[SPARK-15457][MLLIB][ML] Eliminate some warnings from MLlib about deprecations

## What changes were proposed in this pull request?

Several classes and methods have been deprecated and are creating lots of build warnings in branch-2.0. This issue is to identify and fix those items:
* WithSGD classes: Change to make class not deprecated, object deprecated, and public class constructor deprecated. Any public use will require a deprecated API. We need to keep a non-deprecated private API since we cannot eliminate certain uses: Python API, streaming algs, and examples.
  * Use in PythonMLlibAPI: Change to using private constructors
  * Streaming algs: No warnings after we un-deprecate the classes
  * Examples: Deprecate or change ones which use deprecated APIs
* MulticlassMetrics fields (precision, etc.)
* LinearRegressionSummary.model field

## How was this patch tested?

Existing tests.  Checked for warnings manually.

Author: Sean Owen <sowen@cloudera.com>
Author: Joseph K. Bradley <joseph@databricks.com>

Closes #13314 from jkbradley/warning-cleanups.

7 files changed, 44 insertions, 39 deletions

diff --git a/mllib/src/main/scala/org/apache/spark/ml/evaluation/MulticlassClassificationEvaluator.scala b/mllib/src/main/scala/org/apache/spark/ml/evaluation/MulticlassClassificationEvaluator.scala
index 390e9b6444..0b84e0a3fa 100644
--- a/mllib/src/main/scala/org/apache/spark/ml/evaluation/MulticlassClassificationEvaluator.scala
+++ b/mllib/src/main/scala/org/apache/spark/ml/evaluation/MulticlassClassificationEvaluator.scala
@@ -82,8 +82,8 @@ class MulticlassClassificationEvaluator @Since("1.5.0") (@Since("1.5.0") overrid
     val metrics = new MulticlassMetrics(predictionAndLabels)
     val metric = $(metricName) match {
       case "f1" => metrics.weightedFMeasure
-      case "precision" => metrics.precision
-      case "recall" => metrics.recall
+      case "precision" => metrics.accuracy
+      case "recall" => metrics.accuracy
       case "weightedPrecision" => metrics.weightedPrecision
       case "weightedRecall" => metrics.weightedRecall
       case "accuracy" => metrics.accuracy
diff --git a/mllib/src/main/scala/org/apache/spark/ml/regression/LinearRegression.scala b/mllib/src/main/scala/org/apache/spark/ml/regression/LinearRegression.scala
index ff1038cbf1..37552194c5 100644
--- a/mllib/src/main/scala/org/apache/spark/ml/regression/LinearRegression.scala
+++ b/mllib/src/main/scala/org/apache/spark/ml/regression/LinearRegression.scala
@@ -558,16 +558,18 @@ class LinearRegressionSummary private[regression] (
     val predictionCol: String,
     val labelCol: String,
     val featuresCol: String,
-    @deprecated("The model field is deprecated and will be removed in 2.1.0.", "2.0.0")
-    val model: LinearRegressionModel,
+    private val privateModel: LinearRegressionModel,
     private val diagInvAtWA: Array[Double]) extends Serializable {
 
+  @deprecated("The model field is deprecated and will be removed in 2.1.0.", "2.0.0")
+  val model: LinearRegressionModel = privateModel
+
   @transient private val metrics = new RegressionMetrics(
     predictions
       .select(col(predictionCol), col(labelCol).cast(DoubleType))
       .rdd
       .map { case Row(pred: Double, label: Double) => (pred, label) },
-    !model.getFitIntercept)
+    !privateModel.getFitIntercept)
 
   /**
    * Returns the explained variance regression score.
@@ -631,10 +633,10 @@ class LinearRegressionSummary private[regression] (
   lazy val numInstances: Long = predictions.count()
 
   /** Degrees of freedom */
-  private val degreesOfFreedom: Long = if (model.getFitIntercept) {
-    numInstances - model.coefficients.size - 1
+  private val degreesOfFreedom: Long = if (privateModel.getFitIntercept) {
+    numInstances - privateModel.coefficients.size - 1
   } else {
-    numInstances - model.coefficients.size
+    numInstances - privateModel.coefficients.size
   }
 
