## What changes were proposed in this pull request?
jira: https://issues.apache.org/jira/browse/SPARK-16045
2.0 Audit: Update document for StopWordsRemover and Binarizer.
## How was this patch tested?
manual review for doc
Author: Yuhao Yang <hhbyyh@gmail.com>
Author: Yuhao Yang <yuhao.yang@intel.com>
Closes#13375 from hhbyyh/stopdoc.
## What changes were proposed in this pull request?
Update docs for two parameters `spark.sql.files.maxPartitionBytes` and `spark.sql.files.openCostInBytes ` in Other Configuration Options.
## How was this patch tested?
N/A
Author: Takeshi YAMAMURO <linguin.m.s@gmail.com>
Closes#13797 from maropu/SPARK-15894-2.
## What changes were proposed in this pull request?
Update doc as per discussion in PR #13592
## How was this patch tested?
manual
shivaram liancheng
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#13799 from felixcheung/rsqlprogrammingguide.
This has changed from 1.6, and now stores memory off-heap using spark's off-heap support instead of in tachyon.
Author: Eric Liang <ekl@databricks.com>
Closes#13744 from ericl/spark-16025.
## What changes were proposed in this pull request?
Initial SQL programming guide update for Spark 2.0. Contents like 1.6 to 2.0 migration guide are still incomplete.
We may also want to add more examples for Scala/Java Dataset typed transformations.
## How was this patch tested?
N/A
Author: Cheng Lian <lian@databricks.com>
Closes#13592 from liancheng/sql-programming-guide-2.0.
## What changes were proposed in this pull request?
roxygen2 doc, programming guide, example updates
## How was this patch tested?
manual checks
shivaram
Author: Felix Cheung <felixcheung_m@hotmail.com>
Closes#13751 from felixcheung/rsparksessiondoc.
## What changes were proposed in this pull request?
In the 2.0 document, Line "A full example that produces the experiment described in the PIC paper can be found under examples/." is redundant.
There is already "Find full example code at "examples/src/main/scala/org/apache/spark/examples/mllib/PowerIterationClusteringExample.scala" in the Spark repo.".
We should remove the first line, which is consistent with other documents.
## How was this patch tested?
(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
Manual test
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#13755 from wangmiao1981/doc.
## What changes were proposed in this pull request?
Make user guide changes to SparkR documentation for all changes that happened in 2.0 to Machine Learning APIs
Author: GayathriMurali <gayathri.m@intel.com>
Closes#13285 from GayathriMurali/SPARK-15129.
## What changes were proposed in this pull request?
add ml doc for ml isotonic regression
add scala example for ml isotonic regression
add java example for ml isotonic regression
add python example for ml isotonic regression
modify scala example for mllib isotonic regression
modify java example for mllib isotonic regression
modify python example for mllib isotonic regression
add data/mllib/sample_isotonic_regression_libsvm_data.txt
delete data/mllib/sample_isotonic_regression_data.txt
## How was this patch tested?
N/A
Author: WeichenXu <WeichenXu123@outlook.com>
Closes#13381 from WeichenXu123/add_isotonic_regression_doc.
## What changes were proposed in this pull request?
Reduce `spark.memory.fraction` default to 0.6 in order to make it fit within default JVM old generation size (2/3 heap). See JIRA discussion. This means a full cache doesn't spill into the new gen. CC andrewor14
## How was this patch tested?
Jenkins tests.
Author: Sean Owen <sowen@cloudera.com>
Closes#13618 from srowen/SPARK-15796.
## What changes were proposed in this pull request?
minor typo
## How was this patch tested?
minor typo in the doc, should be self explanatory
Author: Mortada Mehyar <mortada.mehyar@gmail.com>
Closes#13639 from mortada/typo.
## What changes were proposed in this pull request?
- Deprecate old Java accumulator API; should use Scala now
- Update Java tests and examples
- Don't bother testing old accumulator API in Java 8 (too)
- (fix a misspelling too)
## How was this patch tested?
Jenkins tests
Author: Sean Owen <sowen@cloudera.com>
Closes#13606 from srowen/SPARK-15086.
## What changes were proposed in this pull request?
SPARK_MASTER_IP is a deprecated environment variable. It is replaced by SPARK_MASTER_HOST according to MasterArguments.scala.
## How was this patch tested?
Manually verified.
Author: bomeng <bmeng@us.ibm.com>
Closes#13543 from bomeng/SPARK-15806.
