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Posted to reviews@spark.apache.org by yanboliang <gi...@git.apache.org> on 2016/05/10 09:09:01 UTC
[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
GitHub user yanboliang opened a pull request:
https://github.com/apache/spark/pull/13023
[SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New R APIs and API docs for mllib.R
## What changes were proposed in this pull request?
SparkR 2.0 QA: New R APIs and API docs for mllib.R
## How was this patch tested?
Existing unit tests.
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/yanboliang/spark spark-15177
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/13023.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #13023
----
commit 1a7700f5902f0439b40b7f6726303ee7489b553b
Author: Yanbo Liang <yb...@gmail.com>
Date: 2016-05-10T09:07:41Z
SparkR 2.0 QA: New R APIs and API docs for mllib.R
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New R APIs an...
Posted by vectorijk <gi...@git.apache.org>.
Github user vectorijk commented on the pull request:
https://github.com/apache/spark/pull/13023
Suggested by this [comment](https://github.com/apache/spark/pull/13394#issuecomment-222560187), I was wondering if we also need to update the docs for k-means and naive bayes in [http://people.apache.org/~pwendell/spark-nightly/spark-master-docs/latest/sparkr.html](url). Maybe we can include that change in this PR.
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/13023#discussion_r64106271
--- Diff: R/pkg/R/mllib.R ---
@@ -269,9 +349,29 @@ setMethod("summary", signature(object = "NaiveBayesModel"),
return(list(apriori = apriori, tables = tables))
})
+#' Makes predictions from a model produced by spark.naiveBayes(),
+#' similarly to R package e1071's predict.
+#'
+#' @param object A fitted naive Bayes model
+#' @param newData SparkDataFrame for testing
+#' @return SparkDataFrame containing predicted labels in a column named "prediction"
+#' @rdname predict
+#' @name predict
+#' @export
+#' @examples
+#' \dontrun{
+#' model <- spark.naiveBayes(trainingData, y ~ x)
+#' predicted <- predict(model, testData)
+#' showDF(predicted)
+#'}
+setMethod("predict", signature(object = "NaiveBayesModel"),
+ function(object, newData) {
+ return(dataFrame(callJMethod(object@jobj, "transform", newData@sdf)))
+ })
+
#' Fit a k-means model
#'
-#' Fit a k-means model, similarly to R's kmeans().
+#' Fits a k-means model, similarly to R's kmeans().
--- End diff --
I'm referring to line
```
#' Fit a k-means model
#'
#' Fit a k-means model, similarly to R's kmeans().
```
ie. the first line and the third line.
For example, it shows up for `glm` like this http://spark.apache.org/docs/latest/api/R/glm.html
Which I'd think would be rather odd if they are not consistent.
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/13023#issuecomment-218110989
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[GitHub] spark issue #13023: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New R APIs an...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/13023
@mengxr @yanboliang Is this PR still active ? Just checking if this is something we should track for the 2.0 release
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/13023#issuecomment-218110900
**[Test build #58225 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/58225/consoleFull)** for PR 13023 at commit [`1a7700f`](https://github.com/apache/spark/commit/1a7700f5902f0439b40b7f6726303ee7489b553b).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on a diff in the pull request:
https://github.com/apache/spark/pull/13023#discussion_r64070351
--- Diff: R/pkg/R/mllib.R ---
@@ -269,9 +349,29 @@ setMethod("summary", signature(object = "NaiveBayesModel"),
return(list(apriori = apriori, tables = tables))
})
+#' Makes predictions from a model produced by spark.naiveBayes(),
+#' similarly to R package e1071's predict.
+#'
+#' @param object A fitted naive Bayes model
+#' @param newData SparkDataFrame for testing
+#' @return SparkDataFrame containing predicted labels in a column named "prediction"
+#' @rdname predict
+#' @name predict
+#' @export
+#' @examples
+#' \dontrun{
+#' model <- spark.naiveBayes(trainingData, y ~ x)
+#' predicted <- predict(model, testData)
+#' showDF(predicted)
+#'}
+setMethod("predict", signature(object = "NaiveBayesModel"),
+ function(object, newData) {
+ return(dataFrame(callJMethod(object@jobj, "transform", newData@sdf)))
+ })
+
#' Fit a k-means model
#'
-#' Fit a k-means model, similarly to R's kmeans().
+#' Fits a k-means model, similarly to R's kmeans().
--- End diff --
`Fits`. See https://docs.oracle.com/javase/8/docs/api/java/lang/Object.html for examples.
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/13023#issuecomment-218762059
**[Test build #58484 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/58484/consoleFull)** for PR 13023 at commit [`9065535`](https://github.com/apache/spark/commit/906553504d4bb66a09ae35add183cfdd7f042b86).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/13023#issuecomment-218762204
Test PASSed.
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/13023#discussion_r63113352
--- Diff: R/pkg/R/mllib.R ---
@@ -269,9 +349,29 @@ setMethod("summary", signature(object = "NaiveBayesModel"),
return(list(apriori = apriori, tables = tables))
})
+#' Makes predictions from a model produced by spark.naiveBayes(),
+#' similarly to R package e1071's predict.
+#'
+#' @param object A fitted naive Bayes model
+#' @param newData SparkDataFrame for testing
+#' @return SparkDataFrame containing predicted labels in a column named "prediction"
+#' @rdname predict
+#' @name predict
+#' @export
+#' @examples
+#' \dontrun{
+#' model <- spark.naiveBayes(trainingData, y ~ x)
+#' predicted <- predict(model, testData)
+#' showDF(predicted)
+#'}
+setMethod("predict", signature(object = "NaiveBayesModel"),
+ function(object, newData) {
+ return(dataFrame(callJMethod(object@jobj, "transform", newData@sdf)))
+ })
+
#' Fit a k-means model
#'
-#' Fit a k-means model, similarly to R's kmeans().