   /**
@@ -642,13 +644,15 @@ class LinearRegressionSummary private[regression] (
    * the square root of the instance weights.
    */
   lazy val devianceResiduals: Array[Double] = {
-    val weighted = if (!model.isDefined(model.weightCol) || model.getWeightCol.isEmpty) {
-      lit(1.0)
-    } else {
-      sqrt(col(model.getWeightCol))
-    }
-    val dr = predictions.select(col(model.getLabelCol).minus(col(model.getPredictionCol))
-      .multiply(weighted).as("weightedResiduals"))
+    val weighted =
+      if (!privateModel.isDefined(privateModel.weightCol) || privateModel.getWeightCol.isEmpty) {
+        lit(1.0)
+      } else {
+        sqrt(col(privateModel.getWeightCol))
+      }
+    val dr = predictions
+      .select(col(privateModel.getLabelCol).minus(col(privateModel.getPredictionCol))
+        .multiply(weighted).as("weightedResiduals"))
       .select(min(col("weightedResiduals")).as("min"), max(col("weightedResiduals")).as("max"))
       .first()
     Array(dr.getDouble(0), dr.getDouble(1))
@@ -668,14 +672,15 @@ class LinearRegressionSummary private[regression] (
       throw new UnsupportedOperationException(
         "No Std. Error of coefficients available for this LinearRegressionModel")
     } else {
-      val rss = if (!model.isDefined(model.weightCol) || model.getWeightCol.isEmpty) {
-        meanSquaredError * numInstances
-      } else {
-        val t = udf { (pred: Double, label: Double, weight: Double) =>
-          math.pow(label - pred, 2.0) * weight }
-        predictions.select(t(col(model.getPredictionCol), col(model.getLabelCol),
-          col(model.getWeightCol)).as("wse")).agg(sum(col("wse"))).first().getDouble(0)
-      }
+      val rss =
+        if (!privateModel.isDefined(privateModel.weightCol) || privateModel.getWeightCol.isEmpty) {
+          meanSquaredError * numInstances
+        } else {
+          val t = udf { (pred: Double, label: Double, weight: Double) =>
+            math.pow(label - pred, 2.0) * weight }
+          predictions.select(t(col(privateModel.getPredictionCol), col(privateModel.getLabelCol),
+            col(privateModel.getWeightCol)).as("wse")).agg(sum(col("wse"))).first().getDouble(0)
+        }
       val sigma2 = rss / degreesOfFreedom
       diagInvAtWA.map(_ * sigma2).map(math.sqrt)
     }
@@ -695,10 +700,10 @@ class LinearRegressionSummary private[regression] (
       throw new UnsupportedOperationException(
         "No t-statistic available for this LinearRegressionModel")
     } else {
-      val estimate = if (model.getFitIntercept) {
-        Array.concat(model.coefficients.toArray, Array(model.intercept))
+      val estimate = if (privateModel.getFitIntercept) {
+        Array.concat(privateModel.coefficients.toArray, Array(privateModel.intercept))
       } else {
-        model.coefficients.toArray
+        privateModel.coefficients.toArray
       }
       estimate.zip(coefficientStandardErrors).map { x => x._1 / x._2 }
     }
diff --git a/mllib/src/main/scala/org/apache/spark/mllib/api/python/PythonMLLibAPI.scala b/mllib/src/main/scala/org/apache/spark/mllib/api/python/PythonMLLibAPI.scala
index 90d3827531..667290ece3 100644
--- a/mllib/src/main/scala/org/apache/spark/mllib/api/python/PythonMLLibAPI.scala
+++ b/mllib/src/main/scala/org/apache/spark/mllib/api/python/PythonMLLibAPI.scala
@@ -152,7 +152,7 @@ private[python] class PythonMLLibAPI extends Serializable {
       intercept: Boolean,
       validateData: Boolean,
       convergenceTol: Double): JList[Object] = {
-    val lrAlg = new LinearRegressionWithSGD()
+    val lrAlg = new LinearRegressionWithSGD(1.0, 100, 0.0, 1.0)
     lrAlg.setIntercept(intercept)
       .setValidateData(validateData)
     lrAlg.optimizer
@@ -181,7 +181,7 @@ private[python] class PythonMLLibAPI extends Serializable {
       intercept: Boolean,
       validateData: Boolean,
       convergenceTol: Double): JList[Object] = {
-    val lassoAlg = new LassoWithSGD()
+    val lassoAlg = new LassoWithSGD(1.0, 100, 0.01, 1.0)
     lassoAlg.setIntercept(intercept)
       .setValidateData(validateData)
     lassoAlg.optimizer
@@ -209,7 +209,7 @@ private[python] class PythonMLLibAPI extends Serializable {
       intercept: Boolean,
       validateData: Boolean,
       convergenceTol: Double): JList[Object] = {
-    val ridgeAlg = new RidgeRegressionWithSGD()
+    val ridgeAlg = new RidgeRegressionWithSGD(1.0, 100, 0.01, 1.0)
     ridgeAlg.setIntercept(intercept)
       .setValidateData(validateData)
     ridgeAlg.optimizer
@@ -268,7 +268,7 @@ private[python] class PythonMLLibAPI extends Serializable {
       intercept: Boolean,
       validateData: Boolean,
       convergenceTol: Double): JList[Object] = {
-    val LogRegAlg = new LogisticRegressionWithSGD()
+    val LogRegAlg = new LogisticRegressionWithSGD(1.0, 100, 0.01, 1.0)
     LogRegAlg.setIntercept(intercept)
       .setValidateData(validateData)
     LogRegAlg.optimizer
diff --git a/mllib/src/main/scala/org/apache/spark/mllib/classification/LogisticRegression.scala b/mllib/src/main/scala/org/apache/spark/mllib/classification/LogisticRegression.scala
index f3c52f61a3..adbcdd302a 100644
--- a/mllib/src/main/scala/org/apache/spark/mllib/classification/LogisticRegression.scala
+++ b/mllib/src/main/scala/org/apache/spark/mllib/classification/LogisticRegression.scala
@@ -200,13 +200,12 @@ object LogisticRegressionModel extends Loader[LogisticRegressionModel] {
 /**
  * Train a classification model for Binary Logistic Regression
  * using Stochastic Gradient Descent. By default L2 regularization is used,
- * which can be changed via [[LogisticRegressionWithSGD.optimizer]].
+ * which can be changed via `LogisticRegressionWithSGD.optimizer`.
  * NOTE: Labels used in Logistic Regression should be {0, 1, ..., k - 1}
  * for k classes multi-label classification problem.
  * Using [[LogisticRegressionWithLBFGS]] is recommended over this.
  */
 @Since("0.8.0")
-@deprecated("Use ml.classification.LogisticRegression or LogisticRegressionWithLBFGS", "2.0.0")
 class LogisticRegressionWithSGD private[mllib] (
     private var stepSize: Double,
     private var numIterations: Int,
@@ -229,6 +228,7 @@ class LogisticRegressionWithSGD private[mllib] (
    * numIterations: 100, regParm: 0.01, miniBatchFraction: 1.0}.
    */
   @Since("0.8.0")
+  @deprecated("Use ml.classification.LogisticRegression or LogisticRegressionWithLBFGS", "2.0.0")
   def this() = this(1.0, 100, 0.01, 1.0)
 
