From b98bb18b69f30537fd235ef73d525c0f59f27293 Mon Sep 17 00:00:00 2001
From: Xiangrui Meng <meng@databricks.com>
Date: Tue, 12 Aug 2014 23:19:26 -0700
Subject: [PATCH] add comments

---
 .../correlation/SpearmanCorrelation.scala     | 36 +++++++++----------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/mllib/src/main/scala/org/apache/spark/mllib/stat/correlation/SpearmanCorrelation.scala b/mllib/src/main/scala/org/apache/spark/mllib/stat/correlation/SpearmanCorrelation.scala
index 8b6cd07a42c01..c7efad6b0401f 100644
--- a/mllib/src/main/scala/org/apache/spark/mllib/stat/correlation/SpearmanCorrelation.scala
+++ b/mllib/src/main/scala/org/apache/spark/mllib/stat/correlation/SpearmanCorrelation.scala
@@ -17,14 +17,13 @@
 
 package org.apache.spark.mllib.stat.correlation
 
-import org.apache.spark.storage.StorageLevel
-
 import scala.collection.mutable.ArrayBuffer
 
-import org.apache.spark.{Logging, HashPartitioner}
+import org.apache.spark.Logging
 import org.apache.spark.SparkContext._
-import org.apache.spark.mllib.linalg.{Vectors, DenseVector, Matrix, Vector}
-import org.apache.spark.rdd.{CoGroupedRDD, RDD}
+import org.apache.spark.mllib.linalg.{Matrix, Vector, Vectors}
+import org.apache.spark.rdd.RDD
+import org.apache.spark.storage.StorageLevel
 
 /**
  * Compute Spearman's correlation for two RDDs of the type RDD[Double] or the correlation matrix
@@ -45,18 +44,18 @@ private[stat] object SpearmanCorrelation extends Correlation with Logging {
   /**
    * Compute Spearman's correlation matrix S, for the input matrix, where S(i, j) is the
    * correlation between column i and j.
-   *
-   * Input RDD[Vector] should be cached or checkpointed if possible since it would be split into
-   * numCol RDD[Double]s, each of which sorted, and the joined back into a single RDD[Vector].
    */
   override def computeCorrelationMatrix(X: RDD[Vector]): Matrix = {
-    val transposed = X.zipWithUniqueId().flatMap { case (vec, uid) =>
+    // ((columnIndex, value), rowId)
+    val colBased = X.zipWithUniqueId().flatMap { case (vec, uid) =>
       vec.toArray.view.zipWithIndex.map { case (v, j) =>
         ((j, v), uid)
       }
-    }.persist(StorageLevel.MEMORY_AND_DISK)
-    val sorted = transposed.sortByKey().persist(StorageLevel.MEMORY_AND_DISK)
-    val ranked = sorted.zipWithIndex().mapPartitions { iter =>
+    }.persist(StorageLevel.MEMORY_AND_DISK) // used by sortByKey
+    // global sort by (columnIndex, value)
+    val sorted = colBased.sortByKey().persist(StorageLevel.MEMORY_AND_DISK) // used by zipWithIndex
+    // Assign global ranks (using average ranks for tied values)
+    val globalRanks = sorted.zipWithIndex().mapPartitions { iter =>
       var preCol = -1
       var preVal = Double.NaN
       var startRank = -1.0
@@ -85,14 +84,15 @@ private[stat] object SpearmanCorrelation extends Correlation with Logging {
         flush()
       }
     }
-    val ranks = tied.groupByKey().map { case (uid, iter) =>
-      val values = iter.toSeq.sortBy(_._1).map(_._2).toArray
-      println(values.toSeq)
-      Vectors.dense(values)
+    // Replace values in the input matrix by their ranks compared with values in the same column.
+    // Note that shifting all ranks in a column by a constant value doesn't affect result.
+    val groupedRanks = globalRanks.groupByKey().map { case (uid, iter) =>
+      // sort by column index and then convert values to a vector
+      Vectors.dense(iter.toSeq.sortBy(_._1).map(_._2).toArray)
     }
-    val corrMatrix = PearsonCorrelation.computeCorrelationMatrix(ranks)
+    val corrMatrix = PearsonCorrelation.computeCorrelationMatrix(groupedRanks)
 
-    transposed.unpersist(blocking = false)
+    colBased.unpersist(blocking = false)
     sorted.unpersist(blocking = false)
 
     corrMatrix