## What changes were proposed in this pull request?
Like `SPARK_JAVA_OPTS` and `SPARK_CLASSPATH`, we will remove the document for `SPARK_WORKER_INSTANCES` to discourage user not to use them. If they are actually used, SparkConf will show a warning message as before.
## How was this patch tested?
Manually tested.
Author: bomeng <bmeng@us.ibm.com>
Closes#13533 from bomeng/SPARK-15781.
## What changes were proposed in this pull request?
Use new Spark logo including "Apache" (now, with crushed PNGs). Remove old unreferenced logo files.
## How was this patch tested?
Manual check of generated HTML site and Spark UI. I searched for references to the deleted files to make sure they were not used.
Author: Sean Owen <sowen@cloudera.com>
Closes#13609 from srowen/SPARK-15879.
## What changes were proposed in this pull request?
fixing documentation for the groupby/agg example in python
## How was this patch tested?
the existing example in the documentation dose not contain valid syntax (missing parenthesis) and is not using `Column` in the expression for `agg()`
after the fix here's how I tested it:
```
In [1]: from pyspark.sql import Row
In [2]: import pyspark.sql.functions as func
In [3]: %cpaste
Pasting code; enter '--' alone on the line to stop or use Ctrl-D.
:records = [{'age': 19, 'department': 1, 'expense': 100},
: {'age': 20, 'department': 1, 'expense': 200},
: {'age': 21, 'department': 2, 'expense': 300},
: {'age': 22, 'department': 2, 'expense': 300},
: {'age': 23, 'department': 3, 'expense': 300}]
:--
In [4]: df = sqlContext.createDataFrame([Row(**d) for d in records])
In [5]: df.groupBy("department").agg(df["department"], func.max("age"), func.sum("expense")).show()
+----------+----------+--------+------------+
|department|department|max(age)|sum(expense)|
+----------+----------+--------+------------+
| 1| 1| 20| 300|
| 2| 2| 22| 600|
| 3| 3| 23| 300|
+----------+----------+--------+------------+
Author: Mortada Mehyar <mortada.mehyar@gmail.com>
Closes#13587 from mortada/groupby_agg_doc_fix.
## What changes were proposed in this pull request?
Mentioned Scala version in the sbt configuration file is 2.11, so the path of the target JAR should be `/target/scala-2.11/simple-project_2.11-1.0.jar`
## How was this patch tested?
n/a
Author: prabs <prabsmails@gmail.com>
Author: Prabeesh K <prabsmails@gmail.com>
Closes#13554 from prabeesh/master.
## What changes were proposed in this pull request?
When fitting ```LinearRegressionModel```(by "l-bfgs" solver) and ```LogisticRegressionModel``` w/o intercept on dataset with constant nonzero column, spark.ml produce same model as R glmnet but different from LIBSVM.
When fitting ```AFTSurvivalRegressionModel``` w/o intercept on dataset with constant nonzero column, spark.ml produce different model compared with R survival::survreg.
We should output a warning message and clarify in document for this condition.
## How was this patch tested?
Document change, no unit test.
cc mengxr
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#12731 from yanboliang/spark-13590.
While there, also document spark.files and spark.jars. Text is the
same as the spark-submit help text with some minor adjustments.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#13502 from vanzin/SPARK-15760.
## What changes were proposed in this pull request?
I use spell check tools checks typo in spark documents and fix them.
## How was this patch tested?
N/A
Author: WeichenXu <WeichenXu123@outlook.com>
Closes#13538 from WeichenXu123/fix_doc_typo.
## What changes were proposed in this pull request?
1, del precision,recall in `ml.MulticlassClassificationEvaluator`
2, update user guide for `mlllib.weightedFMeasure`
## How was this patch tested?
local build
Author: Ruifeng Zheng <ruifengz@foxmail.com>
Closes#13390 from zhengruifeng/clarify_f1.
## What changes were proposed in this pull request?
The patch updates the codes & docs in the example module as well as the related doc module:
- [ ] [docs] `streaming-programming-guide.md`
- [x] scala code part
- [ ] java code part
- [ ] python code part
- [x] [examples] `RecoverableNetworkWordCount.scala`
- [ ] [examples] `JavaRecoverableNetworkWordCount.java`
- [ ] [examples] `recoverable_network_wordcount.py`
## How was this patch tested?
Ran the examples and verified results manually.
Author: Liwei Lin <lwlin7@gmail.com>
Closes#12981 from lw-lin/accumulatorV2-examples.
