ChoR, a R package for Chordalysis

ChoR is a R package for the Chordalysis algorithm, developed at Monash University, Melbourne, Australia

Changelog

2018-04-05

• Updated java requirement en checking

2017-10-13

• Updated rJava to 0.9-9

2017-10-06

• Update Chordalysis jar 2017-07-10
• Replace Apache Commons Mathematics by https://cran.r-project.org/package=commonsMath
  • Post modification of NAMESPACE in the makefile
• Update the example:
  • flare.data2 URL now points to https://raw.githubusercontent.com/jeffheaton/proben1/master/flare/flare.data2
  • Check for optional package "graph"

2017-02-20

• Original version

Notes

About rJava

The Chordalysis algorithm is coded in Java and use commonsMath. This package contains an R layer allowing to use the java code through rJava.

The rJava and commonsMath packages can be install in R with:

install.packages('rJava')
install.packages('commonsMath')

R may need to be reconfigure with Java support. In the shell (may require sudo):

R CMD javareconf

If you need more memory for Java, use the following R line before loading a package performing a JVM initialization.

options( java.parameters = "-Xmx4g" )

Installation of other useful software

install.packages('Rcpp')
install.packages('roxygen2')

Example

See the ChoR/inst/examples/script.R for some examples. The Rgraphviz package from bioconductor is needed to plot the obtained graphs.

source("https://bioconductor.org/biocLite.R")
biocLite("Rgraphviz")
library(Rgraphviz)

ARFF data

If you need to work with ARFF data, use the RWeka package:

library(RWeka)
myARFFdata = read.arff("/path/to/myfile.arff")

Submission to CRAN and documentation on package development

• https://cran.r-project.org/web/packages/policies.html
• https://cran.r-project.org/doc/manuals/r-release/R-exts.html
• "For Java .class and .jar files, the sources should be in a top-level java directory in the source package (or that directory should explain how they can be obtained)."