+#' Fits a k-means model, similarly to R's kmeans().
--- End diff --
seems to be changing a few times here - should this be `Fits a ...` or `Fit a ...`?
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/13023#issuecomment-218751253
**[Test build #58484 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/58484/consoleFull)** for PR 13023 at commit [`9065535`](https://github.com/apache/spark/commit/906553504d4bb66a09ae35add183cfdd7f042b86).
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[GitHub] spark issue #13023: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New R APIs an...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on the issue:
https://github.com/apache/spark/pull/13023
It would be nice to get this in. @yanboliang is traveling. I can help send a PR based on this one.
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New R APIs an...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on the pull request:
https://github.com/apache/spark/pull/13023
@vectorijk There is a separate PR focus on updating machine learning section of SparkR users guide. FYI #13285. Thanks.
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:
https://github.com/apache/spark/pull/13023#issuecomment-218102009
**[Test build #58225 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/58225/consoleFull)** for PR 13023 at commit [`1a7700f`](https://github.com/apache/spark/commit/1a7700f5902f0439b40b7f6726303ee7489b553b).
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/13023#issuecomment-218110987
Merged build finished. Test PASSed.
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:
https://github.com/apache/spark/pull/13023#issuecomment-218762202
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on a diff in the pull request:
https://github.com/apache/spark/pull/13023#discussion_r63016149
--- Diff: R/pkg/R/mllib.R ---
@@ -377,32 +476,9 @@ setMethod("predict", signature(object = "KMeansModel"),
return(dataFrame(callJMethod(object@jobj, "transform", newData@sdf)))
})
-#' Fit a Bernoulli naive Bayes model
+#' Saves a fitted MLlib model to the input path
--- End diff --
Sounds good, updated. Thanks!
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on the pull request:
https://github.com/apache/spark/pull/13023#issuecomment-218116416
cc @mengxr
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by sun-rui <gi...@git.apache.org>.
Github user sun-rui commented on a diff in the pull request:
https://github.com/apache/spark/pull/13023#discussion_r62782265
--- Diff: R/pkg/R/mllib.R ---
@@ -377,32 +476,9 @@ setMethod("predict", signature(object = "KMeansModel"),
return(dataFrame(callJMethod(object@jobj, "transform", newData@sdf)))
})
-#' Fit a Bernoulli naive Bayes model
+#' Saves a fitted MLlib model to the input path
--- End diff --
We need have an agreement on the style of the title for a method. That is, whether or not to add "s" suffix to a verb. Seems R's tradition is not. for example, the title for "lapply":
Apply a Function over a List or Vector
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on a diff in the pull request:
https://github.com/apache/spark/pull/13023#discussion_r62643605
--- Diff: R/pkg/R/mllib.R ---
@@ -108,28 +107,32 @@ setMethod(
#' @param maxit Integer giving the maximal number of IRLS iterations.
#' @return a fitted generalized linear model
#' @rdname glm
+#' @name glm
#' @export
#' @examples
#' \dontrun{
#' sc <- sparkR.init()
#' sqlContext <- sparkRSQL.init(sc)
#' data(iris)
#' df <- createDataFrame(sqlContext, iris)
-#' model <- glm(Sepal_Length ~ Sepal_Width, df, family="gaussian")
+#' model <- glm(Sepal_Length ~ Sepal_Width, df, family = "gaussian")
#' summary(model)
#' }
setMethod("glm", signature(formula = "formula", family = "ANY", data = "SparkDataFrame"),
function(formula, family = gaussian, data, epsilon = 1e-06, maxit = 25) {
spark.glm(data, formula, family, epsilon, maxit)
})
--- End diff --
Because ```glm``` is R-compliant function, so I left the argument names consistent with native R.
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[GitHub] spark pull request #13023: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New R ...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang closed the pull request at:
https://github.com/apache/spark/pull/13023
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[GitHub] spark issue #13023: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New R APIs an...
Posted by mengxr <gi...@git.apache.org>.
Github user mengxr commented on the issue:
https://github.com/apache/spark/pull/13023
@yanboliang We are going to split the work into multiple PRs (SPARK-16090). Do you mind closing this PR for now? Thanks!
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on a diff in the pull request:
https://github.com/apache/spark/pull/13023#discussion_r62644513
--- Diff: R/pkg/R/mllib.R ---
@@ -195,9 +198,9 @@ print.summary.GeneralizedLinearRegressionModel <- function(x, ...) {
"Number of Fisher Scoring iterations: ", x$iter, "\n", sep = "")
cat("\n")
invisible(x)
- }
+}
-#' Make predictions from a generalized linear model
+#' Makes predictions from a fitted MLlib model
--- End diff --
This line appeared in the ```Description``` section of each ```rdname```, so ```predict``` for all models will share this description and it should be general.
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[GitHub] spark pull request: [SPARK-15177] [SparkR] [ML] SparkR 2.0 QA: New...
Posted by yanboliang <gi...@git.apache.org>.
Github user yanboliang commented on a diff in the pull request:
https://github.com/apache/spark/pull/13023#discussion_r62644703
--- Diff: R/pkg/R/mllib.R ---
@@ -377,32 +476,9 @@ setMethod("predict", signature(object = "KMeansModel"),
return(dataFrame(callJMethod(object@jobj, "transform", newData@sdf)))
})
-#' Fit a Bernoulli naive Bayes model
+#' Saves a fitted MLlib model to the input path
--- End diff --
Ditto with ```predict```, it shared by all ```write.ml``` and should be general.
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