## What changes were proposed in this pull request?
Update document programming-guide accumulator section (scala language)
java and python version, because the API haven't done, so I do not modify them.
## How was this patch tested?
N/A
Author: WeichenXu <WeichenXu123@outlook.com>
Closes#13441 from WeichenXu123/update_doc_accumulatorV2_clean.
## What changes were proposed in this pull request?
Fixed broken java code examples in streaming documentation
Attn: tdas
Author: Matthew Wise <matthew.rs.wise@gmail.com>
Closes#13388 from mawise/fix_docs_java_streaming_example.
## What changes were proposed in this pull request?
* Document ```WeightedLeastSquares```(normal equation) and ```IterativelyReweightedLeastSquares```.
* Copy ```L-BFGS``` documents from ```spark.mllib``` to ```spark.ml```.
Due to the session ```Optimization of linear methods``` is used for developers, I think we should provide the brief introduction of the optimization method, necessary references and how it implements in Spark. It's not necessary to paste all mathematical formula and derivation here. If developers/users want to learn more, they can track reference.
## How was this patch tested?
Document update, no tests.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#13262 from yanboliang/spark-15484.
## What changes were proposed in this pull request?
This patch adds a user guide section for generalized linear regression and includes the examples from [#12754](https://github.com/apache/spark/pull/12754).
## How was this patch tested?
Documentation only, no tests required.
## Approach
In general, it is a bit unclear what level of detail ought to be included in the user guide since there is a lot of variability within the current user guide. I tried to give a fairly brief mathematical introduction to GLMs, and cover what types of problems they could be used for. Additionally, I included a brief blurb on the IRLS solver. The input/output columns are given in a table as is found elsewhere in the docs (though, again, these appear rather intermittently in the current docs), as well as a table providing the supported families and their link functions.
Author: sethah <seth.hendrickson16@gmail.com>
Closes#13139 from sethah/SPARK-15186.
## What changes were proposed in this pull request?
Remove several obsolete env variables not supported for Spark on YARN now, also updates the docs to include several changes with 2.0.
## How was this patch tested?
N/A
CC vanzin tgravescs
Author: jerryshao <sshao@hortonworks.com>
Closes#13296 from jerryshao/yarn-doc.
## What changes were proposed in this pull request?
`a` -> `an`
I use regex to generate potential error lines:
`grep -in ' a [aeiou]' mllib/src/main/scala/org/apache/spark/ml/*/*scala`
and review them line by line.
## How was this patch tested?
local build
`lint-java` checking
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#13317 from zhengruifeng/a_an.
## What changes were proposed in this pull request?
Follow up on the earlier PR - in here we are fixing up roxygen2 doc examples.
Also add to the programming guide migration section.
## How was this patch tested?
SparkR tests
Author: felixcheung <felixcheung_m@hotmail.com>
Closes#13340 from felixcheung/sqlcontextdoc.
This patch provides detail on what to do for keytabless Oozie launches of spark apps, and adds some debug-level diagnostics of what credentials have been submitted
Author: Steve Loughran <stevel@hortonworks.com>
Author: Steve Loughran <stevel@apache.org>
Closes#11033 from steveloughran/stevel/feature/SPARK-13148-oozie.
## What changes were proposed in this pull request?
Under Upgrading From SparkR 1.5.x to 1.6.x section added the information, SparkSQL converts `NA` in R to `null`.
## How was this patch tested?
Document update, no tests.
Author: Krishna Kalyan <krishnakalyan3@gmail.com>
Closes#13268 from krishnakalyan3/spark-12071-1.
## What changes were proposed in this pull request?
PySpark: Add links to the predictors from the models in regression.py, improve linear and isotonic pydoc in minor ways.
User guide / R: Switch the installed package list to be enough to build the R docs on a "fresh" install on ubuntu and add sudo to match the rest of the commands.
User Guide: Add a note about using gem2.0 for systems with both 1.9 and 2.0 (e.g. some ubuntu but maybe more).
## How was this patch tested?
built pydocs locally, tested new user build instructions
Author: Holden Karau <holden@us.ibm.com>
Closes#13199 from holdenk/SPARK-15412-improve-linear-isotonic-regression-pydoc.
This PR adds a note to clarify that the ML API for ALS only supports integers for user/item ids, and that other types for these columns can be used but the ids must fall within integer range.
(Refer [SPARK-14891](https://issues.apache.org/jira/browse/SPARK-14891)).
