RCaller
RCaller: A Java package for interfacing R - Published in JOSS (2020)
Science Score: 93.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org, zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Keywords from Contributors
Scientific Fields
Repository
A Java library for calling R.
Basic Info
- Host: GitHub
- Owner: jbytecode
- License: lgpl-2.1
- Language: Java
- Default Branch: master
- Homepage: https://joss.theoj.org/papers/10.21105/joss.02722
- Size: 3.19 MB
Statistics
- Stars: 76
- Watchers: 12
- Forks: 39
- Open Issues: 4
- Releases: 6
Topics
Metadata Files
README.md
Overview
RCaller is a software library which is developed to simplify calling R from Java. Despite it is not the most efficient way of calling R codes from Java, it is very simple to use and its learning curve is steep. It successfully simplifies and wraps type conversations and makes variables in each languages accessible between platforms. With the calling sequential commands facility, the performance is not lost through a single external process. Although R is single-threaded, multiple R processes can be created and handled by multiple RCaller instances in Java. A Servlet based application can instantiate many RCaller objects as well as it can use a single object by using sequential command invocation ability. The former use multiple environments which do not share the same variable pool, whereas, the latter shares a mutual variable pool and clients can communicate as well. RCaller is written purely in Java and it does not depend on any external libraries, that is, it is ready to run in any machines that Java and R installed. Simulation studies show that the other libraries such as Rserve and rJava outperform the RCaller by means of interaction times. As a result of this, RCaller is not suitable for the projectts which have many clients that request relatively single and small computations. [RCaller: A Software Library for Calling R from Java - M. Hakan Satman]
Who uses RCaller?
RCaller is a production ready library for calling R functions from within Java. If you are developing Java software that needs enhanced statistical calculations, RCaller is a practical solution to integrate these languages. R has many well-tested and matured packages for automatic time series model selection, clustering, segmentation and classification, non-linear and robust regression estimations, data and text mining, linear and non-linear programming, generating plots, function optimization besides other research tools. RCaller brings all of the functionality that R serves in Java. Easy installation and integration steps and steep learning curve make RCaller a suitable solution. RCaller's computation overhead is generating XML files in R side and parsing XML to Java objects in Java side.
Dependencies
RCaller compiled jar library requires JRE (v11 or higher) and R installed in the runtime environment. If you want to compile from source, JDK (v11 or higher) and Maven (or Gradle) are also required for building process. Maven is responsible for downloading and install additional Java dependencies defined in pom file. RCaller does not use any version specific property of R.
Usage
It is recommended to take a look at the existing tests and examples
Here is a set of selected examples:
Performance details
RCaller uses XML for reading R output by default. This is lightweight but not very fast way. For speeding up the IO, install R arrow package and add dependencies org.apache.arrow:arrow-vector and org.apache.arrow:arrow-memory-netty to your Java projectt. RCaller will use Arrow format automatically if it is available both in R and Java.
Errors handling can impact performance in online mode and is disabled by default.
Use RCaller.runAndReturnResultOnline(String var, boolean addTryCatch) method with addTryCatch = true for throwing R exceptions to Java.
API Docs
Here is the auto-generated Javadocs.
Building and Installing RCaller
There are many options to integrate RCaller with a Java projectt. First option is to download pre-compiled jar file and add it to the classpath or pom.xml. pre-compiled jar files are here.
The second option is to compile from source. R should be installed to run tests. After building process, if everything is okay, a jar file is located in the target directory.
BASH
$ git clone https://github.com/jbytecode/rcaller.git
$ cd RCaller
$ mvn package
The last option is to use maven dependency:
XML
<dependency>
<groupId>com.github.jbytecode</groupId>
<artifactId>RCaller</artifactId>
<version>4.0.2</version>
</dependency>
The RCaller is located in the Maven Central Repository.
Benchmarks
You can test the performance of the library using the benchmark tool hosted here. This file tests costs of passing vectors and matrices from Java to R and vice versa.
Join us
If you want to join us, please follow the community guidelines here. We look forward to seeing your contributions.
Citation
Please refer to citation information given in file bibtex in your publications.
