Call R from JAVA to get Chi-squared statistic and p-value

Question

I have two 4*4 matrices in JAVA, where one matrix holds observed counts and the other expected counts.

I need an automated way to calculate the p-value from the chi

Answer 1

1) Outputting my matrices from JAVA into .csv files

Use any of CSV libraies, I would recommend http://opencsv.sourceforge.net/

2) Uploading the .csv files into R 3) Calling the chisq.test on the .csv files into R

2 & 3 a pretty the same, You better create parametrized script to be run in R.

obs<-read.csv(args[1])
exp<-read.csv(args[2])
chisq.test(obs,exp)

So you can run

RScript your_script.r path_to_csv1 path_to_csv2, 

and use unique names for the csv files for example:

UUID.randomUUID().toString().replace("-","")

And then you use

Runtime.getRuntime().exec(command, environments, dataDir);

4) Returning the outputted p-value back into JAVA? You can only read the output of R if you are using getRuntime().exec() to invoke R.

I would also recommend to take a look at Apache's Statistics Lib & How to calculate PValue from ChiSquare. Maybe you can live without R at all :)