   override protected[mllib] def createModel(weights: Vector, intercept: Double) = {
diff --git a/mllib/src/main/scala/org/apache/spark/mllib/regression/Lasso.scala b/mllib/src/main/scala/org/apache/spark/mllib/regression/Lasso.scala
index ef8c80f0cb..e14bddf97d 100644
--- a/mllib/src/main/scala/org/apache/spark/mllib/regression/Lasso.scala
+++ b/mllib/src/main/scala/org/apache/spark/mllib/regression/Lasso.scala
@@ -85,9 +85,7 @@ object LassoModel extends Loader[LassoModel] {
  * See also the documentation for the precise formulation.
  */
 @Since("0.8.0")
-@deprecated("Use ml.regression.LinearRegression with elasticNetParam = 1.0. Note the default " +
-  "regParam is 0.01 for LassoWithSGD, but is 0.0 for LinearRegression.", "2.0.0")
-class LassoWithSGD private (
+class LassoWithSGD private[mllib] (
     private var stepSize: Double,
     private var numIterations: Int,
     private var regParam: Double,
@@ -108,6 +106,8 @@ class LassoWithSGD private (
    * regParam: 0.01, miniBatchFraction: 1.0}.
    */
   @Since("0.8.0")
+  @deprecated("Use ml.regression.LinearRegression with elasticNetParam = 1.0. Note the default " +
+    "regParam is 0.01 for LassoWithSGD, but is 0.0 for LinearRegression.", "2.0.0")
   def this() = this(1.0, 100, 0.01, 1.0)
 
