Using R language with Anaconda — Anaconda Enterprise 4.4 documentation

Anaconda Enterprise: Documentation

# Using R language with Anaconda

With Anaconda you can easily install the R programming language and over 80 of the most used R packages for data science, and easily create and share your own custom R packages.

The R Essentials bundle contains the IRKernel and more than 80 of the most popular R packages for data science, including dplyr, shiny, ggplot2, tidyr, caret and nnet.

As of early 2018, the default R interpreter installed into new environments is MRO. You can specify the MRO interpreter with the `mro-base` package or the R interpreter with the `r-base` package. Unless you request a change, conda will continue to use the existing interpreter in each environment.

To run the commands below on Windows use Start - Anaconda Prompt. On macOS or Linux open a Terminal.

## MRO supported operating systems

- 64-bit systems only for all operating systems—Windows, macOS and Linux.
- Windows 7.0 SP1, Windows 8.1, Windows 10, Windows Server 2008 R2 SP1 and Windows Server 2012.
- Linux—CentOS, Red Hat Enterprise Linux, Debian and Ubuntu.

Anaconda with MRO is not currently supported on macOS but will soon be supported on macOS El Capitan (10.11) and later.

Anaconda with R is supported on macOS Yosemite (10.10) and later.

## Creating an environment with MRO and R Essentials

1. Download and install Anaconda.

- Create a new conda environment with MRO and all the r-essentials conda packages built from MRAN:

      conda create -n mro_env r-essentials

- Activate the environment:

      conda activate mro_env

- List the packages in the environment:

      conda list

The list shows that the package `mro-base` is installed and `mro` is listed in the build string of the other R packages in the environment.

When using MRO conda packages, starting the R interactive interpreter shows Microsoft R Open in the startup message.

Anaconda Navigator, the Anaconda graphical package manager and application launcher, also creates MRO environments by default. You may instead select R when creating a new conda environment from within Navigator.

## Microsoft R Client

Microsoft R Client is a free, community-supported data science tool for high performance analytics built on top of MRO. Additionally, R Client introduces the powerful ScaleR technology and its proprietary functions to benefit from parallelization and remote computing.

Microsoft R Client is now available as a conda package (`r-mrclient`). Users of Windows or RHEL-7/CentOS7/Ubuntu 14.04 and above also have the option to `conda install` the MicrosoftML R package for machine learning (`r-mrclient-mml`) and the pre-trained models for sentiment analysis and image detection (`r-mrclient-mlm`).

## Updating R packages

- Update all of the packages and their dependencies with one command:

      conda update r-essentials

- If a new version of a package is available in the R channel, you can use `conda update` to update specific packages.

## Creating a new environment with R instead of MRO

When creating a new environment, you can use R and not MRO by explicitly including `r-base` in your list of packages. This option will continue to be supported for users who prefer R or use platforms that do not support MRO, including 32-bit operating systems and older versions of macOS.

With conda 4.4:

    conda create -n r-environment r-essentials r-base
    conda activate r-environment

## Switch an environment from R to MRO

- Activate the environment containing R.

- If you use conda 4.4 or later, run:

      conda install mro-base

- If you use conda 4.3, run:

      conda remove --force r-base _r-mutex
      conda install mro-base

The environment’s R interpreter will switch from R to MRO.

## Switch the default R interpreter from MRO to R

- Run `conda info` and check your version of conda.

- If your version of conda is below 4.4, run `conda update conda` to update conda to the latest version.

- Run:

      conda config --system --set pinned_packages _r-mutex=*=anacondar*

The default R interpreter will switch from MRO to R.

## Creating and sharing custom R bundles

Creating and sharing custom R bundles is similar to creating and sharing conda packages.

EXAMPLE: Create a simple custom R bundle metapackage named “Custom-R-Bundle” that contains several popular programs and their dependencies:

    conda metapackage custom-r-bundle 0.1.0 --dependencies r-irkernel jupyter r-ggplot2 r-dplyr --summary "My custom R bundle"

Share the new metapackage by uploading it to your channel on Anaconda Cloud:

    conda install anaconda-client
    anaconda login
    anaconda upload custom-r-bundle-0.1.0-0.tar.bz2

Anyone can now access your custom R bundle from any computer:

    conda install -c <your anaconda.org username> custom-r-bundle

For more information, see Jupyter and conda for R language.

## Mirroring the R channel

Many Anaconda Enterprise customers maintain a local mirror of the R channel.

When mirroring the R channel for the first time after the early 2018 update, clean the existing packages by running the command `anaconda-server-sync-conda` with the option `--clean`.

## R packages

- `r-essentials`: The R Essentials bundle contains the IRKernel and more than 80 of the most popular R packages for data science, including dplyr, shiny, ggplot2, tidyr, caret and nnet.
- `mro-basics`: The MRO Basics metapackage contains everything in the Microsoft MRO installers. It does not include `r-mrclient`, `r-mrclient-mml`, or `r-mrclient-mlm`.
- `r-mrclient`: Microsoft R Client is a free, community-supported, data science tool for high performance analytics.
- `r-mrclient-mml`: MicrosoftML provides state-of-the-art fast, scalable machine learning algorithms and transforms for R. Depends on `r-mrclient`.
- `r-mrclient-mlm`: MicrosoftML Machine Learning Models are pre-trained machine learning models for sentiment analysis and image detection. Depends on `r-mrclient-mml`.

## Uninstalling R Essentials

To uninstall the R Essentials package, run:

    conda remove r-essentials

NOTE: This removes only R Essentials and disables R Language support. Other R language packages are not removed.

## User group

For community help on using conda with MRO, join the conda email group.

## Resources

Here are our more popular resources on using Anaconda with the R programming language:

- R Language packages available for use with Anaconda–There are hundreds of R language packages now available, and several ways to get them.
- Navigator tutorial–Use the R programming language with Anaconda Navigator. The Anaconda Navigator graphical interface (GUI) makes it easy for even new users to use and run the R language in a Jupyter Notebook.
- Using R packages with Anaconda and Cloudera CDH–Anaconda Scale provides resource management tools to easily deploy Anaconda across a cluster. It helps you manage multiple conda environments and packages, including Python and R language, on bare-metal or cloud-based clusters.
- Blog post: Jupyter and conda for R–The many benefits that Jupyter, the IRKernel and conda can provide for data scientists working with the R programming language.
- Blog post: Anaconda for R users: SparkR and rBokeh– Data Scientist Christine Doig presents two projects for the R programming language that are powered by Anaconda. rBokeh allows you to create beautiful interactive visualizations. Scale your predictive models with SparkR through Anaconda’s cluster management capabilities.
- Using Anaconda with Hadoop: Distributed language processing with PySpark– This notebook example shows how Anaconda for cluster management makes it easy to manage packages, including Python and R, on a Hadoop cluster with PySpark.
- Webinar: Predict. Share. Deploy.–Download the webinar video to:
  - Build predictive models in Python with Anaconda using Python packages such as pandas and scikit-learn in Jupyter Notebooks.
  - Use modern open data science languages including Python and R together in your analysis.
  - Share your results with your entire data science team.
- Webinar: Anaconda for R Users–Download the slides from the webinar to see how Anaconda makes package, dependency and environment management easy with R language and other Open Data Science languages.