Owner
- Name: Mehmet Hakan Satman
- Login: jbytecode
- Kind: user
- Location: Istanbul
- Company: Istanbul University
- Twitter: mhsatman
- Repositories: 14
- Profile: https://github.com/jbytecode
Professor of Numerical Methods
JOSS Publication
RCaller: A Java package for interfacing R
Authors
Department of Econometrics, Istanbul University, Istanbul, Turkey
Department of Mathematical Optimization and Modeling, BIA-Technologies, Saint Petersburg, Russian Federation
Editor
Mikkel Meyer Andersen
Tags
statistics data scienceGitHub Events
Total
- Watch event: 4
- Push event: 5
- Pull request event: 2
- Fork event: 1
Last Year
- Watch event: 4
- Push event: 5
- Pull request event: 2
- Fork event: 1
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| mhsatman | m****n@g****m | 239 |
| Paul Curcean | c****l@g****m | 97 |
| Kopilov Aleksandr | k****d@g****m | 44 |
| jbytecode | 7 | |
| Alexander Bondarev | a****v@t****m | 5 |
| hako | h****o@h****p | 4 |
| Paul Curcean | p****l@b****t | 4 |
| mbatchkarov | m****v@g****m | 4 |
| Manuel Muradas | m****s@d****r | 4 |
| oem | o****m@o****r | 3 |
| simon.carter | s****r@e****k | 3 |
| hako | = | 3 |
| Volker Boerchers | v****s | 3 |
| dependabot[bot] | 4****] | 2 |
| SKYLAKE-2016\celthana | g****k@g****m | 2 |
| kstarosta | k@k****e | 2 |
| info | i****o@i****r | 2 |
| hako | h****o@h****p | 2 |
| mbatchkarov | m****v@l****t | 1 |
| jbytecode | j****e@l****t | 1 |
| hako | h****o@l****2 | 1 |
| Paul Curcean | p****n@i****t | 1 |
| Luke Lai | L****i | 1 |
| Edinei Piovesan | e****e@g****m | 1 |
| Making GitHub Delicious | i****n@w****o | 1 |
| The Gitter Badger | b****r@g****m | 1 |
| marecabo | 2****o | 1 |
| stevensotelo | s****t@h****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 37
- Total pull requests: 32
- Average time to close issues: 10 months
- Average time to close pull requests: 20 days
- Total issue authors: 25
- Total pull request authors: 15
- Average comments per issue: 4.73
- Average comments per pull request: 0.81
- Merged pull requests: 30
- Bot issues: 0
- Bot pull requests: 2
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: 1 day
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- jbytecode (5)
- wongjoel (3)
- VineelaKantamneni (3)
- mullon-ch (3)
- dieresys (2)
- xin-huang (2)
- d0dge (1)
- Georim (1)
- TomDePauw (1)
- benleblanket (1)
- bclarens (1)
- limhi (1)
- fbastian (1)
- antonkulaga (1)
- choweiyuan (1)
Pull Request Authors
- Kopilov (11)
- jbytecode (3)
- dependabot[bot] (3)
- dieresys (2)
- mirasrael (2)
- sjcetx (2)
- wongjoel (2)
- waffle-iron (1)
- gitter-badger (1)
- vboerchers (1)
- marecabo (1)
- ksfx (1)
- heebtob (1)
- limhi (1)
- edineipiovesan (1)
Top Labels
Issue Labels
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Packages
- Total packages: 1
- Total downloads: unknown
- Total docker downloads: 33
- Total dependent packages: 3
- Total dependent repositories: 59
- Total versions: 7
repo1.maven.org: com.github.jbytecode:RCaller
RCaller is a software library which simplifies performing data analysis and statistical calculations in Java using R. The details are hidden from users including transferring data between platforms, function calls, and retrieving results.
- Homepage: https://github.com/jbytecode/rcaller
- Documentation: https://appdoc.app/artifact/com.github.jbytecode/RCaller/
- License: GNU LGPL
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Latest release: 4.0.2
published over 4 years ago
Rankings
Dependencies
- org.apache.commons:commons-lang3 3.12.0 implementation
- junit:junit 4.13.2 testImplementation
- org.apache.arrow:arrow-vector [5.0.0,) provided
- org.apache.commons:commons-lang3 3.12.0
- junit:junit 4.13.2 test
- org.apache.arrow:arrow-memory-netty [5.0.0,) test
- actions/checkout v2 composite
- actions/setup-java v1 composite
- actions/checkout v2 composite
- actions/setup-java v1 composite