   override protected def createModel(weights: Vector, intercept: Double) = {
diff --git a/mllib/src/main/scala/org/apache/spark/mllib/regression/LinearRegression.scala b/mllib/src/main/scala/org/apache/spark/mllib/regression/LinearRegression.scala
index 9e9d98bc5e..2ceac4b8cc 100644
--- a/mllib/src/main/scala/org/apache/spark/mllib/regression/LinearRegression.scala
+++ b/mllib/src/main/scala/org/apache/spark/mllib/regression/LinearRegression.scala
@@ -86,7 +86,6 @@ object LinearRegressionModel extends Loader[LinearRegressionModel] {
  * See also the documentation for the precise formulation.
  */
 @Since("0.8.0")
-@deprecated("Use ml.regression.LinearRegression or LBFGS", "2.0.0")
 class LinearRegressionWithSGD private[mllib] (
     private var stepSize: Double,
     private var numIterations: Int,
@@ -108,6 +107,7 @@ class LinearRegressionWithSGD private[mllib] (
    * numIterations: 100, miniBatchFraction: 1.0}.
    */
   @Since("0.8.0")
+  @deprecated("Use ml.regression.LinearRegression or LBFGS", "2.0.0")
   def this() = this(1.0, 100, 0.0, 1.0)
 
   override protected[mllib] def createModel(weights: Vector, intercept: Double) = {
diff --git a/mllib/src/main/scala/org/apache/spark/mllib/regression/RidgeRegression.scala b/mllib/src/main/scala/org/apache/spark/mllib/regression/RidgeRegression.scala
index 512fb9a712..301f02fd98 100644
--- a/mllib/src/main/scala/org/apache/spark/mllib/regression/RidgeRegression.scala
+++ b/mllib/src/main/scala/org/apache/spark/mllib/regression/RidgeRegression.scala
@@ -86,9 +86,7 @@ object RidgeRegressionModel extends Loader[RidgeRegressionModel] {
  * See also the documentation for the precise formulation.
  */
 @Since("0.8.0")
-@deprecated("Use ml.regression.LinearRegression with elasticNetParam = 0.0. Note the default " +
-  "regParam is 0.01 for RidgeRegressionWithSGD, but is 0.0 for LinearRegression.", "2.0.0")
-class RidgeRegressionWithSGD private (
+class RidgeRegressionWithSGD private[mllib] (
     private var stepSize: Double,
     private var numIterations: Int,
     private var regParam: Double,
@@ -109,6 +107,8 @@ class RidgeRegressionWithSGD private (
    * regParam: 0.01, miniBatchFraction: 1.0}.
    */
   @Since("0.8.0")
+  @deprecated("Use ml.regression.LinearRegression with elasticNetParam = 0.0. Note the default " +
+    "regParam is 0.01 for RidgeRegressionWithSGD, but is 0.0 for LinearRegression.", "2.0.0")
   def this() = this(1.0, 100, 0.01, 1.0)
 
   override protected def createModel(weights: Vector, intercept: Double) = {