R

R implementation of the Tracker Commons WCON File Format

R can run a Scala interpreter via the rscala package. This gives R access to the Scala implementation of the WCON file format.

This project just contains minimal utility routines needed to get up and running quickly.

Requirements

You need Java 8 and R installed.

Installation

First, make sure the Scala installation works properly (you can run sbt package successfully).

Then, with R installed, type install.packages("rscala"). If a recent version of Scala is installed, you should be able to run library(rscala) and nothing will happen; otherwise it will throw errors. If you don't have a recent version of Scala installed, either install one or use rscala::scalaInstall() to get one automatically.

Finally, enter

sbt assembly

to build a .jar for use with R. (You'll want to rerun this any time the Scala version changes and you want the updates.)

Example usage

From within R, start with the source('wcon-ready.r'). This will load a Scala interpreter (called si) which you can call using the syntax si %~% 'scala.code("here")'.

Here is an example of reading WCON data from R:

source('wcon-ready.r')
si %~% 'val i = ReadWrite.read("../../tests/intermediate.wcon").right.get'
si %~% 'val w = ct.Wcon from i'
numrecords = si %~% 'w.datas.length'
firstid = si %~% 'w.datas(0).id'
first_time_of_first = si %~% 'w.datas(0).t(0)'
first_y_points = si %~% 'w.datas(0).ys(0)'

Documentation

You mostly want to use the Scala documentation since the R implementation just calls through to the Scala. You can use either the standard org.openworm.trackercommons structures, or the wrapped org.openworm.trackercommons.compatibility ones that use simpler data structures. Either way, the Scaladocs can be built with sbt doc in the Scala project directory.

To learn more about how to use rscala to interface between R and Scala, see the rscala documentation.