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R_interop

A simple example to help the interaction with R and Clojure in GraalVM

Status

Clearly alpha. The goal is to keep the function call mechanism but creating a better interop story with R objects (lm or ggplot). That being said, the bindings to R should work and stay stable.

Usage

Install GraalVM first. See this guide for a how to. Note that alternatives is actually update-alternatives on most linux distribution.

Install FastR

If you created the symbolic link /usr/lib/jvm/graalvm to target the content of the graalvm tar file, then

sudo /usr/lib/jvm/graalvm/bin/gu install R

A local ~/R directory should be created to install packages and I would strongly recommend to create an alias under ~/binto FastR in order to not messup with your usual R.

ln -s /usr/lib/jvm/graalvm/bin/R ~/bin/FastR

Clojure

On the Clojure part:

;; inside core.clj

(require '[r-interop.core :as rc])

;; define the rnorm function in clojure linked to the R rnorm function
(rc/defn-r rnorm)

;; positional call to the rnorm function (n=10, mean=2, sd=3)
(rnorm 10 2 3)

;; Same as above for the qnorm, but accepts a maps of arguments
(rc/defn-r qnorm)
;; usual 0.95 and 0.975 quantile
(qnorm :** {:p [0.95, 0.975]})

;; Same as above with standard deviation of 2,
;; observe we did not specify (which then takes the default value 0)
(qnorm :** {:p [0.95, 0.975] :sd 2})

;; you don't need to define all the R function like that
;; I created these packages and it easy to create your own with rc/create-package-bindings

(require '[r-interop.packages.base :as r-base])
(require '[r-interop.packages.stats :as st])
(rc/argslists st/qnorm)

Naming in r_interop.packages.*

All R word split like.this, snake_case, camelCase, PascalCase are converted to lisp kebab-case. The conversion is automatic, but some control is performed to not split terms that belong together (e.g. SVD).

Moreover, all conversion function including a 2 are replaced with -> (e.g. cov2cor is converted to cov->cor).

Caveat

  • Matrix dimensions are sometimes not respected (see the lm) example.
  • Classes are not kept after conversion. [big issue, write R snippets to keep the class of the object, killing the whole python interop].
  • Clojure rational numbers (e.g 3/2) should be avoided as they are not properly converted into R representation.

License

Copyright © 2019 David Pham

This program and the accompanying materials are made available under the terms of the Eclipse Public License 2.0 which is available at http://www.eclipse.org/legal/epl-2.0.

This Source Code may also be made available under the following Secondary Licenses when the conditions for such availability set forth in the Eclipse Public License, v. 2.0 are satisfied: GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version, with the GNU Classpath Exception which is available at https://www.gnu.org/software/classpath/license.html.