[SPARK-17315][SparkR] Kolmogorov-Smirnov test SparkR wrapper

R/pkg/NAMESPACE

@@ -35,7 +35,8 @@ exportMethods("glm",
               "spark.perplexity",
               "spark.isoreg",
               "spark.gaussianMixture",
-              "spark.als")
+              "spark.als",
+              "spark.kstest")
 
 # Job group lifecycle management methods
 export("setJobGroup",
@@ -335,7 +336,8 @@ export("as.DataFrame",
        "tables",
        "uncacheTable",
        "print.summary.GeneralizedLinearRegressionModel",
-       "read.ml")
+       "read.ml",
+       "print.summary.KSTest")
 
 export("structField",
        "structField.jobj",
@@ -359,6 +361,7 @@ S3method(print, jobj)
 S3method(print, structField)
 S3method(print, structType)
 S3method(print, summary.GeneralizedLinearRegressionModel)
+S3method(print, summary.KSTest)
 S3method(structField, character)
 S3method(structField, jobj)
 S3method(structType, jobj)

R/pkg/R/generics.R

@@ -1375,3 +1375,7 @@ setGeneric("write.ml", function(object, path, ...) { standardGeneric("write.ml")
 #' @rdname spark.als
 #' @export
 setGeneric("spark.als", function(data, ...) { standardGeneric("spark.als") })
+
+#' @rdname spark.kstest
+#' @export
+setGeneric("spark.kstest", function(data, ...) { standardGeneric("spark.kstest") })

R/pkg/R/mllib.R

@@ -88,6 +88,13 @@ setClass("GaussianMixtureModel", representation(jobj = "jobj"))
 #' @note ALSModel since 2.1.0
 setClass("ALSModel", representation(jobj = "jobj"))
 
+#' S4 class that represents an KSTest
+#'
+#' @param jobj a Java object reference to the backing Scala KSTestWrapper
+#' @export
+#' @note KSTest since 2.1.0
+setClass("KSTest", representation(jobj = "jobj"))
+
 #' Saves the MLlib model to the input path
 #'
 #' Saves the MLlib model to the input path. For more information, see the specific
@@ -1308,3 +1315,104 @@ setMethod("write.ml", signature(object = "ALSModel", path = "character"),
           function(object, path, overwrite = FALSE) {
             write_internal(object, path, overwrite)
           })
+
+#' (One-Sample) Kolmogorov-Smirnov Test
+#'
+#' @description
+#' \code{spark.kstest} Conduct the two-sided Kolmogorov-Smirnov (KS) test for data sampled from a
+#' continuous distribution.
+#'
+#' By comparing the largest difference between the empirical cumulative
+#' distribution of the sample data and the theoretical distribution we can provide a test for the
+#' the null hypothesis that the sample data comes from that theoretical distribution.
+#'
+#' Users can call \code{summary} to obtain a summary of the test, and \code{print.summary.KSTest}
+#' to print out a summary result.
+#'
+#' @details
+#' For more details, see
+#' \href{http://spark.apache.org/docs/latest/mllib-statistics.html#hypothesis-testing}{
+#' MLlib: Hypothesis Testing}.
+#'
+#' @param data a SparkDataFrame of user data.
+#' @param testCol column name where the test data is from. It should be a column of double type.
+#' @param nullHypothesis name of the theoretical distribution tested against. Currently only
+#'                       \code{"norm"} for normal distribution is supported.
+#' @param distParams parameters(s) of the distribution. For \code{nullHypothesis = "norm"},
+#'                   we can provide as a vector the mean and standard deviation of
+#'                   the distribution. If none is provided, then standard normal will be used.
+#'                   If only one is provided, then the standard deviation will be set to be one.
+#' @param ... additional argument(s) passed to the method.
+#' @return \code{spark.kstest} returns a test result object.
+#' @rdname spark.kstest
+#' @aliases spark.kstest,SparkDataFrame-method
+#' @name spark.kstest
+#' @export
+#' @examples
+#' \dontrun{
+#' data <- data.frame(test = c(0.1, 0.15, 0.2, 0.3, 0.25))
+#' df <- createDataFrame(data)
+#' test <- spark.ktest(df, "test", "norm", c(0, 1))
+#'
+#' # get a summary of the test result
+#' testSummary <- summary(test)
+#' testSummary
+#'
+#' # print out the summary in an organized way
+#' print.summary.KSTest(test)
+#' }
+#' @note spark.kstest since 2.1.0
+setMethod("spark.kstest", signature(data = "SparkDataFrame"),
+          function(data, testCol = "test", nullHypothesis = c("norm"), distParams = c(0, 1)) {
+            tryCatch(match.arg(nullHypothesis),
+                     error = function(e) {
+                       msg <- paste("Distribution", nullHypothesis, "is not supported.")
+                       stop(msg)
+                     })
+            if (nullHypothesis == "norm") {
+              distParams <- as.numeric(distParams)
+              mu <- ifelse(length(distParams) < 1, 0, distParams[1])
+              sigma <- ifelse(length(distParams) < 2, 1, distParams[2])
+              jobj <- callJStatic("org.apache.spark.ml.r.KSTestWrapper",
+                                  "test", data@sdf, testCol, nullHypothesis,
+                                  as.array(c(mu, sigma)))
+              new("KSTest", jobj = jobj)
+            }
+})
+
+#  Get the summary of Kolmogorov-Smirnov (KS) Test.
+#' @param object test result object of KS.
+#' @return \code{summary} returns a list containing the p-value, test statistic computed for the
+#'         test, the null hypothesis with its parameters tested against
+#'         and degrees of freedom of the test.
+#' @rdname spark.kstest
+#' @aliases summary,KSTest-method
+#' @export
+#' @note summary(KSTest) since 2.1.0
+setMethod("summary", signature(object = "KSTest"),
+          function(object) {
+            jobj <- object@jobj
+            pValue <- callJMethod(jobj, "pValue")
+            statistic <- callJMethod(jobj, "statistic")
+            nullHypothesis <- callJMethod(jobj, "nullHypothesis")
+            distName <- callJMethod(jobj, "distName")
+            distParams <- unlist(callJMethod(jobj, "distParams"))
+            degreesOfFreedom <- callJMethod(jobj, "degreesOfFreedom")
+
+            list(p.value = pValue, statistic = statistic, nullHypothesis = nullHypothesis,
+                 nullHypothesis.name = distName, nullHypothesis.parameters = distParams,
+                 degreesOfFreedom = degreesOfFreedom)
+          })
+
+#  Prints the summary of GeneralizedLinearRegressionModel
+
+#' @rdname spark.kstest
+#' @param x test result object of KS.
+#' @export
+#' @note print.summary.KSTest since 2.1.0
+print.summary.KSTest <- function(x, ...) {
+  jobj <- x@jobj
+  summaryStr <- callJMethod(jobj, "summary")
+  cat(summaryStr)
+  invisible(summaryStr)
+}