Also cleaned up a reference to `mllib` in the ML doc.
## How was this patch tested?
Built and viewed User Guide doc locally.
Author: Nick Pentreath <nickp@za.ibm.com>
Closes#13278 from MLnick/SPARK-15502-als-int-id-doc-note.
## What changes were proposed in this pull request?
Correct some typos and incorrectly worded sentences.
## How was this patch tested?
Doc changes only.
Note that many of these changes were identified by whomfire01
Author: sethah <seth.hendrickson16@gmail.com>
Closes#13180 from sethah/ml_guide_audit.
## What changes were proposed in this pull request?
Update the unit test code, examples, and documents to remove calls to deprecated method `dataset.registerTempTable`.
## How was this patch tested?
This PR only changes the unit test code, examples, and comments. It should be safe.
This is a follow up of PR https://github.com/apache/spark/pull/12945 which was merged.
Author: Sean Zhong <seanzhong@databricks.com>
Closes#13098 from clockfly/spark-15171-remove-deprecation.
## What changes were proposed in this pull request?
We should now begin copying algorithm details from the spark.mllib guide to spark.ml as needed, rather than just linking back to the corresponding algorithms in the spark.mllib user guide.
## How was this patch tested?
manual review for doc.
Author: Yuhao Yang <hhbyyh@gmail.com>
Author: Yuhao Yang <yuhao.yang@intel.com>
Closes#12957 from hhbyyh/tfidfdoc.
## What changes were proposed in this pull request?
See JIRA for the motivation. The changes are almost entirely movement of text and edits to sections. Minor changes to text include:
- Copying in / merging text from the "Useful Developer Tools" wiki, in areas of
- Docker
- R
- Running one test
- standardizing on ./build/mvn not mvn, and likewise for ./build/sbt
- correcting some typos
- standardizing code block formatting
No text has been removed from this doc; text has been imported from the https://cwiki.apache.org/confluence/display/SPARK/Useful+Developer+Tools wiki
## How was this patch tested?
Jekyll doc build and inspection of resulting HTML in browser.
Author: Sean Owen <sowen@cloudera.com>
Closes#13124 from srowen/SPARK-15333.
## What changes were proposed in this pull request?
(Please fill in changes proposed in this fix)
Add guide doc and examples for GaussianMixture in Spark.ml in Java, Scala and Python.
## How was this patch tested?
(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
Manual compile and test all examples
Author: wm624@hotmail.com <wm624@hotmail.com>
Closes#12788 from wangmiao1981/example.
## What changes were proposed in this pull request?
1,Rename matrix args in BreezeUtil to upper to match the doc
2,Fix several typos in ML and SQL
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#13078 from zhengruifeng/fix_ann.
## What changes were proposed in this pull request?
Renaming the streaming-kafka artifact to include kafka version, in anticipation of needing a different artifact for later kafka versions
## How was this patch tested?
Unit tests
Author: cody koeninger <cody@koeninger.org>
Closes#12946 from koeninger/SPARK-15085.
## What changes were proposed in this pull request?
1,create a libsvm-type dataset for lda: `data/mllib/sample_lda_libsvm_data.txt`
2,add python example
3,directly read the datafile in examples
4,BTW, change to `SparkSession` in `aft_survival_regression.py`
## How was this patch tested?
manual tests
`./bin/spark-submit examples/src/main/python/ml/lda_example.py`
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#12927 from zhengruifeng/lda_pe.
This PR:
* Clarifies that Spark *does* support Python 3, starting with Python 3.4.
Author: Nicholas Chammas <nicholas.chammas@gmail.com>
Closes#13017 from nchammas/supported-python-versions.
## What changes were proposed in this pull request?
Python example for ml.kmeans already exists, but not included in user guide.
1,small changes like: `example_on` `example_off`
2,add it to user guide
3,update examples to directly read datafile
## How was this patch tested?
manual tests
`./bin/spark-submit examples/src/main/python/ml/kmeans_example.py
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#12925 from zhengruifeng/km_pe.
## What changes were proposed in this pull request?
1, add BisectingKMeans to ml-clustering.md
2, add the missing Scala BisectingKMeansExample
3, create a new datafile `data/mllib/sample_kmeans_data.txt`
## How was this patch tested?
manual tests
Author: Zheng RuiFeng <ruifengz@foxmail.com>
Closes#11844 from zhengruifeng/doc_bkm.
