
-            {
-                if (n > 2)
-                {
-                    Skewness = (double)n / ((n - 1) * (n - 2)) * (skewness / (Variance * StandardDeviation));
-                }
 
-                if (n > 3)
-                {
-                    Kurtosis = (((double)n * (n + 1))
-                                / ((n - 1) * (n - 2) * (n - 3))
-                                * (kurtosis / (Variance * Variance)))
-                               - ((3.0 * (n - 1) * (n - 1)) / ((n - 2) * (n - 3)));
-                }
-            }
-        }
 
         /// <summary>
         /// Computes descriptive statistics from a stream of nullable data values.
@@ -222,9 +220,8 @@ namespace MathNet.Numerics.Statistics
         /// <param name="data">A sequence of datapoints.</param>
         private void Compute(IEnumerable<double?> data)
         {
-            Mean = data.Mean();
+            double mean = 0;
             double variance = 0;
-            double correction = 0;
             double skewness = 0;
             double kurtosis = 0;
             double minimum = Double.PositiveInfinity;
@@ -234,43 +231,25 @@ namespace MathNet.Numerics.Statistics
             {
                 if (xi.HasValue)
                 {
-                    double diff = xi.Value - Mean;
+                    double delta = xi.Value - mean;
-                    double tmp = diff * diff;
+                    double scaleDelta = delta / ++n;
-                    correction += diff;
+                    double scaleDeltaSQR = scaleDelta * scaleDelta;
-                    variance += tmp;
+                    double tmpDelta = delta * (n - 1);
-                    tmp *= diff;
+
-                    skewness += tmp;
+                    mean += scaleDelta;
-                    tmp *= diff;
+
-                    kurtosis += tmp;
+                    kurtosis += tmpDelta * scaleDelta * scaleDeltaSQR * (n * n - 3 * n + 3)
+                        + 6 * scaleDeltaSQR * variance - 4 * scaleDelta * skewness;
+
+                    skewness += tmpDelta * scaleDeltaSQR * (n - 2) - 3 * scaleDelta * variance;
+                    variance += tmpDelta * scaleDelta;
                     if (minimum > xi) { minimum = xi.Value; }
                     if (maximum < xi) { maximum = xi.Value; }
-                    n++;
                 }
             }
 
-            Count = n;
+            SetStatistics(mean, variance, skewness, kurtosis, minimum, maximum, n);
-            if (n > 0)
-            {
-                Minimum = minimum;
-                Maximum = maximum;
-                Variance = (variance - (correction * correction / n)) / (n - 1);
-                StandardDeviation = Math.Sqrt(Variance);
-                if (Variance != 0)
-                {
-                    if (n > 2)
-                    {
-                        Skewness = (double)n / ((n - 1) * (n - 2)) * (skewness / (Variance * StandardDeviation));
-                    }
 
-                    if (n > 3)
-                    {
-                        Kurtosis = (((double)n * (n + 1))
-                                    / ((n - 1) * (n - 2) * (n - 3))
-                                    * (kurtosis / (Variance * Variance)))
-                                   - ((3.0 * (n - 1) * (n - 1)) / ((n - 2) * (n - 3)));
-                    }
-                }
-            }
         }
 
         /// <summary>
@@ -279,10 +258,8 @@ namespace MathNet.Numerics.Statistics
         /// <param name="data">A sequence of datapoints.</param>
         private void ComputeHA(IEnumerable<double> data)
         {
-            Mean = data.Mean();
+            decimal mean = 0;
-            decimal mean = (decimal)Mean;
             decimal variance = 0;
-            decimal correction = 0;
             decimal skewness = 0;
             decimal kurtosis = 0;
             decimal minimum = Decimal.MaxValue;
@@ -290,39 +267,24 @@ namespace MathNet.Numerics.Statistics
             int n = 0;
             foreach (decimal xi in data)
             {
-                decimal diff = xi - mean;
+                decimal delta = xi - mean;
-                decimal tmp = diff * diff;
+                decimal scaleDelta = delta / ++n;
-                correction += diff;
+                decimal scaleDeltaSQR = scaleDelta * scaleDelta;
-                variance += tmp;
+                decimal tmpDelta = delta * (n - 1);
-                tmp *= diff;
+
-                skewness += tmp;
+                mean += scaleDelta;
-                tmp *= diff;
+
-                kurtosis += tmp;
+                kurtosis += tmpDelta * scaleDelta * scaleDeltaSQR * (n * n - 3 * n + 3)
+                    + 6 * scaleDeltaSQR * variance - 4 * scaleDelta * skewness;
+
+                skewness += tmpDelta * scaleDeltaSQR * (n - 2) - 3 * scaleDelta * variance;
+                variance += tmpDelta * scaleDelta;
                 if (minimum > xi) { minimum = xi; }
                 if (maximum < xi) { maximum = xi; }
-                n++;
             }
 
-            Count = n;
+            SetStatistics((double)mean, (double)variance, (double)skewness, (double)kurtosis, (double)minimum, (double)maximum, n);
-            Minimum = (double)minimum;
-            Maximum = (double)maximum;
-            Variance = (double)(variance - (correction * correction / n)) / (n - 1);
-            StandardDeviation = Math.Sqrt(Variance);
-            if (Variance != 0)
-            {
-                if (n > 2)
-                {
-                    Skewness = (double)n / ((n - 1) * (n - 2)) * ((double)skewness / (Variance * StandardDeviation));
-                }
 
