[SPARK-2850] [SPARK-2626] [mllib] MLlib stats examples + small fixes

Added examples for statistical summarization:
* Scala: StatisticalSummary.scala
** Tests: correlation, MultivariateOnlineSummarizer
* python: statistical_summary.py
** Tests: correlation (since MultivariateOnlineSummarizer has no Python API)

Added examples for random and sampled RDDs:
* Scala: RandomAndSampledRDDs.scala
* python: random_and_sampled_rdds.py
* Both test:
** RandomRDDGenerators.normalRDD, normalVectorRDD
** RDD.sample, takeSample, sampleByKey

Added sc.stop() to all examples.

CorrelationSuite.scala
* Added 1 test for RDDs with only 1 value

RowMatrix.scala
* numCols(): Added check for numRows = 0, with error message.
* computeCovariance(): Added check for numRows <= 1, with error message.

Python SparseVector (pyspark/mllib/linalg.py)
* Added toDense() function

python/run-tests script
* Added stat.py (doc test)

CC: mengxr dorx  Main changes were examples to show usage across APIs.

Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>

Closes #1878 from jkbradley/mllib-stats-api-check and squashes the following commits:

ea5c047 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
dafebe2 [Joseph K. Bradley] Bug fixes for examples SampledRDDs.scala and sampled_rdds.py: Check for division by 0 and for missing key in maps.
8d1e555 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
60c72d9 [Joseph K. Bradley] Fixed stat.py doc test to work for Python versions printing nan or NaN.
b20d90a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
4e5d15e [Joseph K. Bradley] Changed pyspark/mllib/stat.py doc tests to use NaN instead of nan.
32173b7 [Joseph K. Bradley] Stats examples update.
c8c20dc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
cf70b07 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
0b7cec3 [Joseph K. Bradley] Small updates based on code review.  Renamed statistical_summary.py to correlations.py
ab48f6e [Joseph K. Bradley] RowMatrix.scala * numCols(): Added check for numRows = 0, with error message. * computeCovariance(): Added check for numRows <= 1, with error message.
65e4ebc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
8195c78 [Joseph K. Bradley] Added examples for random and sampled RDDs: * Scala: RandomAndSampledRDDs.scala * python: random_and_sampled_rdds.py * Both test: ** RandomRDDGenerators.normalRDD, normalVectorRDD ** RDD.sample, takeSample, sampleByKey
064985b [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
ee918e9 [Joseph K. Bradley] Added examples for statistical summarization: * Scala: StatisticalSummary.scala ** Tests: correlation, MultivariateOnlineSummarizer * python: statistical_summary.py ** Tests: correlation (since MultivariateOnlineSummarizer has no Python API)

3 files changed, 23 insertions, 10 deletions

diff --git a/python/pyspark/mllib/linalg.py b/python/pyspark/mllib/linalg.py
index 9a239abfbb..f485a69db1 100644
--- a/python/pyspark/mllib/linalg.py
+++ b/python/pyspark/mllib/linalg.py
@@ -23,6 +23,7 @@ object from MLlib or pass SciPy C{scipy.sparse} column vectors if
 SciPy is available in their environment.
 """
 
+import numpy
 from numpy import array, array_equal, ndarray, float64, int32
 
 
@@ -160,6 +161,15 @@ class SparseVector(object):
                 j += 1
             return result
 
+    def toArray(self):
+        """
+        Returns a copy of this SparseVector as a 1-dimensional NumPy array.
+        """
+        arr = numpy.zeros(self.size)
+        for i in xrange(self.indices.size):
+            arr[self.indices[i]] = self.values[i]
+        return arr
+
     def __str__(self):
         inds = "[" + ",".join([str(i) for i in self.indices]) + "]"
         vals = "[" + ",".join([str(v) for v in self.values]) + "]"
diff --git a/python/pyspark/mllib/stat.py b/python/pyspark/mllib/stat.py
index a73abc5ff9..feef0d16cd 100644
--- a/python/pyspark/mllib/stat.py
+++ b/python/pyspark/mllib/stat.py
@@ -118,16 +118,18 @@ class Statistics(object):
         >>> from linalg import Vectors
         >>> rdd = sc.parallelize([Vectors.dense([1, 0, 0, -2]), Vectors.dense([4, 5, 0, 3]),
         ...                       Vectors.dense([6, 7, 0,  8]), Vectors.dense([9, 0, 0, 1])])
-        >>> Statistics.corr(rdd)
-        array([[ 1.        ,  0.05564149,         nan,  0.40047142],
-               [ 0.05564149,  1.        ,         nan,  0.91359586],
-               [        nan,         nan,  1.        ,         nan],
-               [ 0.40047142,  0.91359586,         nan,  1.        ]])
-        >>> Statistics.corr(rdd, method="spearman")
-        array([[ 1.        ,  0.10540926,         nan,  0.4       ],
-               [ 0.10540926,  1.        ,         nan,  0.9486833 ],
-               [        nan,         nan,  1.        ,         nan],
-               [ 0.4       ,  0.9486833 ,         nan,  1.        ]])
+        >>> pearsonCorr = Statistics.corr(rdd)
+        >>> print str(pearsonCorr).replace('nan', 'NaN')
+        [[ 1.          0.05564149         NaN  0.40047142]
+         [ 0.05564149  1.                 NaN  0.91359586]
+         [        NaN         NaN  1.                 NaN]
+         [ 0.40047142  0.91359586         NaN  1.        ]]
+        >>> spearmanCorr = Statistics.corr(rdd, method="spearman")
+        >>> print str(spearmanCorr).replace('nan', 'NaN')
+        [[ 1.          0.10540926         NaN  0.4       ]
+         [ 0.10540926  1.                 NaN  0.9486833 ]
+         [        NaN         NaN  1.                 NaN]
+         [ 0.4         0.9486833          NaN  1.        ]]
         >>> try:
         ...     Statistics.corr(rdd, "spearman")
         ...     print "Method name as second argument without 'method=' shouldn't be allowed."
diff --git a/python/run-tests b/python/run-tests
index a6271e0cf5..b506559a5e 100755
--- a/python/run-tests
+++ b/python/run-tests
@@ -78,6 +78,7 @@ run_test "pyspark/mllib/linalg.py"
 run_test "pyspark/mllib/random.py"
 run_test "pyspark/mllib/recommendation.py"
 run_test "pyspark/mllib/regression.py"
+run_test "pyspark/mllib/stat.py"
 run_test "pyspark/mllib/tests.py"
 run_test "pyspark/mllib/tree.py"
 run_test "pyspark/mllib/util.py"