R/pkg/inst/tests/testthat/test_mllib.R

@@ -736,4 +736,24 @@ test_that("spark.als", {
   unlink(modelPath)
 })
 
+test_that("spark.kstest", {
+  data <- data.frame(test = c(0.1, 0.15, 0.2, 0.3, 0.25, -1, -0.5))
+  df <- createDataFrame(data)
+  testResult <- spark.kstest(df, "test", "norm")
+  stats <- summary(testResult)
+
+  rStats <- ks.test(data$test, "pnorm", alternative = "two.sided")
+
+  expect_equal(stats$p.value, rStats$p.value, tolerance = 1e-4)
+  expect_equal(stats$statistic, unname(rStats$statistic), tolerance = 1e-4)
+
+  testResult <- spark.kstest(df, "test", "norm", -0.5)
+  stats <- summary(testResult)
+
+  rStats <- ks.test(data$test, "pnorm", -0.5, 1, alternative = "two.sided")
+
+  expect_equal(stats$p.value, rStats$p.value, tolerance = 1e-4)
+  expect_equal(stats$statistic, unname(rStats$statistic), tolerance = 1e-4)
+})
+
 sparkR.session.stop()

mllib/src/main/scala/org/apache/spark/ml/r/KSTestWrapper.scala

@@ -0,0 +1,57 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.spark.ml.r
+
+import org.apache.spark.mllib.stat.Statistics.kolmogorovSmirnovTest
+import org.apache.spark.mllib.stat.test.KolmogorovSmirnovTestResult
+import org.apache.spark.sql.{DataFrame, Row}
+
+private[r] class KSTestWrapper private (
+    val testResult: KolmogorovSmirnovTestResult,
+    val distName: String,
+    val distParams: Array[Double]) {
+
+  lazy val pValue = testResult.pValue
+
+  lazy val statistic = testResult.statistic
+
+  lazy val nullHypothesis = testResult.nullHypothesis
+
+  lazy val degreesOfFreedom = testResult.degreesOfFreedom
+
+  def summary: String = testResult.toString
+}
+
+private[r] object KSTestWrapper {
+
+  def test(
+      data: DataFrame,
+      featureName: String,
+      distName: String,
+      distParams: Array[Double]): KSTestWrapper = {
+
+    val rddData = data.select(featureName).rdd.map {
+      case Row(feature: Double) => feature
+    }
+
+    val ksTestResult = kolmogorovSmirnovTest(rddData, distName, distParams : _*)
+
+    new KSTestWrapper(ksTestResult, distName, distParams)
+  }
+}
+