-                if (n > 3)
-                {
-                    Kurtosis = (((double)n * (n + 1))
-                                / ((n - 1) * (n - 2) * (n - 3))
-                                * ((double)kurtosis / (Variance * Variance)))
-                               - ((3.0 * (n - 1) * (n - 1)) / ((n - 2) * (n - 3)));
-                }
-            }
         }
 
         /// <summary>
@@ -331,10 +293,8 @@ namespace MathNet.Numerics.Statistics
         /// <param name="data">A sequence of datapoints.</param>
         private void ComputeHA(IEnumerable<double?> data)
         {
-            Mean = data.Mean();
+            decimal mean = 0;
-            decimal mean = (decimal)Mean;
             decimal variance = 0;
-            decimal correction = 0;
             decimal skewness = 0;
             decimal kurtosis = 0;
             decimal minimum = Decimal.MaxValue;
@@ -344,43 +304,66 @@ namespace MathNet.Numerics.Statistics
             {
                 if (xi.HasValue)
                 {
-                    decimal diff = xi.Value - mean;
+                    decimal delta = xi.Value - mean;
-                    decimal tmp = diff * diff;
+                    decimal scaleDelta = delta / ++n;
-                    correction += diff;
+                    decimal scaleDeltaSQR = scaleDelta * scaleDelta;
-                    variance += tmp;
+                    decimal tmpDelta = delta * (n - 1);
-                    tmp *= diff;
+
-                    skewness += tmp;
+                    mean += scaleDelta;
-                    tmp *= diff;
+
-                    kurtosis += tmp;
+                    kurtosis += tmpDelta * scaleDelta * scaleDeltaSQR * (n * n - 3 * n + 3)
+                        + 6 * scaleDeltaSQR * variance - 4 * scaleDelta * skewness;
+
+                    skewness += tmpDelta * scaleDeltaSQR * (n - 2) - 3 * scaleDelta * variance;
+                    variance += tmpDelta * scaleDelta;
                     if (minimum > xi) { minimum = xi.Value; }
                     if (maximum < xi) { maximum = xi.Value; }
-                    n++;
                 }
             }
+            SetStatistics((double)mean, (double)variance, (double)skewness, (double)kurtosis, (double)minimum, (double)maximum, n);
 
+        }
+
+        /// <summary>
+        /// Internal use. Method use for setting the statistics.
+        /// </summary>
+        /// <param name="mean">For setting Mean.</param>
+        /// <param name="variance">For setting Variance.</param>
+        /// <param name="skewness">For setting Skewness.</param>
+        /// <param name="kurtosis">For setting Kurtosis.</param>
+        /// <param name="minimum">For setting Minimum.</param>
+        /// <param name="maximum">For setting Maximum.</param>
+        /// <param name="n">For setting Count.</param>
+        private void SetStatistics(double mean, double variance, double skewness, double kurtosis, double minimum, double maximum, int n)
+        {
+            Mean = mean;
             Count = n;
             if (n > 0)
             {
-                Minimum = (double) minimum;
+                Minimum = minimum;
-                Maximum = (double) maximum;
+                Maximum = maximum;
-                Variance = (double)(variance - (correction * correction / n)) / (n - 1);
+                if (n > 1)
-                StandardDeviation = Math.Sqrt(Variance);
+                {
+                    Variance = variance / (n - 1);
+                    StandardDeviation = Math.Sqrt(Variance);
+                }
                 if (Variance != 0)
                 {
                     if (n > 2)
                     {
-                        Skewness = (double)n / ((n - 1) * (n - 2)) * ((double)skewness / (Variance * StandardDeviation));
+                        Skewness = (double)n / ((n - 1) * (n - 2)) * (skewness / (Variance * StandardDeviation));
                     }
 
                     if (n > 3)
                     {
                         Kurtosis = (((double)n * (n + 1))
                                     / ((n - 1) * (n - 2) * (n - 3))
-                                    * ((double)kurtosis / (Variance * Variance)))
+                                    * (kurtosis / (Variance * Variance)))
                                    - ((3.0 * (n - 1) * (n - 1)) / ((n - 2) * (n - 3)));
                     }
                 }
             }
         }
     }
+
 }

src/Numerics/Statistics/Statistics.cs

@@ -32,6 +32,7 @@ namespace MathNet.Numerics.Statistics
 {
     using System;
     using System.Collections.Generic;
+    using System.Linq;
     using Properties;
 
     /// <summary>
@@ -455,7 +456,7 @@ namespace MathNet.Numerics.Statistics
             if (dataArray.Count % 2 == 0)
             {
                 double lower = OrderSelect(dataArray, 0, dataArray.Count - 1, index - 1);
-                double upper = OrderSelect(dataArray, 0, dataArray.Count - 1, index);
+                double upper = dataArray.Skip(index - 1).Minimum();
                 return (lower + upper) / 2.0;
             }
 
@@ -543,12 +544,23 @@ namespace MathNet.Numerics.Statistics
                     return samples[left];
                 }
 
-                // The pivot point.
+                
+                // The pivot point. Choose median of left, right and center
+                //to be the pivot and arrange so that
+                //samples[left]<=samples[right]<=samples[center]
+                int center = (left + right) / 2;
+                if (samples[center] < samples[left])
+                    Sorting.Swap(samples, left, center);
+                if (samples[center] < samples[right])
+                    Sorting.Swap(samples, right, center);
+                if (samples[right] < samples[left])
+                    Sorting.Swap(samples, right, left);
+
                 double pivot = samples[right];
 
                 // The partioning code.
-                int i = left - 1;
+                int i = left;
-                for (int j = left; j <= right - 1; j++)
+                for (int j = left+1; j <= right - 1; j++)
                 {
                     if (samples[j] <= pivot)
                     {